Heterogeneity of gene expression of the hemagglutinin-esterase (HE) protein of murine coronaviruses.

The hemagglutinin-esterase (HE) membrane glycoprotein is present only in some members of the coronavirus family, including some strains of mouse hepatitis virus (MHV). In the JHM strain of MHV, expression of the HE gene is variable and corresponds to the number of copies of a UCUAA pentanucleotide sequence present at the 3'-end of the leader RNA. This copy number varies among MHV strains, depending on their passage history. The JHM isolates with two copies of UCUAA in their leader RNA showed a high level of HE expression, whereas the JHM isolate with three copies had a low-level expression. In this study, the analysis of HE gene expression was extended to other MHV strains. The synthesis of HE mRNA in these viruses also correlates with the copy number of UCUAA in the leader RNA and the particular intergenic sequence preceding the HE gene. In one MHV strain, MHV-1, no detectable HE mRNA was synthesized, despite the presence of a proper transcription initiation signal. This lack of HE mRNA expression was consistent with a leader RNA containing three UCUAA copies. However, mutations and deletions within the coding region of the MHV-1 HE gene have generated a stretch of sequence which resembled the transcriptional initiation motif, and was shown to initiate the synthesis of a novel smaller mRNA. These findings strengthened the theory that interactions between leader RNA and transcriptional initiation sequences regulate MHV subgenomic mRNA transcription. Sequence analysis revealed that most MHV strains, through extensive mutations, deletions, or insertions, have lost the complete HE open reading frame, thus turning HE into a pseudogene. This high degree of variation is unusual as the other three structural proteins (spike, membrane, and nucleocapsid) are well-maintained. In contrast to bovine coronavirus, which apparently requires HE for viral replication, the HE protein in MHV may be only an accessory protein which is not necessary for viral replication. JHM and MHV-S, however, have preserved the expression of HE protein

On the Properties of Language Classes Defined by Bounded Reaction Automata

Reaction automata are a formal model that has been introduced to investigate the computing powers of interactive behaviors of biochemical reactions([14]). Reaction automata are language acceptors with multiset rewriting mechanism whose basic frameworks are based on reaction systems introduced in [4]. In this paper we continue the investigation of reaction automata with a focus on the formal language theoretic properties of subclasses of reaction automata, called linearbounded reaction automata (LRAs) and exponentially-bounded reaction automata (ERAs). Besides LRAs, we newly introduce an extended model (denoted by lambda-LRAs) by allowing lambda-moves in the accepting process of reaction, and investigate the closure properties of language classes accepted by both LRAs and lambda-LRAs. Further, we establish new relationships of language classes accepted by LRAs and by ERAs with the Chomsky hierarchy. The main results include the following : (i) the class of languages accepted by lambda-LRAs forms an AFL with additional closure properties, (ii) any recursively enumerable language can be expressed as a homomorphic image of a language accepted by an LRA, (iii) the class of languages accepted by ERAs coincides with the class of context-sensitive languages.Comment: 23 pages with 3 figure

Coronavirus mRNA synthesis: identification of novel transcription initiation signals which are differentially regulated by different leader sequences.

The mRNA synthesis of mouse hepatitis virus (MHV) has been proposed to be the result of interaction between the leader RNA and the intergenic sites. Previously, we have identified a transcription initiation site (for mRNA 2-1), which is more efficiently transcribed by viruses containing two copies of UCUAA sequence in the leader RNA than by those with three copies. In this study, we have identified several sites which are regulated in the opposite way, namely, they are efficiently transcribed by the leader RNA with three UCUAA copies but not by those with two copies. These sites were characterized by primer extension and amplification by polymerase chain reaction. One of these sites is in the gene 3 region of a recombinant virus between A59 and JHM strains of MHV. Another is in the gene 2 region of MHV-1 strain. Both of these sites have a sequence similar to but different from the consensus transcription initiation signal (UCUAAUCUAUC and UUUAAUCUU, as opposed to UCUAAAC). These two novel intergenic sequences are not present in the genome of the JHM strain, consistent with the absence of these mRNAs in the JHM-infected cells. The discovery of this type of transcription initiation site provides additional evidence for the importance of the leader RNA in the transcription initiation of MHV mRNAs

On purely morphic characterizations of context-free languages

AbstractIn this paper we show the following: For any λ-free context-free language L there effectively exist a weak coding g, a homomorphism h such that L=gh−1 (∣cD2), where D2 is the Dyck set over a two-letter alphabet. As an immediate corollary it follows that for any λ-free context-free language L there exist a weak coding g and a mapping F such that L=gF−1(∣c)

Biosynthesis, structure, and biological activities of envelope protein gp65 of murine coronavirus.

We have previously shown that gp65 (E3) is a virion structural protein which varies widely in quantity among different strains of mouse hepatitis virus (MHV). In this study, the biosynthetic pathway and possible biological activities of this protein were examined. The glycosylation of gp65 in virus-infected cells was inhibited by tunicamycin but not by monensin, suggesting that it contains an N-glycosidic linkage. Glycosylation is cotranslational and appears to be complete before the glycoprotein reaches the Golgi complex. Pulse-chase experiments showed that this protein decreased in size after 30 min of chase, suggesting that the carbohydrate chains of gp65 undergo trimming during its transport across the Golgi. This interpretation is supported by the endoglycosidase treatment of gp65, which showed that the peptide backbone of gp65 did not decrease in size after pulse-chase periods. This maturation pathway is distinct from that of the E1 or E2 glycoproteins. Partial endoglycosidase treatment indicated that gp65 contains 9 to 10 carbohydrate side chains; thus, almost all of the potential glycosylation sites of gp65 were glycosylated. In vitro translation studies coupled with protease digestion suggest that gp65 is an integral membrane protein. The presence of gp65 in the virion is correlated with the presence of an acetylesterase activity. No hemagglutinin activity was detected

Projective/retrospective linking of a contrastive idea: Interactional practices of turn-initial and turn-final uses of kedo ‘but’ in Japanese

Projection and retrospection are the two primary factors in understanding how talk-in-interaction is structured in real-time. Powerful resources to mark a projective or retrospective relation between turns include conjunctions, and the contrastive conjunction kedo ‘but, ’ which can be used in both turn-initial and turn-final positions, is one of the most prominent devices in Japanese conversation. Focusing on the cases where turns with kedo are used as responses to the prior turn of the interlocutor, this study compares the interactional functions of the turn-initial and turn-final kedo. Through detailed analysis of excerpts taken from the Corpus of Everyday Japanese Conversation, it is shown that while both turn-initial kedo and turn-final kedo are similar in that the speaker presents his or her own turn as more or less contrasting to the preceding turn, they differ in the typical sequential contexts and the subsequent trajectories of the interaction. Specifically, kedo-prefaced turns are used to bring in a new perspective and thereby project a sequence dealing with the newly introduced perspective. By contrast, kedo-ending turns do not invite further topical development but provide a supplementary comment retrospectively on a prior part of the conversation

Who Made This Copy? An Empirical Analysis of Code Clone Authorship

Code clones are code snippets that are identical or similar to other snippets within the same or different files. They are often created through copy-and-paste practices during development and maintenance activities. Since code clones may require consistent updates and coherent management, they present a challenging issue in software maintenance. Therefore, many studies have been conducted to find various types of clones with accuracy, scalability, or performance. However, the exploration of the nature of code clones has been limited. Even the fundamental question of whether code snippets in the same clone set were written by the same author or different authors has not been thoroughly investigated. In this paper, we investigate the characteristics of code clones with a focus on authorship. We analyzed the authorship of code clones at the line-level granularity for Java files in 153 Apache projects stored on GitHub and addressed three research questions. Based on these research questions, we found that there are a substantial number of clone lines across all projects (an average of 18.5\% for all projects). Furthermore, authors who contribute to many non-clone lines also contribute to many clone lines. Additionally, we found that one-third of clone sets are primarily contributed to by multiple leading authors. These results confirm our intuitive understanding of clone characteristics, although no previous publications have provided empirical validation data from multiple projects. As the results could assist in designing better clone management techniques, we will explore the implications of developing an effective clone management tool.Comment: An extended version of the 17th International Workshop on Software Clones IWSC 2023 in Bogota, Colombi

Reaction Automata

Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that feature (string) language acceptors with multiset manipulation as a computing mechanism, and show that reaction automata are computationally Turing universal. Further, some subclasses of reaction automata with space complexity are investigated and their language classes are compared to the ones in the Chomsky hierarchy.Comment: 19 pages, 6 figure

Membrane Computing Schema Based on String Insertions

In this note we introduce the notion of a membrane computing schema for string objects. We propose a computing schema for a membrane network (i.e., tissue-like membrane system) where each membrane performs unique type of operations at a time and sends the result to others connected through the channel. The distinguished features of the computing models obtained from the schema are: 1. only context-free insertion operations are used for string generation, 2. some membranes assume ltering functions for structured objects(molecules), 3. the generating model and accepting model are obtained in the same schema, and both are computationally universal, 4. several known rewriting systems with universal computability can be reformulated in terms of membrane computing schema in a uniform manner. The rst feature provides the model with a simple uniform structure which facilitates a biological implementation of the model, while the second feature suggests further feasibility of the model in terms of DNA complementarity. Through the third and fourth features, one may have a uni ed view of a variety of existing rewriting systems with Turing computability in the framework of membrane computing paradigm

Chromatin Dynamics during DNA Repair Revealed by Pair Correlation Analysis of Molecular Flow in the Nucleus

AbstractChromatin dynamics modulate DNA repair factor accessibility throughout the DNA damage response. The spatiotemporal scale upon which these dynamics occur render them invisible to live cell imaging. Here we present a believed novel assay to monitor the in vivo structural rearrangements of chromatin during DNA repair. By pair correlation analysis of EGFP molecular flow into chromatin before and after damage, this assay measures millisecond variations in chromatin compaction with submicron resolution. Combined with laser microirradiation we employ this assay to monitor the real-time accessibility of DNA at the damage site. We find from comparison of EGFP molecular flow with a molecule that has an affinity toward double-strand breaks (Ku-EGFP) that DNA damage induces a transient decrease in chromatin compaction at the damage site and an increase in compaction to adjacent regions, which together facilitate DNA repair factor recruitment to the lesion with high spatiotemporal control