Non-canonical (non-B) DNA structures-e.g. bent DNA, hairpins, G-quadruplexes (G4s), Z-DNA, etc.-which form at certain sequence motifs (e.g. A-phased repeats, inverted repeats, etc.), have emerged as important regulators of cellular processes and drivers of genome evolution. Yet, they have been understudied due to their repetitive nature and potentially inaccurate sequences generated with short-read technologies. Here we comprehensively characterize such motifs in the long-read telomere-to-telomere (T2T) genomes of human, bonobo, chimpanzee, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. Non-B DNA motifs are enriched at the genomic regions added to T2T assemblies and occupy 9%-15%, 9%-11%, and 12%-38% of autosomes and chromosomes X and Y, respectively. G4s and Z-DNA are enriched at promoters and enhancers, as well as at origins of replication. Repetitive sequences harbor more non-B DNA motifs than non-repetitive sequences, especially in the short arms of acrocentric chromosomes. Most centromeres and/or their flanking regions are enriched in at least one non-B DNA motif type, consistent with a potential role of non-B structures in determining centromeres. Our results highlight the uneven distribution of predicted non-B DNA structures across ape genomes and suggest their novel functions in previously inaccessible genomic regions.

• MeSH
• DNA * chemie   genetika   MeSH
• G-kvadruplexy MeSH
• genom lidský MeSH
• genom * MeSH
• Hominidae * genetika   MeSH
• lidé MeSH
• nukleotidové motivy MeSH
• Pan troglodytes genetika   MeSH
• repetitivní sekvence nukleových kyselin MeSH
• telomery * genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

An organism is considered "alive" if it can grow, reproduce, respond to external stimuli, metabolize nutrients, and maintain stability. By this definition, both mitochondria and viruses exhibit the key characteristics of independent life. In addition to their capacity for self-replication under specifically defined conditions, both mitochondria and viruses can communicate via shared biochemical elements, alter cellular energy metabolism, and adapt to their local environment. To explain this phenomenon, we hypothesize that early viral prototype species evolved from ubiquitous environmental DNA and gained the capacity for self-replication within coacervate-like liquid droplets. The high mutation rates experienced in this environment streamlined their acquisition of standard genetic codes and adaptation to a diverse set of host environments. Similarly, mitochondria, eukaryotic intracellular organelles that generate energy and resolve oxygen toxicity, originally evolved from an infectious bacterial species and maintain their capacity for active functionality within the extracellular space. Thus, while mitochondria contribute profoundly to eukaryotic cellular homeostasis, their capacity for freestanding existence may lead to functional disruptions over time, notably, the overproduction of reactive oxygen species, a phenomenon strongly linked to aging-related disorders. Overall, a more in-depth understanding of the full extent of the evolution of both viruses and mitochondria from primordial precursors may lead to novel insights and therapeutic strategies to address neurodegenerative processes and promote healthy aging.

• MeSH
• energetický metabolismus MeSH
• lidé MeSH
• mitochondrie * metabolismus   MeSH
• původ života * MeSH
• viry * metabolismus   genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

BACKGROUND: The Advanced Trauma Life Support classification (ATLS) of hypovolemic shock is a widely used teaching and treatment reference in emergency medicine, but oversimplifies clinical reality. A decade ago, a landmark study compared vital parameters to base deficit (BD) in trauma patients. The investigators concluded that BD had higher accuracy to detect the need for early blood product administration. BD was subsequently introduced in the ATLS shock classification and has since been widely accepted as a laboratory standard for hypovolemia. The aim of this study is to investigate whether a methodological bias may have inadvertently contributed to the study's results and interpretation. METHODS: In the current study, we replicate the original study by simulating a cohort of trauma patients with randomly generated data and applying the same methodological strategies. First, a predefined correlation between all predictor variables (vital parameters and BD) and outcome variable (transfusion) was set at 0.55. Then, in accordance with the methods of the original study we created a composite of ATLS parameters (highest class amongst heart rate, systolic blood pressure, and Glasgow Coma Scale) and compared it with BD for resulting transfusion quantity. Given the preset correlations between predictors and outcome, no predictor should exhibit a stronger association unless influenced by methodological bias. RESULTS: Applying the original imbalanced grouping and composite allocation strategies caused a systematic overestimation of shock class for traditional ATLS parameters, favoring the association between BD and transfusion. This effect persisted when the correlation between BD and transfusion was set substantially worse (rho = 0.3) than the correlation between ATLS parameters and transfusion (rho = 0.8). CONCLUSIONS: In this fully reproducible simulation, we confirm the inadvertent presence of methodological bias. It is physiologically reasonable to include a metabolic parameter to classify hypovolemic shock, but more evidence is needed to support widespread and preferred use of BD.

• MeSH
• hypovolemie diagnóza   klasifikace   MeSH
• krevní transfuze MeSH
• lidé MeSH
• neodkladná péče o pacienty s traumatem metody   MeSH
• poruchy acidobazické rovnováhy diagnóza   MeSH
• šok * klasifikace   diagnóza   patofyziologie   MeSH
• zkreslení výsledků (epidemiologie) MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

Oncogene-induced replication stress has been recognized as a major cause of genome instability in cancer cells. Increased expression of cyclin E1 caused by amplification of the CCNE1 gene is a common cause of replication stress in various cancers. Protein phosphatase magnesium-dependent 1 delta (PPM1D) is a negative regulator of p53 and has been implicated in termination of the cell cycle checkpoint. Amplification of the PPM1D gene or frameshift mutations in its final exon promote tumorigenesis. Here, we show that PPM1D activity further increases the replication stress caused by overexpression of cyclin E1. In particular, we demonstrate that cells expressing a truncated mutant of PPM1D progress faster from G1 to S phase and fail to complete licensing of the replication origins. In addition, we show that transcription-replication collisions and replication fork slowing caused by CCNE1 overexpression are exaggerated in cells expressing the truncated PPM1D. Finally, replication speed and accumulation of focal DNA copy number alterations caused by induction of CCNE1 expression was rescued by pharmacological inhibition of PPM1D. We propose that increased activity of PPM1D suppresses the checkpoint function of p53 and thus promotes genome instability in cells expressing the CCNE1 oncogene.

• MeSH
• cyklin E genetika   metabolismus   MeSH
• lidé MeSH
• nádorový supresorový protein p53 * genetika   metabolismus   MeSH
• nádory * MeSH
• nestabilita genomu MeSH
• proteinfosfatasa 2C genetika   metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

PURPOSE: Endoscopically assisted sagittal strip craniotomy with subsequent cranial orthosis is a frequently used surgical approach for non-syndromic sagittal synostosis. Originally, this technique involved a wide sagittal strip craniectomy with bilateral wedge osteotomies. More recent studies suggest omitting wedge osteotomies, achieving similar outcomes. The controversy surrounding wedge osteotomies and our efforts to refine our technique led us to create models and evaluate the mechanical impact of wedge osteotomies. METHODS: We conducted a 3D-print study involving preoperative CT scans of non-syndromic scaphocephaly patients undergoing minimally invasive-assisted remodelation (MEAR) surgery. The sagittal strip collected during surgery underwent thickness measurement, along with a 3-point bending test. These results were used to determine printing parameters for accurately replicating the skull model. Model testing simulated gravitational forces during the postoperative course and assessed lateral expansion under various wedge osteotomy conditions. RESULTS: The median sagittal strip thickness was 2.00 mm (range 1.35-3.46 mm) and significantly positively correlated (p = 0.037) with the median force (21.05 N) of the 3-point bending test. Model testing involving 40 models demonstrated that biparietal wedge osteotomies significantly reduced the force required for lateral bone shift, with a trend up to 5-cm-long cuts (p = 0.007). Additional cuts beyond this length or adding the occipital cut did not provide further significant advantage (p = 0.1643; p = 9.6381). CONCLUSION: Biparietal wedge osteotomies reduce the force needed for lateral expansion, provide circumstances for accelerated head shape correction, and potentially reduce the duration of cranial orthosis therapy.

• MeSH
• 3D tisk * MeSH
• anatomické modely MeSH
• endoskopie metody   MeSH
• kojenec MeSH
• kraniosynostózy * chirurgie   MeSH
• kraniotomie metody   MeSH
• lidé MeSH
• osteotomie * metody   MeSH
• počítačová rentgenová tomografie MeSH
• Check Tag
• kojenec MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

Organoids are 3-dimensional (3D) self-assembled structures capable of replicating the microanatomy and physiology of the epithelial components of their organ of origin. Adult stem cell (ASC) derived organoids from the liver have previously been shown to differentiate into primarily mature cholangiocytes, and their partial differentiation into functional hepatocytes can be promoted using specific media compositions. While full morphological differentiation of mature hepatocytes from ASCs has not yet been reported for any species, the functional differentiation can be approximated using various media compositions. Six differentiation media formulations from published studies on hepatic organoids were used for the differentiation protocol. Target species for these protocols were humans, mice, cats, and dogs, and encompassed various combinations and concentrations of four major hepatocyte media components: Bone morphogenetic protein 7 (BMP7), Fibroblast Growth Factor 19 (FGF19), Dexamethasone (Dex), and Gamma-Secretase Inhibitor IX (DAPT). Additionally, removing R-spondin from basic organoid media has previously been shown to drive the differentiation of ASC into mature hepatocytes. Differentiation media (N = 20) were designed to encompass combinations of the four major hepatocyte media components. The preferred differentiation of ASC-derived organoids from liver tissue into mature hepatocytes over cholangiocytes was confirmed by albumin production in the culture supernatant. Out of the twenty media compositions tested, six media resulted in the production of the highest amounts of albumin in the supernatant of the organoids. The cell lines cultured using these six media were further characterized via histological staining, transmission electron microscopy, RNA in situ hybridization, analysis of gene expression patterns, immunofluorescence, and label-free proteomics. The results indicate that preferential hepatocyte maturation from canine ADC-derived organoids from liver tissue is mainly driven by Dexamethasone and DAPT components. FGF19 did not enhance organoid differentiation but improved cell culture survival. Furthermore, we confirm that removing R-spondin from the media is crucial for establishing mature hepatic organoid cultures.

• Publikační typ
• časopisecké články MeSH

• MeSH
• biologie MeSH
• lékařská genetika MeSH
• molekulární medicína MeSH

• Konspekt
• Lékařské vědy. Lékařství
• Učební osnovy. Vyučovací předměty. Učebnice
• NLK Obory
• biologie
• NLK Publikační typ
• učebnice vysokých škol

Accurate and complete replication of genetic information is a fundamental process of every cell division. The replication licensing is the first essential step that lays the foundation for error-free genome duplication. During licensing, minichromosome maintenance protein complexes, the molecular motors of DNA replication, are loaded to genomic sites called replication origins. The correct quantity and functioning of licensed origins are necessary to prevent genome instability associated with severe diseases, including cancer. Here, we delve into recent discoveries that shed light on the novel functions of licensed origins, the pathways necessary for their proper maintenance, and their implications for cancer therapies.

• MeSH
• lidé MeSH
• MCM proteiny genetika   metabolismus   MeSH
• nádory * genetika   MeSH
• replikace DNA * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

Robust scientific knowledge is contingent upon replication of original findings. However, replicating researchers are constrained by resources, and will almost always have to choose one replication effort to focus on from a set of potential candidates. To select a candidate efficiently in these cases, we need methods for deciding which out of all candidates considered would be the most useful to replicate, given some overall goal researchers wish to achieve. In this article we assume that the overall goal researchers wish to achieve is to maximize the utility gained by conducting the replication study. We then propose a general rule for study selection in replication research based on the replication value of the set of claims considered for replication. The replication value of a claim is defined as the maximum expected utility we could gain by conducting a replication of the claim, and is a function of (a) the value of being certain about the claim, and (b) uncertainty about the claim based on current evidence. We formalize this definition in terms of a causal decision model, utilizing concepts from decision theory and causal graph modeling. We discuss the validity of using replication value as a measure of expected utility gain, and we suggest approaches for deriving quantitative estimates of replication value. Our goal in this article is not to define concrete guidelines for study selection, but to provide the necessary theoretical foundations on which such concrete guidelines could be built. (PsycInfo Database Record (c) 2023 APA, all rights reserved).

• MeSH
• lidé MeSH
• nejistota MeSH
• teoretické modely * MeSH
• znalosti * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: During the worldwide COVID-19 pandemic crisis, the role of digital contact tracing (DCT) intensified. However, the uptake of this technology expectedly differed among age cohorts and national cultures. Various conceptual tools were introduced to strengthen DCT research from a theoretical perspective. However, little has been done to compare theory-supported findings across different cultural contexts and age cohorts. OBJECTIVE: Building on the original study conducted in Belgium in April 2020 and theoretically underpinned by the Health Belief Model (HBM), this study attempted to confirm the predictors of DCT adoption in a cultural environment different from the original setting, that is, the Czech Republic. In addition, by using brief qualitative evidence, it aimed to shed light on the possible limitations of the HBM in the examined context and to propose certain extensions of the HBM. METHODS: A Czech version of the original instrument was administered to a convenience sample of young (aged 18-29 y) Czech adults in November 2020. After filtering, 519 valid responses were obtained and included in the quantitative data analysis, which used structural equation modeling and followed the proposed structure of the relationships among the HBM constructs. Furthermore, a qualitative thematic analysis of the free-text answers was conducted to provide additional insights about the model's validity in the given context. RESULTS: The proposed measurement model exhibited less optimal fit (root mean square error of approximation=0.065, 90% CI 0.060-0.070) than in the original study (root mean square error of approximation=0.036, 90% CI 0.033-0.039). Nevertheless, perceived benefits and perceived barriers were confirmed as the main, statistically significant predictors of DCT uptake, consistent with the original study (β=.60, P<.001 and β=-.39; P<.001, respectively). Differently from the original study, self-efficacy was not a significant predictor in the strict statistical sense (β=.12; P=.003). In addition, qualitative analysis demonstrated that in the given cohort, perceived barriers was the most frequent theme (166/354, 46.9% of total codes). Under this category, psychological fears and concerns was a subtheme, notably diverging from the original operationalization of the perceived barriers construct. In a similar sense, a role for social influence in DCT uptake processes was suggested by some respondents (12/354, 1.7% of total codes). In summary, the quantitative and qualitative results indicated that the proposed quantitative model seemed to be of limited value in the examined context. CONCLUSIONS: Future studies should focus on reconceptualizing the 2 underperforming constructs (ie, perceived severity and cues to action) by considering the qualitative findings. This study also provided actionable insights for policy makers and app developers to mitigate DCT adoption issues in the event of a future pandemic caused by unknown viral agents.

• MeSH
• COVID-19 * epidemiologie   MeSH
• lidé MeSH
• mladiství MeSH
• mobilní aplikace * MeSH
• pandemie MeSH
• srovnání kultur MeSH
• trasování kontaktů metody   MeSH
• Check Tag
• lidé MeSH
• mladiství MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH