Chromatin and Nuclear Dynamics in the Maintenance of Replication Fork Integrity

Replication of the eukaryotic genome is a highly regulated process and stringent control is required to maintain genome integrity. In this review, we will discuss the many aspects of the chromatin and nuclear environment that play key roles in the regulation of both unperturbed and stressed replication. Firstly, the higher order organisation of the genome into A and B compartments, topologically associated domains (TADs) and sub-nuclear compartments has major implications in the control of replication timing. In addition, the local chromatin environment defined by non-canonical histone variants, histone post-translational modifications (PTMs) and enrichment of factors such as heterochromatin protein 1 (HP1) plays multiple roles in normal S phase progression and during the repair of replicative damage. Lastly, we will cover how the spatial organisation of stalled replication forks facilitates the resolution of replication stress.

Emerging Complexity of Nuclear South Asia

South Asia is a geo-political system which has its unique security characters. The emerging complex nature of a system could lead either to the security or insecurity of that system. India and Pakistan are the emerging nuclear powers of South Asia. The nuclear doctrines and behavior of India and Pakistan promote the advancement of their nuclear programs in both strategic and civil domains. Both countries desire stability, the balance of power and security through the possession of nuclear options. However, the author argues that South Asia’s existing nuclear environment and its emerging complexity have produced insecurity and instability in the region at large. This paper is an attempt to identify the complexity of actors and behaviors and their emerging threats to the security of the region. There is also a lack of literature to portray the nuclear risk that the non-nuclear states face in South Asia. This paper tries to fill that gap as well.

Nuclear morphogenesis: forming a heterogeneous nucleus during embryogenesis

An embryo experiences progressively complex spatial and temporal patterns of gene expression that guide the morphogenesis of its body plan as it matures. Using super-resolution fluorescence microscopy in Drosophila melanogaster embryos, we observed a similar increase in complexity in the nucleus: the spatial distributions of transcription factors became increasingly heterogeneous as the embryo matured. We also observed a similar trend in chromatin conformation with the establishment of specific histone modification patterns. However, transcription sites of specific genes had distinct local preferences for histone marks separate from the average nuclear trend, depending on the time and location of their expression. These results suggest that reconfiguring the nuclear environment is an integral part of embryogenesis and that the physical organization of the nucleus a key element in developmental gene regulation.

RNA Sequencing of Medusavirus Suggests Remodeling of the Host Nuclear Environment at an Early Infection Stage

Medusavirus is an amoeba-infecting giant virus that was isolated from a hot spring in Japan. It belongs to the proposed family “ Medusaviridae ” in the phylum Nucleocytoviricota .

A merger between compatible but divergent genomes supports allopolyploidization in the Brassicaceae family

Hybridization and polyploidization are pivotal to plant evolution. Genetic crosses between distantly related species rarely occur in nature mainly due to reproductive barriers but how such hurdles can be overcome is largely unknown. xBrassicoraphanus is a fertile intergeneric allopolyploid synthesized between Brassica rapa and Raphanus sativus in the Brassicaceae family. Genomes of B. rapa and R. sativus are diverged enough to suppress synapsis formation between non-homologous progenitor chromosomes during meiosis, and we found that both genomes reside in the single nucleus of xBrassicoraphanus without genome loss or rearrangement. Expressions of syntenic orthologs identified in B. rapa and R. sativus were adjusted to a hybrid nuclear environment of xBrassicoraphanus, which necessitates reconfiguration of transcription network by rewiring cis-trans interactions. B. rapa coding sequences have a higher level of gene-body methylation than R. sativus, and such methylation asymmetry is maintained in xBrassicoraphanus. B. rapa-originated transposable elements were transcriptionally silenced in xBrassicoraphanus, rendered by gain of CHG methylation in trans via small RNAs derived from the same sequences of R. sativus subgenome. Our work proposes that not only transcription compatibility but also a certain extent of genome divergence supports hybrid genome stabilization, which may explain great diversification and expansion of angiosperms during evolution.

USING OF SOME HIGH TECHNOLOGIES AGAINST MODERN INTERNATIONAL TERRORISM

Сегодня главными угрозами для существования всего человечества являются нарастание интенсивности, в том числе широкомасштабные природные и техногенные катастрофы и международный терроризм (МТ). Согласно прогнозам эта негативная тенденция со временем усилится в 21 веке. И к ним добавился очень опасный вирус COVID-19. Здесь мы представляем результаты наших МТ-исследований по результатам участия в международных тематических мероприятиях, таких как международные научные мероприятия НАТО и Международного научно-технического центра (МНТЦ), в том числе некоторые фрагменты моей работы в качестве члена Международного Научный комитет Международной конференции по моделированию и симуляции хаоса (CHAOS) и руководитель его специальной сессии: «Моделирование оценки рисков для ядерных, экологических и техногенных источников». Особое внимание уделяется организации и проведению подобных мероприятий, направленных на повышение их эффективности и проведения. Предоставляется информация о новых методах борьбы с МТ и предотвращения её возможных действий. Обсуждаются вопросы использования новых технологий, посвященных сегодняшней борьбе с COVID-19 и группировкам МТ Талибан в Афганистане. Today the main great treats for existence of all humanity are intensity increasing and including wide scale natural and manmade catastrophes and international terrorism (IT). According to forecasts, this negative trend will increase over time in the 21st century. And very dangerous COVID-19 was added to them. Here we present the results of our IT researches on the results of participation in international thematic events, such as the international scientific events of NATO and the International Science and Technology Center (ISTC), including some fragments of my work as the member of the International Scientific Committee of Chaotic Modeling and Simulation International Conference (CHAOS) and chief of its Special Session: “Modeling risk assessment for nuclear, environment and manmade sources”. The special attention is paid to the organization and conduct of such events aimed at increasing their effectiveness and implementation. Information is provided on new methods of combating IT and preventing its possible acts. Using of new technologies, devoted to today struggle against COVID-19 and IT Taliban groups in Afghanistan are under discussion.

The needle and the haystack: single molecule tracking to probe the transcription factor search in eukaryotes

Transcription factors (TFs) regulate transcription of their target genes by identifying and binding to regulatory regions of the genome among billions of potential non-specific decoy sites, a task that is often presented as a ‘needle in the haystack’ challenge. The TF search process is now well understood in bacteria, but its characterization in eukaryotes needs to account for the complex organization of the nuclear environment. Here we review how live-cell single molecule tracking is starting to shed light on the TF search mechanism in the eukaryotic cell and we outline the future challenges to tackle in order to understand how nuclear organization modulates the TF search process in physiological and pathological conditions.

RNA-seq of the medusavirus suggests remodeling of the host nuclear environment at an early infection stage

Nucleo-cytoplasmic large DNA viruses (NCLDVs) undergo a cytoplasmic or nucleo-cytoplasmic cycle, and the latter involves both nuclear and cytoplasmic compartments to proceed viral replication. Medusavirus, a recently isolated NCLDV, has a nucleo-cytoplasmic replication cycle in amoebas during which the host nuclear membrane apparently remains intact, a unique feature among amoeba-infecting giant viruses. The medusavirus genome lacks most transcription genes but encodes a full set of histone genes. To investigate the infection strategy, we performed a time-course RNA-seq experiment. All the viral genes were transcribed and classified into five temporal expression clusters. The immediate early genes (cluster 1, 42 genes) were mostly (83%) of unknown functions, frequently (95%) associated with a palindromic promoter-like motif, and enriched (45%) in putative nuclear-targeting genes. The later genes (clusters 2-5) were assigned to various functional categories. The viral linker histone H1 gene was in cluster 1, whereas the four core histone genes were in cluster 3, suggesting they had distinct roles during the course of the virus infection. The transcriptional profile of the host amoeba, Acanthamoeba castellanii, genes was greatly altered post-infection. Several encystment-related host genes showed increased representation levels at 48 hours post-infection, which is consistent with the previously reported amoeba encystment upon medusavirus infection. Overall, the transcriptional landscape during the course of medusavirus infection suggests that the virus modifies the host nuclear environment immediately after the initiation of infection.

Nuclear weapons, extinction, and the Anthropocene: Reappraising Jonathan Schell

In the Anthropocene, International Relations must confront the possibility of anthropogenic extinction. Recent, insightful attempts to advance new vocabularies of planet politics tend to demote the profound historical and intellectual links between our current predicament and the nuclear age. In contrast, we argue that it is vital to revisit the nuclear-environment nexus of the Cold War to trace genealogies of today's intricate constellation of security problems. We do so by reappraising the work of Jonathan Schell (1943–2014), author of The Fate of the Earth (1982), who came to regard extinction as a defining feature of the nuclear age. We show how a deep engagement with nuclear weapons led Schell to an understanding of the Earth as a complex, delicate ecology and fed into a sophisticated, Arendtian theory of extinction. Despite its limitations and tensions, we argue that Schell's work remains deeply relevant for rethinking human–Earth relations and confronting the Anthropocene.