Replication Patterns Research Articles

Genome-wide identification of alcohol dehydrogenase (ADH) gene family in oilseed rape (Brassica napus L.) and BnADH36 functional verification under salt stress

BackgroundAlcohol dehydrogenase (ADH) is an enzyme that binds to zinc, facilitating the interconversion of ethanol and acetaldehyde or other corresponding alcohols/aldehydes in the pathway of ethanol fermentation. It plays a pivotal role in responding to environmental stress. However, the response of the ADH family to abiotic stress remains unknown in rapeseed.ResultIn this study, we conducted a comprehensive genome-wide investigation of the ADH family in rapeseed, encompassing analysis of their gene structure, replication patterns, conserved motifs, cis-acting elements, and response to stress. A total of 47 ADH genes were identified within the rapeseed genome. Through phylogenetic analysis, BnADHs were classified into four distinct clades (I, II, IV, V). Prediction of protein domains revealed that all BnADH members possessed a GroES-like (ADH_N) domain and a zinc-bound (ADH_zinc_N) domain. Analysis of promoter sequences demonstrated that BnADHs contained numerous cis-acting elements associated with hormone and stress responses, indicating their widespread involvement in various biological regulatory processes. Expression profiling under different concentrations of salt stress treatments (0%, 0.4%, 0.8%, 1.0% NaCl) further highlighted the significant role played by the BnADH family in abiotic stress response mechanisms. Overexpression of BnADH36 in rapeseed significantly improved the salt tolerance of rapeseed.ConclusionThe features of the BnADH family in rapeseed was comprehensively characterized in this study, which could provide reference to the research of BnADHs in abiotic stress response.

Genome organization and stability in mammalian pre-implantation development

A largely stable genome is required for normal development, even as genetic change is an integral aspect of reproduction, genetic adaptation and evolution. Recent studies highlight a critical window of mammalian development with intrinsic DNA replication stress and genome instability in the first cell divisions after fertilization. Patterns of DNA replication and genome stability are established very early in mammals, alongside patterns of nuclear organization, and before the emergence of gene expression patterns, and prior to cell specification and germline formation. The study of DNA replication and genome stability in the mammalian embryo provides a unique cellular system due to the resetting of the epigenome to a totipotent state, and the de novo establishment of the patterns of nuclear organization, gene expression, DNA methylation, histone modifications and DNA replication. Studies on DNA replication and genome stability in the early mammalian embryo is relevant for understanding both normal and disease-causing genetic variation, and to uncover basic principles of genome regulation.

Replication kinetics of pathogenic Eurasian orthohantaviruses in human mesangial cells

BackgroundEurasian pathogenic orthohantaviruses cause hemorrhagic fever with renal syndrome (HFRS) characterized by acute kidney injury (AKI). The virulence of orthohantaviruses varies enormously and direct infection of different renal cell types contribute to pathogenesis. Glomerular mesangial cells play an essential role in the interplay between kidney cells and proper kidney function. Therefore, we analyzed the replication competence of different orthohantavirus species in primary mesangial cells and a mesangial cell line.MethodsWe tested the suitability of the mesangial cell line CIHGM-1 (conditionally immortalized human glomerular mesangial cells) as cell culture model for orthohantavirus kidney infection by comparison with primary human renal mesangial cells (HRMCs). We analyzed infection with high pathogenic Hantaan virus (HTNV), moderate pathogenic Puumala virus (PUUV) and non-/low-pathogenic Tula virus (TULV).ResultsEffective viral spread was observed for PUUV only, whereas infection with HTNV and TULV was abortive. However, in contrast to TULV, HTNV exhibits an initially high infection rate and declines afterwards. This replication pattern was observed in HRMCs and CIHGM-1 cells. Viability or adhesion was neither impaired for PUUV-infected CIHGM-1 nor HRMCs. A loss of migration capacity was observed in PUUV-infected CIHGM-1 cells, but not in HRMCs.ConclusionsThe identification of differences in the replication competence of pathogenic orthohantavirus strains in renal mesangial cells is of special interest and may provide useful insights in the virus-specific mechanisms of orthohantavirus induced AKI. The use of CIHGM-1 cells will facilitate the research in a relevant cell culture system.

THE USE OF MNEMONIC METHODS AND ASSOCIATIVE CARDS IN STUDYING GENETICS ANNOTATION

This article explores the effectiveness of using mnemonic techniques and associative cards in the study of genetics. The focus is on the principles of how associative cards function and their role in enhancing the memorization of complex genetic terms and processes. The literature review supports the positive impact of visualization and associations on students’ cognitive activities, highlighting how these methods facilitate the retention of challenging information in fields like biology and genetics. Mnemonic techniques, which combine verbal and visual elements, help learners build stronger cognitive connections and improve recall accuracy. Associative cards are discussed as a tool for integrating visual and textual information, allowing students to grasp genetic concepts such as DNA replication, mutations, and hereditary patterns more effectively.Moreover, the article examines the practical implementation of mnemonic methods in the modern educational system, particularly focusing on the use of digital platforms like Quizlet and Anki. These platforms utilize spaced repetition techniques to improve long-term retention, making the learning process more flexible and interactive. The research emphasizes how personalized study approaches, using these cognitive tools, contribute to better learning outcomes and overall academic performance.The conclusions show that the incorporation of mnemonic techniques and associative cards into genetics education not only enhances student engagement but also significantly improves the efficiency of mastering complex biological concepts. This study underlines the potential of these methods to be further integrated into educational curricula to address learning challenges in genetic studies.

Moving from the O-Z flap to the O-S flap for scalp reconstruction: A new geometrical model

The O-Z flap is the most commonly used local flap technique to repair round and oval scalp defects in clinical practice. Preoperative flap marking is one of the major technical issues of this reconstructive method and it is essential to achieve an optimal outcome. Nevertheless, the absence of a unified arc design scheme could significantly limit the use of this useful and reliable technique, and flap drawing is sometimes based more on the surgeon's experience than on a real geometrical model. Our aim was to describe an intuitive and standardizable method for O-Z flap marking, that we called "O-S flap," based on a simple and easily replicable geometrical pattern. We reported our experience in this case series of eight patients with skin tumors of the scalp who underwent scalp reconstruction with the "O-S flap" technique at our university hospital. Most patients had defects located on the vertex or parieto-occipital regions of the scalp. The area of the defects ranged from 7 to 78.5 cm2. There were no cases of flap necrosis, wound infection, or positive margins, and no patients required revision surgery. We believe that our technical refinement represents a safe, easy, and reproducible method for O-Z flap marking. It follows a simple geometrical model which could be customized according to different clinical needs.

Global influencers’ content creation strategies: Negotiating with platform affordances to practice vernacular creativity

We examine how globally oriented-influencers from India utilize specific strategies of content creation to negotiate with the dominant logic of platform affordances to engage with global audiences. It involves individual negotiations by the influencers with the platform affordances in creating content that foregrounds their cultural realities and aspirations while remaining relevant to global audiences. We do so by deploying the critical technocultural discourse analysis (CTDA) framework to understand influencers’ strategic choices and discursive practices as they interact and negotiate with the platform affordances. Our analysis shows two processes that help the influencers communicate their content to the global audience and sustain their local connections and followership: (1) Templatization: a process through which influencers from the global South attune themselves to the technological possibilities of the platform and utilize its features to produce content with a set of replicable patterns, formats, and practices; and (2) Cultural brokering: a negotiation strategy which allows the influencers to foreground and express their quotidian lived realities and cultural experiences in an increasingly globalized digital environment.

Cross-cohort replicable resting-state functional connectivity in predicting symptoms and cognition of schizophrenia.

Schizophrenia (SZ) is a debilitating mental illness characterized by adolescence or early adulthood onset of psychosis, positive and negative symptoms, as well as cognitive impairments. Despite a plethora of studies leveraging functional connectivity (FC) from functional magnetic resonance imaging (fMRI) to predict symptoms and cognitive impairments of SZ, the findings have exhibited great heterogeneity. We aimed to identify congruous and replicable connectivity patterns capable of predicting positive and negative symptoms as well as cognitive impairments in SZ. Predictable functional connections (FCs) were identified by employing an individualized prediction model, whose replicability was further evaluated across three independent cohorts (BSNIP, SZ = 174; COBRE, SZ = 100; FBIRN, SZ = 161). Across cohorts, we observed that altered FCs in frontal-temporal-cingulate-thalamic network were replicable in prediction of positive symptoms, while sensorimotor network was predictive of negative symptoms. Temporal-parahippocampal network was consistently identified to be associated with reduced cognitive function. These replicable 23 FCs effectively distinguished SZ from healthy controls (HC) across three cohorts (82.7%, 90.2%, and 86.1%). Furthermore, models built using these replicable FCs showed comparable accuracies to those built using the whole-brain features in predicting symptoms/cognition of SZ across the three cohorts (r = .17-.33, p < .05). Overall, our findings provide new insights into the neural underpinnings of SZ symptoms/cognition and offer potential targets for further research and possible clinical interventions.

5-Formylcytosine mediated DNA-peptide cross-link induces predominantly semi-targeted mutations in both Escherichia coli and human cells

Histone proteins can become trapped on DNA in the presence of 5-formylcytosine (5fC) to form toxic DNA-protein conjugates. Their repair may involve proteolytic digestion resulting in DNA-peptide cross-links (DpCs). Here, we have investigated replication of a model DpC comprised of an 11-mer peptide (NH2-GGGKGLGK∗GGA) containing an oxy-lysine residue (K∗) conjugated to 5fC in DNA. Both CXG and CXT (where X= 5fC-DpC) sequence contexts were examined. Replication of both constructs gave low viability (<10%) in Escherichia coli, whereas TLS efficiency was high (72%) in HEK 293T cells. In E.coli, the DpC was bypassed largely error-free, inducing only 2 to 3% mutations, which increased to 4 to 5% with SOS. For both sequences, semi-targeted mutations were dominant, and for CXG, the predominant mutations were G→T and G→C at the 3'-base to the 5fC-DpC. In HEK 293T cells, 7 to 9% mutations occurred, and the dominant mutations were the semi-targeted G → T for CXG and T → G for CXT. These mutations were reduced drastically in cells deficient in hPol η, hPol ι or hPol ζ, suggesting a role of these TLS polymerases in mutagenic TLS. Steady-state kinetics studies using hPol η confirmed that this polymerase induces G → T and T → G transversions at the base immediately 3' to the DpC. This study reveals a unique replication pattern of 5fC-conjugated DpCs, which are bypassed largely error-free in both E.coli and human cells and induce mostly semi-targeted mutations at the 3' position to the lesion.

In vivo parcellation of the human spinal cord functional architecture

Abstract The spinal cord is a critical component of the central nervous system, transmitting and integrating signals between the brain and the periphery via topographically organized functional levels. Despite its central role in sensorimotor processes and several neuromotor disorders, mapping the functional organization of the spinal cord in vivo in humans has been a long-standing challenge. Here, we test the efficacy of two data-driven connectivity approaches to produce a reliable and temporally stable functional parcellation of the cervical spinal cord through resting-state networks in two different functional magnetic resonance imaging (fMRI) datasets. Our results demonstrate robust and replicable patterns across methods and datasets, effectively capturing the spinal functional levels. Furthermore, we present the first evidence of spinal resting-state networks organized in functional levels in individual participants, unveiling personalized maps of the spinal functional organization. These findings underscore the potential of non-invasive, data-driven approaches to reliably outline the spinal cord’s functional architecture. The implications are far-reaching, from spinal cord fMRI processing to personalized investigations of healthy and impaired spinal cord function.

Periodic tapping mechanisms of skill learning in a fast-paced video game.

Timing plays a critical role when building up motor skill. In this study, we investigated and simulated human skill learning in a simplified variant of the Space Fortress video game named Auto Orbit with a strong timing component. Our principal aim was to test whether a computational model designed to simulate keypress actions repeated at rates slower than 500 ms (>500 ms) could also simulate human learning with repeated keypress actions taking place at very fast rates (≤500 ms). The main finding was that increasing speed stress forced human participants to qualitatively switch their behavior from a cognitively controlled strategy to an inherently rhythmic motor strategy. We show how the adaptive control of thought rational architecture's periodic tapping motor extension can replicate such rhythmic patterns of keypresses in two different computational models of human learning. The first model implements streamed motor actions across hands that are temporally decoupled, while the second model implements a coupled motor strategy in which actions from both hands are executed relative to the same periodic motor clock. Different subsets of subjects correspond to these two models. Our modeling simulations integrate previous psychological and motor control findings within a single cognitive architecture, and successfully replicate human behavioral patterns across a range of experimental measures at fast speed. (PsycInfo Database Record (c) 2024 APA, all rights reserved).

Development of a SYBR Green-Based RT-qPCR Assay for the Detection and Quantification of Lone Star Virus

Objective: Lone Star virus (LSV) is a newly characterized arbovirus with pathogenic potential. However, no detection methods are available to specifically identify and monitor LSV. Methods: Two SYBR green-based RT-qPCRs were developed and validated for the detection and quantification of LSV. Two primer sets were evaluated for reproducibility, specificity, and sensitivity. The primer sets were applied to monitor viral titers in vitro and via surveillance of LSV in collected ticks. Results: One primer set (LSV-S) was the most specific for LSV when tested against 11 other vector-borne viruses. While less specific, the LSV-M primer set detected &lt;2 copies/μl of the viral genome and &lt;1 copy/μL of the viral genome. Viral replication quantified with either primer set yielded similar viral replication patterns, indicating that both primer sets are sufficient to monitor viral titers in vitro. Plaque assays in human and non-human primate cell lines yielded no replicable plaques and could not be used for comparisons of viral titer quantification. LSV was not detected in the 143 ticks collected from southeast Texas. Conclusion: The SYBR green-based RT-qPCRs described herein can be utilized for the detection and monitoring of LSV for laboratory and tick surveillance purposes.

Alyawarr English

Abstract This paper explores Alyawarr English, a new contact language spoken in Ipmangker, a remote Alyawarr community of Central Australia. Focusing on language use by children and drawing on a corpus of 50+ hrs of naturalistic video recordings, several aspects of Alyawarr English are examined in detail. The analysis centres on the origins of nominal and verbal morphology, with comparison to the patterns of replication evidenced in other new Australian contact languages. This reveals that children’s Alyawarr English has several points of symmetry with these languages. Nominal inflectional morphology is primarily derived from Alyawarr sources. Verb morphology is primarily derived from Kriol/English sources. The lexicon is derived from both Kriol/English and Alyawarr sources. Variation between morphology of Alyawarr and Kriol/English sources is also considered in each domain, to further elucidate what gets replicated and why in the ongoing development of new Australian contact languages.

Scientific Evaluation of the Remedies Used in Turkish Folk Medicine to Treat Possible Viral Infections

Background: Plants, with their rich phytochemical treasury, are one of the main sources of drug development. However, a randomized search on plant sources for the discovery of phytochemicals with specified pharmacological activity is expensive and tedious. Therefore, it is logical to constrain the sources to increase success. In the recent four decades, the importance of traditional information has been recognized by the scientific community. Consequently, interest in field surveys for the documentation of traditional worldwide medicines has significantly increased. Aims and Methods: Infectious diseases induced by pathogenic bacteria, fungi, or viruses have been one of the most common health problems for the public, for which traditional remedies have been practiced. Since laypeople could not distinguish the microbial origin of the infection, the remedies used for treatment could not be delineated. The aim of this study was first to search the plants used in Turkish folk medicine for such infectious diseases. The second step was to find scientific evidence in the online databases for the frequently quoted plants whether they may have potential activity against virus replication. Results: A reference survey on the most frequently quoted plants revealed that 16 out of 17 were shown to possess virucide or inhibitory effects on the replication of various viruses. Conclusion: Since each virus type may have a different viral replication pattern, further detailed investigations should be carried out to reveal their exact antiviral potentials.

Do Technology Startups Replicate Internationalization Patterns From Big Companies? Evidence From Latin America

This article discusses the internationalization of technology startups in Latin America. The study analyzed 121 startups from five countries using a quantitative approach and data was collected from the Crunchbase platform. Results indicate that Argentinean, Chilean, and Colombian startups have faster internationalization trajectories than their Brazilian and Mexican counterparts, which tend to remain local during initial stages following the Uppsala model pattern. Our study on startup internationalization in Latin America yielded comparable results to big tech companies from these countries. However, we noticed that Mexican startups have better access to financial support receiving double the investment compared to other organizations. These finding provide valuable insights into promotive international entrepreneurship in emerging countries and can inform public policy accordingly.

Abnormalities in red blood cell production and pathogenesis of anemia in the progression of rock bream iridovirus (RBIV)

Rock bream iridovirus (RBIV), belonging to Megalocytivirus, causes severe mortality in rock bream. Almost all deaths associated with RBIV are accompanied by splenic enlargement and anemia. Although red blood cells (RBCs) are involved in the immune response against viral infections, their involvement in rock bream has not yet been studied in terms of the immune response against RBIV. In this study, the viral replication patterns, blood characteristics and anemia-related factors were evaluated in rock bream post RBIV infection. The virus-infected RBCs of rock bream demonstrated similarities in the expression levels of hemoglobins (HGB) (α and β), cytokine-dependent hematopoietic cell linker (CLNK) and hematopoietic transcription factor GATA (GATA), with significantly decreasing levels from 4 days post infection (dpi) to 17 (dpi), when the viral replication was at its peak. This suggests that the expression of blood-related genes is inadequate for HGB synthesis and RBC production, thereby causing anemia leading to death. Moreover, the levels of complete blood cell count (CBC) indicators, such as RBCs, HGB and hematocrit (HCT), significantly decreased from 10 to 17 dpi. This phenomenon suggests that blood-related gene expression and/or RBC-, HGB- and HCT-related levels are critical factors in RBIV-induced anemia and disease progression. These results highlight the significance of blood-mediated immune responses against RBIV infection in rock bream. Understanding blood-related gene levels to identify blood-related immune response interactions in rock bream will be useful for development of future strategies in controlling RBIV diseases in rock bream.

Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency.

Stochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of four specific genomic loci. MATAC-Seq relies on preferential modification of accessible DNA by methyltransferases combined with Nanopore-Sequencing for direct readout of methylated DNA-bases. Applying MATAC-Seq to selected early-efficient and late-inefficient yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an accessible nucleosome-free region in combination with well-positioned+1 and+2 nucleosomes as a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during eukaryotic DNA replication. Consequently, our single-molecule chromatin accessibility assay will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.

Bird’s Eye View on Lattice Structures: Design Issues and Applications for Best Practices in Mechanical Design

Lattice structures for engineering applications are patterns of unit cells designed to make a larger functional structure. Research on lattice structures ranges in many fields, from mechanical characterization and cell and pattern designs in respect of their applications, to the manufacturing process and its final shape control. From the manufacturing point of view, some kinds of lattice structures can be infeasible when approached with traditional manufacturing methods. It may offer an inevitable limitation of their adoption. However, advancements in Additive Manufacturing (AM) have solved this manufacturing issue to a great extent, allowing to obtain major complexity of the cells that can be achieved. The topology, shape of the unit cell, and the characteristics of its replication pattern allow us to obtain many kinds of structures in respect of the different engineering requirements and manufacturing constraints. Nevertheless, the necessity of new or dedicated CAD-CAE approaches arises to manage the domains of multiscale modeling. These are some of the advantages and disadvantages that may arise while approaching the design of a component using lattice structures. The aim of this paper is to provide an overview that integrates the most recent applications of lattice structures with their related design and manufacturing issues so that, from a practical design point of view, any state-of-the-art improvements may be established in respect of the related field of applications. In this article, engineers and researchers may find a practical summary of the capabilities and processes of lattice structures that are currently available from a design and development point of view.

Reading minds or reading scripts? De-intellectualising theory of mind.

Understanding the origins of human social cognition is a central challenge in contemporary science. In recent decades, the idea of a 'Theory of Mind' (ToM) has emerged as the most popular way of explaining unique features of human social cognition. This default view has been progressively undermined by research on 'implicit' ToM, which suggests that relevant precursor abilities may already be present in preverbal human infants and great apes. However, this area of research suffers from conceptual difficulties and empirical limitations, including explanatory circularity, over-intellectualisation, and inconsistent empirical replication. Our article breaks new ground by adapting 'script theory' for application to both linguistic and non-linguistic agents. It thereby provides a new theoretical framework able to resolve the aforementioned issues, generate novel predictions, and provide a plausible account of how individuals make sense of the behaviour of others. Script theory is based on the premise that pre-verbal infants and great apes are capable of basic forms of agency-detection and non-mentalistic goal understanding, allowing individuals to form event-schemata that are then used to make sense of the behaviour of others. We show how script theory circumvents fundamental problems created by ToM-based frameworks, explains patterns of inconsistent replication, and offers important novel predictions regarding how humans and other animals understand and predict the behaviour of others.

The Situated Assessment Method (SAM2): Establishing individual differences in habitual behavior.

From the perspectives of grounded, situated, and embodied cognition, we have developed a new approach for assessing individual differences. Because this approach is grounded in two dimensions of situatedness-situational experience and the Situated Action Cycle-we refer to it as the Situated Assessment Method (SAM2). Rather than abstracting over situations during assessment of a construct (as in traditional assessment instruments), SAM2 assesses a construct in situations where it occurs, simultaneously measuring factors from the Situated Action Cycle known to influence it. To demonstrate this framework, we developed the SAM2 Habitual Behavior Instrument (SAM2 HBI). Across three studies with a total of 442 participants, the SAM2 HBI produced a robust and replicable pattern of results at both the group and individual levels. Trait-level measures of habitual behavior exhibited large reliable individual differences in the regularity of performing positive versus negative habits. Situational assessments established large effects of situations and large situation by individual interactions. Several sources of evidence demonstrated construct and content validity for SAM2 measures of habitual behavior. At both the group and individual levels, these measures were associated with factors from the Situated Action Cycle known to influence habitual behavior in the literature (consistency, automaticity, immediate reward, long-term reward). Regressions explained approximately 65% of the variance at the group level and a median of approximately 75% at the individual level. SAM2 measures further exhibited well-established interactions with personality measures for self-control and neuroticism. Cognitive-affective processes from the Situated Action Cycle explained nearly all the variance in these interactions. Finally, a composite measure of habitualness established habitual behaviors at both the group and individual levels. Additionally, a composite measure of reward was positively related to the composite measure of habitualness, increasing with self-control and decreasing with neuroticism.

Future time perspective: Factor structure, age pattern, and implications for psychological well-being and life satisfaction.

Emerging research challenges the one-factor model of the future time perspective (FTP) scale by demonstrating two- and three-factor models of the FTP scale. Three samples (i.e., Switzerland and the United States; N = 2022) explored the factor structure, age pattern differences, tested the link between FTP factors, psychological well-being, and life satisfaction, as well as age as a moderator. We distinguished FTP into opportunities, extension, and constraint factors that corroborated previous research. We did not find a replicable curvilinear age pattern difference on any of the FTP factors. The association between extension and life satisfaction was stronger among younger than older adults. Alternatively, the association between constraint and life satisfaction was stronger among younger than older adults in Samples A and C, and the pattern was reversed in Sample B. Lastly, the association between constraint and environmental mastery was stronger among older adults than younger adults in Sample B and the pattern was reversed in Sample C. This variation in the perception of the future is different for people at different periods in life and has an important consequence for living life well, especially a focus on extension and lack of constraint.