Mediator dynamics during heat shock in budding yeast

The Mediator complex is central to transcription by RNA polymerase II (Pol II) in eukaryotes. In budding yeast (Saccharomyces cerevisiae), Mediator is recruited by activators and associates with core promoter regions, where it facilitates pre-initiation complex (PIC) assembly, only transiently prior to Pol II escape. Interruption of the transcription cycle by inactivation or depletion of Kin28 inhibits Pol II escape and stabilizes this association. However, Mediator occupancy and dynamics have not been examined on a genome-wide scale in yeast grown in nonstandard conditions. Here we investigate Mediator occupancy following heat shock or CdCl2 exposure, with and without depletion of Kin28. We find that Pol II occupancy exhibits similar dependence on Mediator under normal and heat shock conditions. However, while Mediator association increases at many genes upon Kin28 depletion under standard growth conditions, little or no increase is observed at most genes upon heat shock, indicating a more stable association of Mediator after heat shock. Mediator remains associated upstream of the core promoter at genes repressed by heat shock or CdCl2 exposure whether or not Kin28 is depleted, suggesting that Mediator is recruited by activators but is unable to engage PIC components at these repressed targets. This persistent association is strongest at promoters that bind the HMGB family member Hmo1, and is reduced but not eliminated in hmo1∆ yeast. Finally, we show a reduced dependence on PIC components for Mediator occupancy at promoters after heat shock, further supporting altered dynamics or stronger engagement with activators under these conditions.

Lateral transduction is inherent to the life cycle of the archetypical Salmonella phage P22

Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with early prophage excision followed by DNA replication and packaging (ERP). This temporal program is considered universal for P22-like temperate phages, though there is no direct evidence to support the timing and sequence of these events. Here we report that the long-standing ERP program is an observation of the experimentally favored Salmonella phage P22 tsc229 heat-inducible mutant, and that wild-type P22 actually follows the replication-packaging-excision (RPE) program. We find that P22 tsc229 excises early after induction, but P22 delays excision to just before it is detrimental to phage production. This allows P22 to engage in lateral transduction. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation.

Metaphorical Perception of Kazan Through the Prism of the Tatar Gastronomic Culture

The relevance of the research topic is due to the interest in urban space and its cultural and symbolic meaning. The city, perceived as a text, helps in interpreting to understand its specifics and represent it at different levels, which increases, among other things, its tourist attractiveness. The purpose of the study is to analyze the metaphor of Kazan-a woman through the prism of the gastronomic culture of the Tatars. Materials and Methods of Research. The methodological basis of the research consists of the cosmosophical ideas of G. D. Gachev, as well as the books of K. F. Fuchs, K. Nasyri, F. Ibragimova, S. Lutfullina, in which there are characteristics of the gastronomic culture of the Tatars. In the original metaphor, analyzed from the point of view of G. D. Gachev’s cosmosophy, where Kazan represents the Cosmos, and a woman represents Psyche, a missing link is found – the Logos. It is this link that, while remaining an open structure, accommodates various spheres of manifestation of the national mind in the field of culture and art, which helps to identify the feminine qualities of the city when interpreting the metaphor. Results. A stable association associated with Kazan is its Tatar national cuisine. This is no coincidence. The very history of the city according to some extant legends and legends is associated with the cauldron, which is a mandatory attribute of the cuisine. Despite the primacy of the man in the family, the mistress of the kitchen is a woman. It is on her that a huge number of duties are assigned to prepare food and create a spiritual atmosphere during the meal. Gastronomic culture, acting as a Logo, allows us to identify such qualities of Kazan, interpreted as an image of a woman-hostess, as hospitality, cordiality, respect, sensitivity, creativity, rationalism, skillful and careful handling of products. Discussion and conclusion. Clarification of the meaning of the Kazan-woman metaphor requires further study. At the same time, other spheres of culture and various texts of art can act as Logos.

A gut commensal niche regulates stable association of a multispecies microbiota

The intestines of animals are typically colonized by a complex, relatively stable microbiota that influences health and fitness, but the underlying mechanisms of colonization remain poorly understood. As a typical animal, the fruit fly, Drosophila melanogaster, is associated with a consistent set of commensal bacterial species, yet the reason for this consistency is unknown. Here, we use gnotobiotic flies, microscopy, and microbial pulse-chase protocols to show that a commensal niche exists within the proventriculus region of the Drosophila foregut that selectively binds bacteria with exquisite strain-level specificity. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus physically remodels the niche to favor secondary colonization by Acetobacter. Our results provide a mechanistic framework for understanding the establishment and stability of an intestinal microbiome.One-Sentence SummaryA strain-specific set of bacteria inhabits a defined spatial region of the Drosophila gut that forms a commensal niche.

Inositol hexakisphosphate is a critical regulator of Integrator assembly and function

Integrator has critical roles in noncoding RNA 3'-end processing as well as transcription attenuation of selected mRNAs. IntS11 is the endonuclease for RNA cleavage, as a part of the IntS4-IntS9-IntS11 complex (Integrator cleavage module, ICM). Our structure of the Drosophila ICM, determined by cryo-electron microscopy at 2.74 A resolution, unexpectedly revealed the stable association of an inositol hexakisphosphate (IP6) molecule. The binding site is located in a highly electropositive pocket at an interface among all three subunits of ICM, 55 A away from the IntS11 active site and generally conserved in other ICMs. IP6 binding is also confirmed in human ICM. Mutations of residues in this binding site or disruption of IP6 biosynthesis significantly reduced Integrator assembly and activity in snRNA 3'-end processing. Our structural and functional studies reveal that Integrator is subject to intricate cellular control and IP6 is a critical regulator of Integrator assembly and function in Drosophila, humans, and likely other organisms.

Only females show a stable association between neuroticism and microstructural asymmetry of the cingulum across childhood and adolescence: A longitudinal DTI study

Neuroticism is characterized by a tendency to experience negative and anxious emotions. This personality trait is linked to an increased risk of anxiety and mood disorders. In a cross-sectional 3T diffusion tensor imaging (DTI) study in children and adolescents, we found an association between neuroticism and a relative imbalance between left and right (i.e., asymmetry) fractional anisotropy (FA) in the cingulum and white matter underlying the ventromedial prefrontal cortex with opposite directions in females and males. Here we analyzed the longitudinal follow-up DTI data, which was acquired in 76 typically-developing 7- to 18-year-olds, including up to 11 scans per subject. Neuroticism was assessed up to four times. Our longitudinal DTI measurements substantiate robust associations between higher neuroticism scores and increased left relative to right cingulum FA in females and decreased left relative to right cingulum FA in males. In females, the association was already present in late childhood and with a stable expression across childhood and adolescence. In males, the association gradually emerged during adolescence. Future longitudinal studies should clarify which neurobiological factors (e.g., genetic variation, prenatal stress, sex hormones) contribute to the sex-specific associations in the relationship between neuroticism and interhemispheric microstructural asymmetry of the cingulum.

Criminal Law Characteristics of an Organized Group

The paper examines the content of the organized criminal group characteristics provided for under the law. The criminal activity of a stable association of persons poses an increased public danger. The identification of such facts and their investigation is fraught with significant difficulties that arise also due to the evaluative nature of the concept of "organized group". Therefore, its essence is analyzed not only on the basis of theoretical sources, but also in the context of judicial practice. The author compares and generalizes the signs listed in the relevant decisions of the Plenum of the Supreme Court of the Russian Federation and in court decisions on specific criminal cases. A correct understanding of the organized group characteristics is necessary for the competent qualification of crimes committed by its members, and the successful proof of their fault. The author summarizes that the sustainability of complicity is based on two complementary aspects. The first provides for a close, relatively long-term relationship between members of the group united by criminal motivation and goals (which ensures the stability of its main composition), as well as the recognition by ordinary participants of the decisions of their leader or the leading core of the group or decisions jointly made by the group as binding. The second aspect of sustainability provides for the implementation of effective criminal activity through the advance development of its plan and a clear distribution of role functions among the group members, ensuring the consistency of their actions, and the implementation of other measures necessary for the successful achievement of the intended goals. In cases where the conspiracy of the members of the group occurred immediately before the commission of the crime or took place in advance, but there was no close relationship and careful joint preparation for it we deal with a group of persons created by prior conspiracy due to the lack of stability of such an association.

The secret life (cycle) of temperate bacteriophages

Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with prophage excision followed by DNA replication and packaging (ERP) – a temporal program that is considered universal for most temperate phages. Here we report that the long-standing ERP program is an artefact of the experimentally favoured Salmonella phage P22 tsc229 heat-inducible mutant, and that wildtype P22 actually follows a replication-packaging-excision (RPE) program. We found that unlike P22 tsc229, P22 delayed excision to just before it was detrimental to phage production. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation.One Sentence SummaryGenetic analyses propose a new life cycle for temperate bacteriophages.

NDC1 is necessary for stable assembly of the nuclear pore scaffold to establish nuclear transport in early C. elegans embryos

Nuclear pore complexes (NPCs) are large protein assemblies that facilitate transport of macromolecules across the nuclear envelope (NE) [1, 2]. How thousands of NPCs rapidly assemble to form a functional NE after open mitosis is not known. Recruitment of the outer ring Nup107-160 complex to the NE initiates NPC assembly. The Nup53/93 complex bridges the outer ring to the central channel to form a functional pore [3-6]. Nup53 interacts with the conserved transmembrane nucleoporin Ndc1; however, how Ndc1 contributes to post-mitotic NPC assembly is unclear [7-9]. Here, we use C. elegans embryos to show that the timely formation of a functional NE after mitosis depends on Ndc1. Endogenously tagged Ndc1 is recruited early to the reforming NE and is highly mobile in the nuclear rim. 3D analysis of NE reformation revealed a significant decrease in NPC density in ndc1 deleted embryos: continuous nuclear membranes contained few holes where NPCs are normally located. Nup160 is highly mobile in NEs depleted of Ndc1 and outer ring scaffold components are less enriched at the rim. Nup160 is not recruited to the nuclear rim when both ndc1 and nup53 are absent and nuclear assembly fails. This suggests that Ndc1 and Nup53 function in part in parallel pathways to drive post-mitotic nuclear assembly in vivo. Together, we show that Ndc1 dynamically associates with the NE and promotes stable association of the outer ring scaffold with nascent NEs to facilitate NPC assembly after open mitosis, revealing a previously uncharacterized role for Ndc1 in forming functional NE.

Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations

Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone mutation affects the function of SETD2 at the nucleosome level, we determined the cryo-EM structure of human SETD2 associated with an H3.3K36M nucleosome and cofactor S-adenosylmethionine (SAM), and revealed that SETD2 is attached to the N-terminal region of histone H3 and the nucleosome DNA at superhelix location 1, accompanied with the partial unwrapping of nucleosome DNA to expose the SETD2-binding site. These structural features were also observed in the previous cryo-EM structure of the fungal Set2–nucleosome complex. By contrast with the stable association of SETD2 with the H3.3K36M nucleosome, the EM densities of SETD2 could not be observed on the wild-type nucleosome surface, suggesting that the association of SETD2 with wild-type nucleosome might be transient. The linker histone H1, which stabilizes the wrapping of nucleosome DNA at the entry/exit sites, exhibits an inhibitory effect on the activities of SETD2 and displays inversely correlated genome distributions with that of the H3K36me3 marks. Cryo-EM analysis of yeast H3K36 methyltransferase Set2 complexed with nucleosomes further revealed evolutionarily conserved structural features for nucleosome recognition in eukaryotes, and provides insights into the mechanism of activity regulation. These findings have advanced our understanding of the structural basis for the tumorigenesis mechanism of the H3.3K36M mutation and highlight the effect of nucleosome conformation on the regulation of histone modification.