Periodicity Forcing Words

The Dual Post Correspondence Problem asks, for a given word α, if there exists a non-periodic morphism g and an arbitrary morphism h such that g(α) = h(α). Thus α satisfies the Dual PCP if and only if it belongs to a non-trivial equality set. Words which do not satisfy the Dual PCP are called periodicity forcing, and are important to the study of word equations, equality sets and ambiguity of morphisms. In this paper, a 'prime' subset of periodicity forcing words is presented. It is shown that when combined with a particular type of morphism it generates exactly the full set of periodicity forcing words. Furthermore, it is shown that there exist examples of periodicity forcing words which contain any given factor/prefix/suffix. Finally, an alternative class of mechanisms for generating periodicity forcing words is developed, resulting in a class of examples which contrast those known already

Modified activities of macrophages’ deubiquitinating enzymes after Francisella infection

Francisella tularensis influences several host molecular/signaling pathways during infection. Ubiquitination and deubiquitination are among the most important regulatory mechanisms and respectively occur through attachment or removal of the ubiquitin molecule. The process is necessary not only to mark molecules for degradation, but also, for example, to the activation of signaling pathways leading to pro-inflammatory host response. Many intracellular pathogens, including Francisella tularensis, have evolved mechanisms of modifying such host immune responses to escape degradation. Here, we describe that F. tularensis interferes with the host’s ubiquitination system. We show increased total activity of deubiquitinating enzymes (DUBs) in human macrophages after infection, while confirm reduced enzymatic activities of two specific DUBs (USP10 and UCH-L5), and demonstrate increased activity of USP25. We further reveal the enrichment of these three enzymes in exosomes derived from F. tularensis-infected cells. The obtained results show the regulatory effect on ubiquitination mechanism in macrophages during F. tularensis infection

Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period

Aim Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter-gatherers as the main cause. In contrast, the impact of humans on rodent populations is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene. Location Europe. Taxon Common vole (Microtus arvalis). Methods We generated a dataset comprised of 4.2 kb long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated. Results We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than most previous estimates. We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57-29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition. In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM) even at high latitudes. Main Conclusions The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas climate deterioration during the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas.info:eu-repo/semantics/publishedVersio

In Vitro Assembly of Virus-Like Particles of a Gammaretrovirus, the Murine Leukemia Virus XMRV

Immature retroviral particles are assembled by self-association of the structural polyprotein precursor Gag. During maturation the Gag polyprotein is proteolytically cleaved, yielding mature structural proteins, matrix (MA), capsid (CA), and nucleocapsid (NC), that reassemble into a mature viral particle. Proteolytic cleavage causes the N terminus of CA to fold back to form a beta-hairpin, anchored by an internal salt bridge between the N-terminal proline and the inner aspartate. Using an in vitro assembly system of capsid-nucleocapsid protein (CANC), we studied the formation of virus-like particles (VLP) of a gammaretrovirus, the xenotropic murine leukemia virus (MLV)-related virus (XMRV). We show here that, unlike other retroviruses, XMRV CA and CANC do not assemble tubular particles characteristic of mature assembly. The prevention of beta-hairpin formation by the deletion of either the N-terminal proline or 10 initial amino acids enabled the assembly of Delta ProCANC or Delta 10CANC into immature-like spherical particles. Detailed three-dimensional (3D) structural analysis of these particles revealed that below a disordered N-terminal CA layer, the C terminus of CA assembles a typical immature lattice, which is linked by rod-like densities with the RNP

Nucleic Acid Binding by Mason-Pfizer Monkey Virus CA Promotes Virus Assembly and Genome Packaging

The Gag polyprotein of retroviruses drives immature virus assembly by forming hexameric protein lattices. The assembly is primarily mediated by protein-protein interactions between capsid (CA) domains and by interactions between nucleocapsid (NC) domains and RNA. Specific interactions between NC and the viral RNA are required for genome packaging. Previously reported cryoelectron microscopy analysis of immature Mason-Pfizer monkey virus (M-PMV) particles suggested that a basic region (residues RKK) in CA may serve as an additional binding site for nucleic acids. Here, we have introduced mutations into the RKK region in both bacterial and proviral M-PMV vectors and have assessed their impact on M-PMV assembly, structure, RNA binding, budding/release, nuclear trafficking, and infectivity using in vitro and in vivo systems. Our data indicate that the RKK region binds and structures nucleic acid that serves to promote virus particle assembly in the cytoplasm. Moreover, the RKK region appears to be important for recruitment of viral genomic RNA into Gag particles, and this function could be linked to changes in nuclear trafficking. Together these observations suggest that in M-PMV, direct interactions between CA and nucleic acid play important functions in the late stages of the viral life cycle

Chemical systematics of Neotropical termite genera with symmetrically snapping soldiers (Termitidae : Termitinae)

Termite soldiers often combine mechanical adaptations with defensive chemicals secreted from the frontal gland. Amongst the most remarkable strategies for mechanical defence, symmetrical and asymmetrical snapping mandibles evolved in several lineages of the diversified subfamily Termitinae (Termitidae). The contribution of the frontal chemical weapon to defence in snapping soldiers has long been doubted and the subfamily Termitinae overlooked with respect to soldier-produced chemicals. We recently reported an active frontal gland secreting unique defensive chemicals in the symmetrically snapping soldiers of Cauitermes tuberosus. The aim of the present study was a larger-scale comparison of chemical defence in symmetrically snapping soldiers. We studied the anatomy of the frontal gland and the chemistry of its secretion in five additional Neotropical species and mapped our observations on a de novo constructed molecular phylogeny of the target group. We show that the soldiers of all studied species possess a functional frontal gland, housed in part in the frontal projections on their heads. Phylogenetic reconstruction groups the studied taxa into two well-defined clades, supported by fundamental differences in defensive chemicals, either arising exclusively from the lipogenic pathway or containing also the products of the isoprenoid pathway. Our results also identify a new genus of symmetrical snappers, related to the genus Cavitermes, incorrectly classified in several previous studies

Ancient DNA reveals interstadials as a driver of the common vole population dynamics during the last glacial period

The common vole is a temperate rodent widespread across Europe. It was also one of the most abundant small mammal species throughout the Late Pleistocene. Phylogeographic studies of its extant populations suggested the Last Glacial Maximum (LGM, 26.5–19 ka ago) as one of the main drivers of the species’ population dynamics. However, analyses based solely on extant genetic diversity may not recover the full complexity of past population history. The main aim of this study was to investigate the evolutionary history and identify the main drivers of the common vole population dynamics during the Late Pleistocene in Europe. We generated a dataset comprising 4.2 kb-long fragment of mitochondrial DNA from 148 63 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of specimens that were not directly dated. We estimate the time to the most recent common ancestor of all Last Glacial and extant common vole lineages to 90 ka ago and the divergence of the main mtDNA lineages present in extantpopulations to between 55 and 40 ka ago, earlier than previous estimates. We find multiple lineage turnovers in Europe in the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition. Conversely, data from the Western Carpathians suggest continuity throughout the LGM even at high latitudes. Our results suggest that the main factor affecting the common vole populations during the last glacial period was the reduction of open habitats during the interstadial periods while the climate deterioration during the LGM had little impact on species’ population dynamics

Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period

Aim: Many species experienced population turnover and local extinction during the Late Pleistocene. In the case of megafauna, it remains challenging to disentangle climate change and the activities of Palaeolithic hunter-gatherers as the main cause. In contrast, the impact of humans on rodent populations is likely to be negligible. This study investigated which climatic and/or environmental factors affect the population dynamics of the common vole. This temperate rodent is widespread across Europe and was one of the most abundant small mammal species throughout the Late Pleistocene. Location: Europe. Taxon: Common vole (Microtus arvalis). Methods: We generated a dataset comprised of 4.2 kb long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51 modern specimens sampled from multiple localities across Europe and covering the last 60 thousand years (ka). We used Bayesian inference to reconstruct their phylogenetic relationships and to estimate the age of the specimens that were not directly dated. Results: We estimated the time to the most recent common ancestor of all last glacial and extant common vole lineages to be 90 ka ago and the divergence of the main mtDNA lineages present in extant populations to between 55 and 40 ka ago, which is earlier than most previous estimates. We detected several lineage turnovers in Europe during the period of high climate variability at the end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those found previously around the Pleistocene/Holocene transition. In contrast, data from the Western Carpathians suggest continuity throughout the Last Glacial Maximum (LGM) even at high latitudes. Main Conclusions: The main factor affecting the common vole populations during the last glacial period was the decrease in open habitat during the interstadials, whereas climate deterioration during the LGM had little impact on population dynamics. This suggests that the rapid environmental change rather than other factors was the major force shaping the histories of the Late Pleistocene faunas