Molecular Characterization of Cold Adaptation of Membrane Proteins in the Vibrionaceae Core-Genome

Cold-adaptation strategies have been studied in multiple psychrophilic organisms, especially for psychrophilic enzymes. Decreased enzyme activity caused by low temperatures as well as a higher viscosity of the aqueous environment require certain adaptations to the metabolic machinery of the cell. In addition to this, low temperature has deleterious effects on the lipid bilayer of bacterial membranes and therefore might also affect the embedded membrane proteins. Little is known about the adaptation of membrane proteins to stresses of the cold. In this study we investigate a set of 66 membrane proteins from the core genome of the bacterial family Vibrionaceae to identify general characteristics that discern psychrophilic and mesophilic membrane proteins. Bioinformatical and statistical methods were used to analyze the alignments of the three temperature groups mesophilic, intermediate and psychrophilic. Surprisingly, our results show little or no adaptation to low temperature for those parts of the proteins that are predicted to be inside the membrane. However, changes in amino acid composition and hydrophobicity are found for complete sequences and sequence parts outside the lipid bilayer. Among others, the results presented here indicate a preference for helix-breaking and destabilizing amino acids Ile, Asp and Thr and an avoidance of the helix-forming amino acid Ala in the amino acid composition of psychrophilic membrane proteins. Furthermore, we identified a lower overall hydrophobicity of psychrophilic membrane proteins in comparison to their mesophilic homologs. These results support the stability-flexibility hypothesis and link the cold-adaptation strategies of membrane proteins to those of loop regions of psychrophilic enzymes. © 2012 Kahlke, Thorvaldsen

Three-dimensional conformation at the H19/Igf2 locus supports a model of enhancer tracking

Insight into how the mammalian genome is structured in vivo is key to understanding transcriptional regulation. This is especially true in complex domains in which genes are coordinately regulated by long-range interactions between cis-regulatory elements. The regulation of the H19/Igf2 imprinted region depends on the presence of several cis-acting sequences, including a methylation-sensitive insulator between Igf2 and H19 and shared enhancers downstream of H19. Each parental allele has a distinct expression pattern. We used chromosome conformation capture to assay the native three-dimensional organization of the H19/Igf2 locus on each parental copy. Furthermore, we compared wild-type chromosomes to several mutations that affect the insulator. Our results show that promoters and enhancers reproducibly co-localize at transcriptionally active genes, i.e. the endodermal enhancers contact the maternal H19 and the paternal Igf2 genes. The active insulator blocks traffic of the enhancers along the chromosome, restricting them to the H19 promoter. Conversely, the methylated inactive insulator allows the enhancers to contact the upstream regions, including Igf2. Mutations that either remove or inhibit insulator activity allow unrestricted access of the enhancers to the whole region. A mutation that allows establishment of an enhancer-blocker on the normally inactive paternal copy diminishes the contact of the enhancer with the Igf2 gene. Based on our results, we propose that physical proximity of cis-acting DNA elements is vital for their activity in vivo. We suggest that enhancers track along the chromosome until they find a suitable promoter sequence to interact with and that insulator elements block further tracking of enhancers

Tissue-specific insulator function at H19/Igf2 revealed by deletions at the imprinting control region

Parent-of-origin-specific expression at imprinted genes is regulated by allele-specific DNA methylation at imprinting control regions (ICRs). This mechanism of gene regulation, where one element controls allelic expression of multiple genes, is not fully understood. Furthermore, the mechanism of gene dysregulation through ICR epimutations, such as loss or gain of DNA methylation, remains a mystery. We have used genetic mouse models to dissect ICR-mediated genetic and epigenetic regulation of imprinted gene expression. The H19/insulin-like growth factor 2 (Igf2) ICR has a multifunctional role including insulation, activation and repression. Microdeletions at the human H19/IGF2 ICR (IC1) are proposed to be responsible for IC1 epimutations associated with imprinting disorders such as Beckwith–Wiedemann syndrome (BWS). Here, we have generated and characterized a mouse model that mimics BWS microdeletions to define the role of the deleted sequence in establishing and maintaining epigenetic marks and imprinted expression at the H19/IGF2 locus. These mice carry a 1.3 kb deletion at the H19/Igf2 ICR [Δ2,3] removing two of four CCCTC-binding factor (CTCF) sites and the intervening sequence, ∼75% of the ICR. Surprisingly, the Δ2,3 deletion does not perturb DNA methylation at the ICR; however, it does disrupt imprinted expression. While repressive functions of the ICR are compromised by the deletion regardless of tissue type, insulator function is only disrupted in tissues of mesodermal origin where a significant amount of CTCF is poly(ADP-ribosyl)ated. These findings suggest that insulator activity of the H19/Igf2 ICR varies by cell type and may depend on cell-specific enhancers as well as posttranslational modifications of the insulator protein CTCF

Humanized H19/Igf2 locus reveals diverged imprinting mechanism between mouse and human and reflects Silver–Russell syndrome phenotypes

Genomic imprinting is essential for mammalian development. Curiously, elements that regulate genomic imprinting, the imprinting control regions (ICRs), often diverge across species. To understand whether the diverged ICR sequence plays a species-specific role at the H19/insulin-like growth factor 2 (Igf2) imprinted locus, we generated a mouse in which the human ICR (hIC1) sequence replaced the endogenous mouse ICR. We show that the imprinting mechanism has partially diverged between mouse and human, depending on the parental origin of the hIC1 in mouse. We also suggest that our mouse model is optimal for studying the imprinting disorders Beckwith–Wiedemann syndrome when hIC1 is maternally transmitted, and Silver–Russell syndrome when hIC1 is paternally transmitted

Mortality of the Orthodox Adult Population in Ekaterinburg during the Late 19th and Early 20th Centuries

Поступила в редакцию: 15.08.2021. Принята к печати: 29.10.2021.Submitted: 15.08.2021. Accepted: 29.10.2021.Традиционно исследования исторической смертности фокусировались на изучении национальной, региональной либо локальной специфики. Создание баз индивидуальных данных позволило изучать смертность на уровне индивидов, отдельных семей и поколений. При этом роль ближайшего окружения, не состоявшего в кровном родстве, учитывалась редко. Между тем, стремительная урбанизация разрушила семейные связи и каналы трансляции традиционных моделей демографического поведения. Одновременно возрастала роль внесемейных факторов, главным из которых был церковный приход, с конца XIX в. постепенно трансформировавшийся в соседское сообщество — прообраз городского микрорайона. Предлагаемая работа нацелена на исследование смертности взрослого населения Екатеринбурга конца XIX — начала XX в. и ее дифференциации между приходами Русской православной церкви. Источниковую базу составили официальная статистика и база данных «Регистр населения Урала», созданная на основе метрических книг за 1880–1919 гг. пяти православных приходов Екатеринбурга. В ходе исследования была выполнена реконструкция динамики смертности по каждому приходу и городу в целом; восстановлена структура смертности; вычислен средний возраст смертности; проведен анализ причин, ее вызвавших; проанализирована сезонность. В итоге можно заключить, что каждый из пяти православных приходов имел определенную демографическую специфику. На смертность влиял экономический профиль района и направление городской застройки, большое значение имело расположение крупных социальных объектов на территории прихода. Проведенное исследование позволило выявить определенную стабильность и респектабельность Богоявленского и отчасти Вознесенского прихода; «мигрантскую» специфику Александро-Невского и Свято-Духовского; и некий средний, близкий общегородскому, характер района, соответствовавшего приходу Екатерининского собора.Traditionally, studies of historical mortality have focused on the national, regional, or local levels. Currently, the creation of individual level databases has made it possible to study mortality at the individual and family levels, also following people over generations. However, this research rarely considered non-family relations; at the same time, rapid urbanisation during the late nineteenth century severed many family ties and hindered the transmission of traditional models for demographic behaviour. Thus, the role of non-family factors increased, the main of which was the church parish, which since the end of the nineteenth century gradually transformed into a neighborhood community — the prototype of the urban microdistrict. This research aims to study the mortality of the adult population of Ekaterinburg during the decades around 1900, differentiating between the parishes of the Russian Orthodox Church. The sources consist of official statistics and the Ural Population Project database, which was created based on the metric (church) books. The authors reconstruct the full development of mortality for each parish and for Ekaterinburg as a whole; map the structure of mortality, calculate the average age at death, as well as analyse the causes of death and its seasonality. As a result, it may be concluded that each of the five Orthodox parishes indeed had a certain demographic specificity. Mortality was influenced by the economic profile of the area and the trend of urban development, where the location of social facilities on the territory of each parish was of great importance.Работа выполнена при финансовой поддержке РФФИ и Правительства Свердловской области, грант № 20-49-660013 «Городские элиты Екатеринбурга конца XVIII — начала XX века: 250 лет социальной и демографической эволюции».The research is sponsored by the Russian Foundation for Basic Research and Government of Sverdlovsk Region, project 20-49-660013 “Urban Elites of Ekaterinburg at the End of the 18th — Beginning of the 20th Centuries: 250 Years of Social and Demographic Evolution”

The SOS Pilot Study: a RCT of routine oxygen supplementation early after acute stroke—effect on recovery of neurological function at one week

Mild hypoxia is common after stroke and associated with poor long-term outcome. Oxygen supplementation could prevent hypoxia and improve recovery. A previous study of routine oxygen supplementation showed no significant benefit at 7 and 12 months. This pilot study reports the effects of routine oxygen supplementation for 72 hours on oxygen saturation and neurological outcomes at 1 week after a stroke

Distinct Methylation Changes at the IGF2-H19 Locus in Congenital Growth Disorders and Cancer

Background: Differentially methylated regions (DMRs) are associated with many imprinted genes. In mice methylation at a DMR upstream of the H19 gene known as the Imprint Control region (IC1) is acquired in the male germline and influences the methylation status of DMRs 100 kb away in the adjacent Insulin-like growth factor 2 (Igf2) gene through long-range interactions. In humans, germline-derived or post-zygotically acquired imprinting defects at IC1 are associated with aberrant activation or repression of IGF2, resulting in the congenital growth disorders Beckwith-Wiedemann (BWS) and Silver-Russell (SRS) syndromes, respectively. In Wilms tumour and colorectal cancer, biallelic expression of IGF2 has been observed in association with loss of methylation at a DMR in IGF2. This DMR, known as DMR0, has been shown to be methylated on the silent maternal IGF2 allele presumably with a role in repression. The effect of IGF2 DMR0 methylation changes in the aetiology of BWS or SRS is unknown. Methodology/Principal Findings: We analysed the methylation status of the DMR0 in BWS, SRS and Wilms tumour patients by conventional bisulphite sequencing and pyrosequencing. We show here that, contrary to previous reports, the IGF2 DMR0 is actually methylated on the active paternal allele in peripheral blood and kidney. This is similar to the IC

Matrilineal diversity and population history of Norwegians

Background While well known for its Viking past, Norway's population history and the influences that have shaped its genetic diversity are less well understood. This is particularly true with respect to its demography, migration patterns, and dialectal regions, despite there being curated historical records for the past several centuries. In this study, we undertook an analysis of mitochondrial DNA (mtDNA) diversity within the country to elaborate this history from a matrilineal genetic perspective. Methods We aggregated 1174 partial modern Norwegian mtDNA sequences from the published literature and subjected them to detailed statistical and phylogenetic analysis by dialectal regions and localities. We further contextualized the matrilineal ancestry of modern Norwegians with data from Mesolithic, Iron Age, and historic period populations. Results Modern Norwegian mtDNAs fell into eight West Eurasian (N, HV, JT, I, U, K, X, W), five East Eurasian (A, F, G, N11, Z), and one African (L2) haplogroups. Pairwise analysis of molecular variance (AMOVA) estimates for all Norwegians indicated they were differentiated from each other at 1.68% (p < 0.001). Norwegians within the same dialectal region also showed genetic similarities to each other, although differences between subpopulations within dialectal regions were also observed. In addition, certain mtDNA lineages in modern Norwegians were also found among prehistoric and historic period populations, suggesting some level of genetic continuity over hundreds to many thousands of years. Conclusions This analysis of mtDNA diversity provides a detailed picture of the genetic variation within Norway in light of its topography, settlement history, and historical migrations over the past several centuries.publishedVersio