DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL

Sophisticated analysis and simplified visualization are crucial for understanding complicated structures of biomacromolecules. DSSR (Dissecting the Spatial Structure of RNA) is an integrated computational tool that has streamlined the analysis and annotation of 3D nucleic acid structures. The program creates schematic block representations in diverse styles that can be seamlessly integrated into PyMOL and complement its other popular visualization options. In addition to portraying individual base blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the minor-groove edges. Notably, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The DSSR-enabled innovative schematics with PyMOL are aesthetically pleasing and highly informative: the base identity, pairing geometry, stacking interactions, double-helical stems, and G-quadruplexes are immediately obvious. These features can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL, the web application, and the web application programming interface. The supplemental PDF serves as a practical guide, with complete and reproducible examples. Thus, even beginners or occasional users can get started quickly, especially via the web application at http://skmatic.x3dna.org.

Motivations for Consonant Epenthesis in Nonstandard Suffixed Forms of Korean Nouns

This paper investigates variation in the treatment of consonant clusters in stem-final position in Korean nouns. Consonant clusters undergo obligatory simplification when nouns are in isolation (e.g., /talk/ [tak] ‘chicken’). Consonant deletion may also occur in nonstandard Korean when a vowel-initial suffix is attached to nouns (e.g., /talk/ [ta.ki] ‘chicken-nom’). Another nonstandard variant discussed in this study is the suffixed forms of nouns with consonant epenthesis—particularly with [s]-epenthesis (e.g., /talk-i/ [tak.si] ‘chicken-nom’). The epenthetic consonant has received little or no attention, or neglected as a speech error in previous research. However, results from a production experiment show that [s]-epenthesis occurs consistently in terms of its position and quality. I propose this is motivated by the Base identity effect required both at the segmental and suprasegmental levels. In addition, the quality of the epenthetic consonant is also consistent: that is, only [s] but not any other consonant is epenthesized. I ascribe this to the frequency effects by which speakers epenthesize a consonant that is frequent in onset position overall in Korean.

Profiling Cybercriminals

Cybercrime has become a growing business. The marketplaces for such businesses tend to be online forums. Much of the research on carding forums has been qualitative, but there have been quantitative analyses as well. One such type of analysis is topic modeling, a clustering technique that groups forum users according to the textual comments they leave. However, this type of research so far has been exclusively quantitative, without qualitatively examining the topics. The following study attempts to add to this research by analyzing the comment histories from 30,469 users from three carding forums. The results have revealed that users belong to one or more of 21 different topics. The topics are grouped into six broader categories, consisting of a customer base, identity fraud market, crimeware market, free content market, and two others. Descriptives are provided displaying how the topics are distributed across the three websites and directions for future research are discussed.

An efficient controlled quantum secure direct communication and authentication by using four particle cluster states

In this paper, a three-party controlled quantum secure direct communication and authentication (QSDCA) protocol is proposed by using four particle cluster states via a quantum one-time pad and local unitary operations. In the present scheme, only under the permission of the controller, the sender and the receiver can implement secure direct communication successfully. But under any circumstances, Charlie cannot obtain the secret message. Eavesdropping detection and identity authentication are achieved with the help of the previously shared reusable base identity strings of users. This protocol is unconditionally secure in both ideal and practical noisy cases. In one transmission, a qubit of each four particle cluster state is used as controller’s permission and the same qubit with another qubit are used to recover two classical bits of information. In the proposed scheme, the efficiency is improved compared with the previous works.

Mutations in 23S rRNA at the Peptidyl Transferase Center and Their Relationship to Linezolid Binding and Cross-Resistance

ABSTRACT The oxazolidinone antibiotic linezolid targets the peptidyl transferase center (PTC) on the bacterial ribosome. Thirteen single and four double 23S rRNA mutations were introduced into a Mycobacterium smegmatis strain with a single rRNA operon. Converting bacterial base identity by single mutations at positions 2032, 2453, and 2499 to human cytosolic base identity did not confer significantly reduced susceptibility to linezolid. The largest decrease in linezolid susceptibility for any of the introduced single mutations was observed with the G2576U mutation at a position that is 7.9 Å from linezolid. Smaller decreases were observed with the A2503G, U2504G, and G2505A mutations at nucleotides proximal to linezolid, showing that the degree of resistance conferred is not simply inversely proportional to the nucleotide-drug distance. The double mutations G2032A-C2499A, G2032A-U2504G, C2055A-U2504G, and C2055A-A2572U had remarkable synergistic effects on linezolid resistance relative to the effects of the corresponding single mutations. This study emphasizes that effects of rRNA mutations at the PTC are organism dependent. Moreover, the data show a nonpredictable cross-resistance pattern between linezolid, chloramphenicol, clindamycin, and valnemulin. The data underscore the significance of mutations at distal nucleotides, either alone or in combination with other mutated nucleotides, in contributing to linezolid resistance.

RNA minihelices as model substrates for ATP/CTP:tRNA nucleotidyltransferase

Twenty-one RNA minihelices, resembling the coaxially stacked acceptor- /T-stems and T-loop found along the top of a tRNA's three-dimensional structure, were synthesized and used as substrates for ATP/CTP:tRNA nucleotidyltransferases from Escherichia coli and Saccharomyces cerevisiae. The sequence of nucleotides in the loop varied at positions corresponding to residues 56, 57 and 58 in the T-loop of a tRNA. All minihelices were substrates for both enzymes, and the identity of bases in the loop affected the interaction. In general, RNAs with purines in the loop were better substrates than those with pyrimidines, although no single base identity absolutely determined the effectiveness of the RNA as substrate. RNAs lacking bases near the 5ʹ-end were good substrates for the E. coli enzyme, but were poor substrates for that from yeast. The apparent Km values for selected minihelices were 2-3 times that for natural tRNA, and values for apparent Vmax were lowered 5-10-fold.