bluuebunny/crossref_metadata_2025 huggingface dataset:
A Decision Support Tool for Social Engagement, Alternative Financing and Risk Mitigation of Geothermal Energy Projects
Authors: Ioannou Anastasia , Falcone Gioia , Baisch Christina , Friederichs Georgie , Hildebrand Jan
Published: January 2023

This paper presents a decision support tool for promoters/investors of geothermal energy projects, based on a decision tree (DT) structure. The DT aims to assist stakeholders to select public engagement strategies, alternative financing solutions and risk mitigation measures (or options) for geothermal energy projects. Public engagement is necessary for the successful development and operation of geothermal projects. Available studies (including toolkits and protocols) commonly list a set of practices for social engagement without providing information on the factors which render certain options more suitable than others. The presented tool offers a transparent framework to how relevant decisions could be managed by providing a sequence of questions that focus on social, environmental, resource risk, and financial influencing factors and to realise community engagement into geothermal projects. This work is part of the Horizon 2020 CROWDTHERMAL project, which aims at empowering the public to directly participate in the development of geothermal projects through social engagement tools and alternative financing schemes, like crowdfunding.
Predicting Spruce Taiga Distribution in Northeast Asia Using Species Distribution Models: Glacial Refugia, Mid-Holocene Expansion and Future Predictions for Global Warming
Authors: Korznikov Kirill , Petrenko Tatyana , Kislov Dmitry , Krestov Pavel , Doležal Jiří
Published: January 2023

Spruce taiga forests in Northeast Asia are of great economic and conservation importance. Continued climate warming may cause profound changes in their distribution. We use prognostic and retrospective species distribution models based on the Random Forest machine learning method to estimate the potential range change of the dominant taiga conifer Jezo spruce (Picea jezoensis (Siebold & Zucc.) Carrière) for the year 2070 climate warming scenarios and for past climate epochs–the Last Glacial Maximum (LGM) (~21,000 years before present) and the mid-Holocene Climatic Optimum (MHO) (~7000 years before the present) using the MIROC-ESM and CCSM4 climate models. The current suitable climatic conditions for P. jezoensis are estimated to be 500,000 km2. Both climatic models show similar trends in past and future ranges but provide different quantitative areal estimates. During the LGM, the main part of the species range was located much further south than today at 35–45° N. Projected climate warming will cause a greater change in the distributional range of P. jezoensis than has occurred since the MHO. Overlapping climatic ranges at different times show that the Changbai Mountains, the central parts of the Japanese Alps, Hokkaido, and the Sikhote-Alin Mountains will remain suitable refugia for Jezo spruce until 2070. The establishment of artificial forest stands of P. jezoensis and intraspecific taxa in the future climate-acceptable regions may be important for the preservation of genetic diversity.
The Fine Root Distribution and Morphology of Mature White Poplar in Natural Temperate Riverside Forests under Periodically Flooded or Dry Hydrological Conditions
Authors: Frymark-Szymkowiak Anna , Kieliszewska-Rokicka Barbara
Published: January 2023

Fine roots are a key component of carbon turnover in the terrestrial environment. Therefore, their distribution allows for the estimation of areas of carbon in the soil. The vertical distribution of roots is the result of both the tree species and various environmental factors. Research on the architecture of root systems most often includes seedlings and young trees growing under experimental conditions; however, little is known about trees in their natural habitats. The aim of this study is to analyze the fine root distribution of mature white poplar trees in natural riverside temperate zone forests of Central Europe (Poland) periodically flooded and in dry hydrological conditions. The length, diameter, and area of the fine roots, as well as the specific root length (SRL) and specific root area (SRA) of white poplar were measured in three layers of the soil, 0–10 cm, 10–20 cm, and 20–30 cm depths, in three forest sites. Two of the sites experience periodic floods, and one has been without flooding for 80 years, due to the construction of a flood embankment. The highest values of the lengths and surface areas of the poplar fine roots were observed at a depth of 0–10 cm at all sites. Soil moisture was positively correlated with the analyzed root parameters. The presence of understory plant roots contributed to the reduction in the fine root length of poplar in the subsurface layer, compared to the site that was not affected by the presence of plants other than poplar. The distribution of fine roots, the most dynamic part of the plant root system, reflects the most active areas in the soil profile. The presented research will allow for a better understanding of the functioning of natural riverside ecosystems, as well as show the great adaptability of white poplar fine roots to various conditions in the soil.
Highlighting the Impact of Lactic-Acid-Bacteria-Derived Flavours or Aromas on Sensory Perception of African Fermented Cereals
Authors: Kayitesi Eugénie , Onojakpor Ogheneyoma , Moyo Siphosanele Mafa
Published: January 2023

Sensory characteristics and flavour profiles of lactic-acid-fermented foods are influenced by lactic acid bacteria (LAB) metabolic activities. The flavour compounds released/produced are directly linked to the sensory characteristics of fermented cereals. African fermented cereals constitute a staple, frequently consumed food group and provide high energy and essential nutrients to many communities on the continent. The flavour and aroma characteristics of fermented cereal products could be correlated with the metabolic pathways of fermenting microorganisms. This report looks at the comprehensive link between LAB-produced flavour metabolites and sensory attributes of African fermented cereals by reviewing previous studies. The evaluation of such data may point to future prospects in the application of flavour compounds derived from African fermented cereals in various food systems and contribute toward the improvement of flavour attributes in existing African fermented cereal products.
Digitalization of Distribution Transformer Failure Probability Using Weibull Approach towards Digital Transformation of Power Distribution Systems
Authors: Attanayake A. M. Sakura R. H. , Ratnayake R. M. Chandima
Published: January 2023

Digitalization of the failure-probability modeling of crucial components in power-distribution systems is important for improving risk and reliability analysis for system-maintenance and asset-management practices. This paper aims to implement a Python programming-based Weibull approach for digitalization of distribution-transformer (DT) failures, considering a regional section of DTs in Sri Lanka as a case study. A comprehensive analysis for DT-failure data for six years has been utilized to derive a Weibull distribution analysis for DTs. The interpretation of the resulting beta and alpha parameters of the Weibull analysis for different categories of DTs in the selected region is also presented. The resulting data can be uploaded to computerized maintenance-management systems (CMMS), to adopt conclusions or resolutions reached by the asset and maintenance managers. Ultimately, failure-probability modeling is beneficial for decision-making processes for higher management aiming for the digital transformation of power-distribution systems.
Wildfire Risk Zone Mapping in Contrasting Climatic Conditions: An Approach Employing AHP and F-AHP Models
Authors: Sinha Aishwarya , Nikhil Suresh , Ajin Rajendran Shobha , Danumah Jean Homian , Saha Sunil , Costache Romulus , Rajaneesh Ambujendran , Sajinkumar Kochappi Sathyan , Amrutha Kolangad , Johny Alfred , Marzook Fahad , Mammen Pratheesh Chacko , Abdelrahman Kamal , Fnais Mohammed S. , Abioui Mohamed
Published: January 2023

Wildfires are one of the gravest and most momentous hazards affecting rich forest biomes worldwide; India is one of the hotspots due to its diverse forest types and human-induced reasons. This research aims to identify wildfire risk zones in two contrasting climate zones, the Wayanad Wildlife Sanctuary in the Western Ghats and the Kedarnath Wildlife Sanctuary in the Himalayas, using geospatial tools, analytical hierarchy process (AHP), and fuzzy-AHP models to assess the impacts of various conditioning factors and compare the efficacy of the two models. Both of the wildlife sanctuaries were severely battered by fires in the past, with more than 100 fire incidences considered for this modeling. This analysis found that both natural and anthropogenic factors are responsible for the fire occurrences in both of the two sanctuaries. The validation of the risk maps, utilizing the receiver operating characteristic (ROC) method, proved that both models have outstanding prediction accuracy for the training and validation datasets, with the F-AHP model having a slight edge over the other model. The results of other statistical validation matrices such as sensitivity, accuracy, and Kappa index also confirmed that F-AHP is better than the AHP model. According to the F-AHP model, about 22.49% of Kedarnath and 17.12% of Wayanad fall within the very-high risk zones. The created models will serve as a tool for implementing effective policies intended to reduce the impact of fires, even in other protected areas with similar forest types, terrain, and climatic conditions.
Recent Advances in Hydrogels via Diels–Alder Crosslinking: Design and Applications
Authors: Morozova Sofia M.
Published: January 2023

The Diels–Alder (DA) reaction is a promising tool for obtaining covalently crosslinked hydrogels due to its reaction bioorthogonality, the absence of by-products, and the application of mild conditions without a catalyst. The resulting hydrogels are in demand for use in various fields of materials science and biomedicine. While the dynamic nature of the cycloaddition of diene and dienophile has previously been used extensively for the fabrication of self-healing materials, it has only recently spread to the expansion of the functional properties of polymer gels for bioapplications. This review describes strategies and recent examples of obtaining hydrogels based on the DA reaction, demonstrating that the emerging functional properties go beyond self-healing. The types of classifications of hydrogels are listed, depending on the type of reaction and the nature of the components. Examples of obtaining hydrogels based on the normal and inverse electron-demand DA reaction, as well as the application of hydrogels for cell culture, drug delivery, injectable gels, and wound dressings, are considered. In conclusion, possible developmental directions are discussed, including the use of diene–dienophile pairs with a low temperature for the reversal of DA reaction, the modification of nanoparticles by diene and/or dienophile fragments, and new applications such as ink for 3D printing, sensing hydrogels, etc.
Synthesis and Characterization of an Novel Intercalated Polyacrylamide/Clay Nanocomposite
Authors: Zhang Song , Wei Falin , Liu Pingde , Cai Cheng , Zeng Zhihui , Yu Zhentao , Wang Zengbao , Bai Yingrui
Published: January 2023

Solving the problem of the low temperature and low salt resistances of conventional polyacrylamide and the high cost of functional monomers, and thus, introducing it to the interlayer space provided by a layered structure for polymer modification, is a promising option. In this study, montmorillonite was used as the inorganic clay mineral, and an intercalated polyacrylamide/clay nanocomposite was synthesized via in situ intercalation polymerization. The optimal synthesis conditions were a clay content of 10.7%, preparation temperature of 11 °C, initiator concentration of 2.5 × 10−4 mol/L, and chain extender concentration of 5%. The IR results showed that the polymer was successfully introduced to the nanocomposite. The synthesized intercalated polyacrylamide/clay nanocomposite exhibited a better thickening effect, good viscoelasticity, and better salt resistance and thermal stability than polyacrylamide. In addition, the thickening capacity and thermal stability were superior to the salt-resistant polymer, with a 16.0% higher thickening viscosity and a 15.1% higher viscosity retention rate at 85 °C for 60 d. The intercalated polyacrylamide/clay nanocomposite further expanded the application of polyacrylamide in petroleum exploitation.
Genetic Diversity and Population Structure of the Native Pulawska and Three Commercial Pig Breeds Based on Microsatellite Markers
Authors: Radko Anna , Koseniuk Anna , Smołucha Grzegorz
Published: January 2023

Swine DNA profiling is highly important for animal identification and parentage verification and also increasingly important for meat traceability. This work aimed to analyze the genetic structure and genetic diversity in selected Polish pig breeds. The study used a set of 14 microsatellite (STR) markers recommended by ISAG for parentage verification in the native Puławska pig (PUL, n = 85) and three commercial pig breeds: Polish Large White (PLW, n = 74), Polish Landrace (PL, n = 85) and foreign breed Duroc (DUR, n = 84). Genetic differentiation among breeds accounted for 18% of the total genetic variability (AMOVA). Bayesian structure analysis (STRUCTURE) indicated that the four distinct genetic clusters obtained corresponded to the four breeds studied. The genetic Reynolds distances (Ɵw) showed a close relationship between PL and PLW breeds and the most distant for DUR and PUL pigs. The genetic differentiation values (FST) were lower between PL and PLW and higher between PUL and DUR. The principal coordinate analysis (PCoA) supported the classification of the populations into four clusters.
Molecular Genetic Characteristics of FANCI, a Proposed New Ovarian Cancer Predisposing Gene
Authors: Fierheller Caitlin T. , Alenezi Wejdan M. , Serruya Corinne , Revil Timothée , Amuzu Setor , Bedard Karine , Subramanian Deepak N. , Fewings Eleanor , Bruce Jeffrey P. , Prokopec Stephenie , Bouchard Luigi , Provencher Diane , Foulkes William D. , El Haffaf Zaki , Mes-Masson Anne-Marie , Tischkowitz Marc , Campbell Ian G. , Pugh Trevor J. , Greenwood Celia M. T. , Ragoussis Jiannis , Tonin Patricia N.
Published: January 2023

FANCI was recently identified as a new candidate ovarian cancer (OC)-predisposing gene from the genetic analysis of carriers of FANCI c.1813C>T; p.L605F in OC families. Here, we aimed to investigate the molecular genetic characteristics of FANCI, as they have not been described in the context of cancer. We first investigated the germline genetic landscape of two sisters with OC from the discovery FANCI c.1813C>T; p.L605F family (F1528) to re-affirm the plausibility of this candidate. As we did not find other conclusive candidates, we then performed a candidate gene approach to identify other candidate variants in genes involved in the FANCI protein interactome in OC families negative for pathogenic variants in BRCA1, BRCA2, BRIP1, RAD51C, RAD51D, and FANCI, which identified four candidate variants. We then investigated FANCI in high-grade serous ovarian carcinoma (HGSC) from FANCI c.1813C>T carriers and found evidence of loss of the wild-type allele in tumour DNA from some of these cases. The somatic genetic landscape of OC tumours from FANCI c.1813C>T carriers was investigated for mutations in selected genes, copy number alterations, and mutational signatures, which determined that the profiles of tumours from carriers were characteristic of features exhibited by HGSC cases. As other OC-predisposing genes such as BRCA1 and BRCA2 are known to increase the risk of other cancers including breast cancer, we investigated the carrier frequency of germline FANCI c.1813C>T in various cancer types and found overall more carriers among cancer cases compared to cancer-free controls (p = 0.007). In these different tumour types, we also identified a spectrum of somatic variants in FANCI that were not restricted to any specific region within the gene. Collectively, these findings expand on the characteristics described for OC cases carrying FANCI c.1813C>T; p.L605F and suggest the possible involvement of FANCI in other cancer types at the germline and/or somatic level.
PyuARF16/33 Are Involved in the Regulation of Lignin Synthesis and Rapid Growth in Populus yunnanensis
Authors: Hu Zhixu , Zong Dan , Zhang Qin , Zhang Xiaolin , Lu Yu , He Chengzhong
Published: January 2023

(1) Background: Lignin is a unique component of the secondary cell wall, which provides structural support for perennial woody plants. ARFs are the core factors of the auxin-signaling pathway, which plays an important role in promoting plant growth, but the specific relationship between auxin response factors (ARFs) and lignin has not been fully elucidated with regard to rapid plant growth in forest trees. (2) Objectives: This study aimed to investigate the relationship between ARFs and lignin with regard to rapid plant growth in forest trees. (3) Methods: We used bioinformatics analysis to investigate the PyuARF family, find genes homologous to ARF6 and ARF8 in Populus yunnanensis, and explore the changes in gene expression and lignin content under light treatment. (4) Results: We identified and characterized 35 PyuARFs based on chromosome-level genome data from P. yunnanensis. In total, we identified 92 ARF genes in P. yunnanensis, Arabidopsis thaliana, and Populus trichocarpa, which were subsequently divided into three subgroups based on phylogenetic analysis and classified the conserved exon–intron structures and motif compositions of the ARFs into the same subgroups. Collinearity analysis suggested that segmental duplication and whole-genome duplication events were majorly responsible for the expansion of the PyuARF family, and the analysis of Ka/Ks indicated that the majority of the duplicated PyuARFs underwent purifying selection. The analysis of cis-acting elements showed that PyuARFs were sensitive to light, plant hormones, and stress. We analyzed the tissue-specific transcription profiles of PyuARFs with transcriptional activation function and the transcription profiles of PyuARFs with high expression under light in the stem. We also measured the lignin content under light treatment. The data showed that the lignin content was lower, and the gene transcription profiles were more limited under red light than under white light on days 1, 7, and 14 of the light treatments. The results suggest that PyuARF16/33 may be involved in the regulation of lignin synthesis, thereby promoting the rapid growth of P. yunnanensis. (5) Conclusions: Collectively, this study firstly reports that PyuARF16/33 may be involved in the regulation of lignin synthesis and in promoting the rapid growth in P. yunnanensis.
Altered Nucleotide Insertion Mechanisms of Disease-Associated TERT Variants
Authors: Welfer Griffin A. , Borin Veniamin A. , Cortez Luis M. , Opresko Patricia L. , Agarwal Pratul K. , Freudenthal Bret D.
Published: January 2023

Telomere biology disorders (TBDs) are a spectrum of diseases that arise from mutations in genes responsible for maintaining telomere integrity. Human telomerase reverse transcriptase (hTERT) adds nucleotides to chromosome ends and is frequently mutated in individuals with TBDs. Previous studies have provided insight into how relative changes in hTERT activity can lead to pathological outcomes. However, the underlying mechanisms describing how disease-associated variants alter the physicochemical steps of nucleotide insertion remain poorly understood. To address this, we applied single-turnover kinetics and computer simulations to the Tribolium castaneum TERT (tcTERT) model system and characterized the nucleotide insertion mechanisms of six disease-associated variants. Each variant had distinct consequences on tcTERT’s nucleotide insertion mechanism, including changes in nucleotide binding affinity, rates of catalysis, or ribonucleotide selectivity. Our computer simulations provide insight into how each variant disrupts active site organization, such as suboptimal positioning of active site residues, destabilization of the DNA 3′ terminus, or changes in nucleotide sugar pucker. Collectively, this work provides a holistic characterization of the nucleotide insertion mechanisms for multiple disease-associated TERT variants and identifies additional functions of key active site residues during nucleotide insertion.
A Network-Based Approach for Improving Annotation of Transcription Factor Functions and Binding Sites in Arabidopsis thaliana
Authors: Najnin Tanzira , Saimon Sakhawat Hossain , Sunter Garry , Ruan Jianhua
Published: January 2023

Transcription factors are an integral component of the cellular machinery responsible for regulating many biological processes, and they recognize distinct DNA sequence patterns as well as internal/external signals to mediate target gene expression. The functional roles of an individual transcription factor can be traced back to the functions of its target genes. While such functional associations can be inferred through the use of binding evidence from high-throughput sequencing technologies available today, including chromatin immunoprecipitation sequencing, such experiments can be resource-consuming. On the other hand, exploratory analysis driven by computational techniques can alleviate this burden by narrowing the search scope, but the results are often deemed low-quality or non-specific by biologists. In this paper, we introduce a data-driven, statistics-based strategy to predict novel functional associations for transcription factors in the model plant Arabidopsis thaliana. To achieve this, we leverage one of the largest available gene expression compendia to build a genome-wide transcriptional regulatory network and infer regulatory relationships among transcription factors and their targets. We then use this network to build a pool of likely downstream targets for each transcription factor and query each target pool for functionally enriched gene ontology terms. The results exhibited sufficient statistical significance to annotate most of the transcription factors in Arabidopsis with highly specific biological processes. We also perform DNA binding motif discovery for transcription factors based on their target pool. We show that the predicted functions and motifs strongly agree with curated databases constructed from experimental evidence. In addition, statistical analysis of the network revealed interesting patterns and connections between network topology and system-level transcriptional regulation properties. We believe that the methods demonstrated in this work can be extended to other species to improve the annotation of transcription factors and understand transcriptional regulation on a system level.
Ablation of Gabra5 Influences Corticosterone Levels and Anxiety-like Behavior in Mice
Authors: Syding Linn Amanda , Kubik-Zahorodna Agnieszka , Reguera David Pajuelo , Nickl Petr , Hruskova Bohdana , Kralikova Michaela , Kopkanova Jana , Novosadova Vendula , Kasparek Petr , Prochazka Jan , Rozman Jan , Turecek Rostislav , Sedlacek Radislav
Published: January 2023

Stress responses are activated by the hypothalamic-pituitary-adrenal axis (HPA axis), culminating in the release of glucocorticoids. During prolonged periods of secretion of glucocorticoids or inappropriate behavioral responses to a stressor, pathologic conditions may occur. Increased glucocorticoid concentration is linked to generalized anxiety, and there are knowledge gaps regarding its regulation. It is known that the HPA axis is under GABAergic control, but the contribution of the individual subunits of the GABA receptor is largely unknown. In this study, we investigated the relationship between the α5 subunit and corticosterone levels in a new mouse model deficient for Gabra5, which is known to be linked to anxiety disorders in humans and phenologs observed in mice. We observed decreased rearing behavior, suggesting lower anxiety in the Gabra5−/− animals; however, such a phenotype was absent in the open field and elevated plus maze tests. In addition to decreased rearing behavior, we also found decreased levels of fecal corticosterone metabolites in Gabra5−/− mice indicating a lowered stress response. Moreover, based on the electrophysiological recordings where we observed a hyperpolarized state of hippocampal neurons, we hypothesize that the constitutive ablation of the Gabra5 gene leads to functional compensation with other channels or GABA receptor subunits in this model.
Novel Insights into Mitochondrial DNA: Mitochondrial Microproteins and mtDNA Variants Modulate Athletic Performance and Age-Related Diseases
Authors: Kumagai Hiroshi , Miller Brendan , Kim Su-Jeong , Leelaprachakul Naphada , Kikuchi Naoki , Yen Kelvin , Cohen Pinchas
Published: January 2023

Sports genetics research began in the late 1990s and over 200 variants have been reported as athletic performance- and sports injuries-related genetic polymorphisms. Genetic polymorphisms in the α-actinin-3 (ACTN3) and angiotensin-converting enzyme (ACE) genes are well-established for athletic performance, while collagen-, inflammation-, and estrogen-related genetic polymorphisms are reported as genetic markers for sports injuries. Although the Human Genome Project was completed in the early 2000s, recent studies have discovered previously unannotated microproteins encoded in small open reading frames. Mitochondrial microproteins (also called mitochondrial-derived peptides) are encoded in the mtDNA, and ten mitochondrial microproteins, such as humanin, MOTS-c (mitochondrial ORF of the 12S rRNA type-c), SHLPs 1–6 (small humanin-like peptides 1 to 6), SHMOOSE (Small Human Mitochondrial ORF Over SErine tRNA), and Gau (gene antisense ubiquitous in mtDNAs) have been identified to date. Some of those microproteins have crucial roles in human biology by regulating mitochondrial function, and those, including those to be discovered in the future, could contribute to a better understanding of human biology. This review describes a basic concept of mitochondrial microproteins and discusses recent findings about the potential roles of mitochondrial microproteins in athletic performance as well as age-related diseases.
Stage-Specific Transcriptomes of the Mussel Mytilus coruscus Reveals the Developmental Program for the Planktonic to Benthic Transition
Authors: Wang Yu-Qing , Liu Qi , Zhou Yan , Chen Lizhi , Yang Yue-Ming , Shi Xue , Power Deborah M. , Li Yi-Feng
Published: January 2023

Many marine invertebrate larvae undergo complex morphological and physiological changes during the planktonic—benthic transition (a.k.a. metamorphosis). In this study, transcriptome analysis of different developmental stages was used to uncover the molecular mechanisms underpinning larval settlement and metamorphosis of the mussel, Mytilus coruscus. Analysis of highly upregulated differentially expressed genes (DEGs) at the pediveliger stage revealed enrichment of immune-related genes. The results may indicate that larvae co-opt molecules of the immune system to sense and respond to external chemical cues and neuroendocrine signaling pathways forecast and trigger the response. The upregulation of adhesive protein genes linked to byssal thread secretion indicates the anchoring capacity required for larval settlement arises prior to metamorphosis. The results of gene expression support a role for the immune and neuroendocrine systems in mussel metamorphosis and provide the basis for future studies to disentangle gene networks and the biology of this important lifecycle transformation.
The Evolutionary History of a DNA Methylase Reveals Frequent Horizontal Transfer and Within-Gene Recombination
Authors: Gosselin Sophia , Arsenault Danielle , Jennings Catherine , Gogarten Johann
Published: January 2023

Inteins, often referred to as protein introns, are highly mobile genetic elements that invade conserved genes throughout the tree of life. Inteins have been found to invade a wide variety of key genes within actinophages. While in the process of conducting a survey of these inteins in actinophages, we discovered that one protein family of methylases contained a putative intein, and two other unique insertion elements. These methylases are known to occur commonly in phages as orphan methylases (possibly as a form of resistance to restriction–modification systems). We found that the methylase family is not conserved within phage clusters and has a disparate distribution across divergent phage groups. We determined that two of the three insertion elements have a patchy distribution within the methylase protein family. Additionally, we found that the third insertion element is likely a second homing endonuclease, and that all three elements (the intein, the homing endonuclease, and what we refer to as the ShiLan domain) have different insertion sites that are conserved in the methylase gene family. Furthermore, we find strong evidence that both the intein and ShiLan domain are partaking in long-distance horizontal gene transfer events between divergent methylases in disparate phage hosts within the already dispersed methylase distribution. The reticulate evolutionary history of methylases and their insertion elements reveals high rates of gene transfer and within-gene recombination in actinophages.
Sleep Quality and Duration in Children That Consume Caffeine: Impact of Dose and Genetic Variation in ADORA2A and CYP1A
Authors: Jessel Chaten D. , Narang Ankita , Zuberi Rayyan , Bousman Chad A.
Published: January 2023

Caffeine is the most consumed drug in the world, and it is commonly used by children. Despite being considered relatively safe, caffeine can have marked effects on sleep. Studies in adults suggest that genetic variants in the adenosine A2A receptor (ADORA2A, rs5751876) and cytochrome P450 1A (CYP1A, rs2472297, rs762551) loci are correlated with caffeine-associated sleep disturbances and caffeine intake (dose), but these associations have not been assessed in children. We examined the independent and interaction effects of daily caffeine dose and candidate variants in ADORA2A and CYP1A on the sleep quality and duration in 6112 children aged 9–10 years who used caffeine and were enrolled in the Adolescent Brain Cognitive Development (ABCD) study. We found that children with higher daily caffeine doses had lower odds of reporting > 9 h of sleep per night (OR = 0.81, 95% CI = 0.74–0.88, and p = 1.2 × 10−6). For every mg/kg/day of caffeine consumed, there was a 19% (95% CI = 12–26%) decrease in the odds of children reporting > 9 h of sleep. However, neither ADORA2A nor CYP1A genetic variants were associated with sleep quality, duration, or caffeine dose. Likewise, genotype by caffeine dose interactions were not detected. Our findings suggest that a daily caffeine dose has a clear negative correlation with sleep duration in children, but this association is not moderated by the ADORA2A or CYP1A genetic variation.
DNA Double-Strand Break-Related Competitive Endogenous RNA Network of Noncoding RNA in Bovine Cumulus Cells
Authors: Liu Jian-Bo , Zhang Jia-Bao , Yan Xiang-Min , Xie Peng-Gui , Fu Yao , Fu Xu-Huang , Sun Xu-Lei , Han Dong-Xu , Li Sheng-Peng , Zheng Yi , Gao Yan , Kim Nam-Hyung , Yuan Bao , Jiang Hao
Published: January 2023

(1) Background: DNA double strand breaks (DSBs) are the most serious form of DNA damage that affects oocyte maturation and the physiological state of follicles and ovaries. Non-coding RNAs (ncRNAs) play a crucial role in DNA damage and repair. This study aims to analyze and establish the network of ncRNAs when DSB occurs and provide new ideas for next research on the mechanism of cumulus DSB. (2) Methods: Bovine cumulus cells (CCs) were treated with bleomycin (BLM) to construct a DSB model. We detected the changes of the cell cycle, cell viability, and apoptosis to determine the effect of DSBs on cell biology, and further evaluated the relationship between the transcriptome and competitive endogenous RNA (ceRNA) network and DSBs. (3) Results: BLM increased γH2AX positivity in CCs, disrupted the G1/S phase, and decreased cell viability. Totals of 848 mRNAs, 75 long noncoding RNAs (lncRNAs), 68 circular RNAs (circRNAs), and 71 microRNAs (miRNAs) in 78 groups of lncRNA–miRNA–mRNA regulatory networks, 275 groups of circRNA–miRNA–mRNA regulatory networks, and five groups of lncRNA/circRNA–miRNA–mRNA co-expression regulatory networks were related to DSBs. Most differentially expressed ncRNAs were annotated to cell cycle, p53, PI3K-AKT, and WNT signaling pathways. (4) Conclusions: The ceRNA network helps to understand the effects of DNA DSBs activation and remission on the biological function of CCs.
Stargardt-like Clinical Characteristics and Disease Course Associated with Variants in the WDR19 Gene
Authors: Sajovic Jana , Meglič Andrej , Volk Marija , Maver Aleš , Jarc-Vidmar Martina , Hawlina Marko , Fakin Ana
Published: January 2023

Variants in WDR19 (IFT144) have been implicated as another possible cause of Stargardt disease. The purpose of this study was to compare longitudinal multimodal imaging of a WDR19-Stargardt patient, harboring p.(Ser485Ile) and a novel c.(3183+1_3184-1)_(3261+1_3262-1)del variant, with 43 ABCA4-Stargardt patients. Age at onset, visual acuity, Ishihara color vision, color fundus, fundus autofluorescence (FAF), spectral-domain optical coherence tomography (OCT) images, microperimetry and electroretinography (ERG) were evaluated. First symptom of WDR19 patient was nyctalopia at the age of 5 years. After the age of 18 years, OCT showed hyper-reflectivity at the level of the external limiting membrane/outer nuclear layer. There was abnormal cone and rod photoreceptor function on ERG. Widespread fundus flecks appeared, followed by perifoveal photoreceptor atrophy. Fovea and peripapillary retina remained preserved until the latest exam at 25 years of age. ABCA4 patients had median age of onset at 16 (range 5–60) years and mostly displayed typical Stargardt triad. A total of 19% had foveal sparing. In comparison to ABCA4 patients, the WDR19 patient had a relatively large foveal preservation and severe rod photoreceptor impairment; however, it was still within the ABCA4 disease spectrum. Addition of WDR19 in the group of genes producing phenocopies of Stargardt disease underlines the importance of genetic testing and may help to understand its pathogenesis.
Candidate Genes for Salt Tolerance in Forage Sorghum under Saline Conditions from Germination to Harvest Maturity
Authors: Fan Shugao , Chen Jianmin , Yang Rongzhen
Published: January 2023

To address the plant adaptability of sorghum (Sorghum bicolor) in salinity, the research focus should shift from only selecting tolerant varieties to understanding the precise whole-plant genetic coping mechanisms with long-term influence on various phenotypes of interest to expanding salinity, improving water use, and ensuring nutrient use efficiency. In this review, we discovered that multiple genes may play pleiotropic regulatory roles in sorghum germination, growth, and development, salt stress response, forage value, and the web of signaling networks. The conserved domain and gene family analysis reveals a remarkable functional overlap among members of the bHLH (basic helix loop helix), WRKY (WRKY DNA-binding domain), and NAC (NAM, ATAF1/2, and CUC2) superfamilies. Shoot water and carbon partitioning, for example, are dominated by genes from the aquaporins and SWEET families, respectively. The gibberellin (GA) family of genes is prevalent during pre-saline exposure seed dormancy breaking and early embryo development at post-saline exposure. To improve the precision of the conventional method of determining silage harvest maturity time, we propose three phenotypes and their underlying genetic mechanisms: (i) the precise timing of transcriptional repression of cytokinin biosynthesis (IPT) and stay green (stg1 and stg2) genes; (ii) the transcriptional upregulation of the SbY1 gene and (iii) the transcriptional upregulation of the HSP90-6 gene responsible for grain filling with nutritive biochemicals. This work presents a potential resource for sorghum salt tolerance and genetic studies for forage and breeding.
OCT and ERG Techniques in High-Throughput Phenotyping of Mouse Vision
Authors: Lindovsky Jiri , Palkova Marcela , Symkina Viktoriia , Raishbrook Miles Joseph , Prochazka Jan , Sedlacek Radislav
Published: January 2023

The purpose of the study is to demonstrate coherent optical tomography and electroretinography techniques adopted from the human clinical practice to assess the morphology and function of the mouse retina in a high-throughput phenotyping environment. We present the normal range of wild-type C57Bl/6NCrl retinal parameters in six age groups between 10 and 100 weeks as well as examples of mild and severe pathologies resulting from knocking out a single protein-coding gene. We also show example data obtained by more detailed analysis or additional methods useful in eye research, for example, the angiography of a superficial and deep vascular complex. We discuss the feasibility of these techniques in conditions demanding a high-throughput approach such as the systemic phenotyping carried out by the International Mouse Phenotyping Consortium.
The Genetic Mechanisms Underlying the Concerted Expression of the yellow and tan Genes in Complex Patterns on the Abdomen and Wings of Drosophila guttifera
Authors: Raja Komal K. B. , Bachman Evan A. , Fernholz Catrina E. , Trine David S. , Hobmeier Rebecca E. , Maki Nathaniel J. , Massoglia Timothy J. , Werner Thomas
Published: January 2023

How complex morphological patterns form is an intriguing question in developmental biology. However, the mechanisms that generate complex patterns remain largely unknown. Here, we sought to identify the genetic mechanisms that regulate the tan (t) gene in a multi-spotted pigmentation pattern on the abdomen and wings of Drosophila guttifera. Previously, we showed that yellow (y) gene expression completely prefigures the abdominal and wing pigment patterns of this species. In the current study, we demonstrate that the t gene is co-expressed with the y gene in nearly identical patterns, both transcripts foreshadowing the adult abdominal and wing melanin spot patterns. We identified cis-regulatory modules (CRMs) of t, one of which drives reporter expression in six longitudinal rows of spots on the developing pupal abdomen, while the second CRM activates the reporter gene in a spotted wing pattern. Comparing the abdominal spot CRMs of y and t, we found a similar composition of putative transcription factor binding sites that are thought to regulate the complex expression patterns of both terminal pigmentation genes y and t. In contrast, the y and t wing spots appear to be regulated by distinct upstream factors. Our results suggest that the D. guttifera abdominal and wing melanin spot patterns have been established through the co-regulation of y and t, shedding light on how complex morphological traits may be regulated through the parallel coordination of downstream target genes.
RAD51 and RAD51B Play Diverse Roles in the Repair of DNA Double Strand Breaks in Physcomitrium patens
Authors: Angelis Karel J. , Záveská Drábková Lenka , Vágnerová Radka , Holá Marcela
Published: January 2023

RAD51 is involved in finding and invading homologous DNA sequences for accurate homologous recombination (HR). Its paralogs have evolved to regulate and promote RAD51 functions. The efficient gene targeting and high HR rates are unique in plants only in the moss Physcomitrium patens (P. patens). In addition to two functionally equivalent RAD51 genes (RAD1-1 and RAD51-2), other RAD51 paralogues were also identified in P. patens. For elucidation of RAD51’s involvement during DSB repair, two knockout lines were constructed, one mutated in both RAD51 genes (Pprad51-1-2) and the second with mutated RAD51B gene (Pprad51B). Both lines are equally hypersensitive to bleomycin, in contrast to their very different DSB repair efficiency. Whereas DSB repair in Pprad51-1-2 is even faster than in WT, in Pprad51B, it is slow, particularly during the second phase of repair kinetic. We interpret these results as PpRAD51-1 and -2 being true functional homologs of ancestral RAD51 involved in the homology search during HR. Absence of RAD51 redirects DSB repair to the fast NHEJ pathway and leads to a reduced 5S and 18S rDNA copy number. The exact role of the RAD51B paralog remains unclear, though it is important in damage recognition and orchestrating HR response.
Occurrence of Sex Chromosomes in Fish of the Genus Ancistrus with a New Description of Multiple Sex Chromosomes in the Ecuadorian Endemic Ancistrus clementinae (Loricariidae)
Authors: Nirchio Mauro , Oliveira Claudio , de Bello Cioffi Marcelo , de Menezes Cavalcante Sassi Francisco , Valdiviezo Jonathan , Paim Fabilene Gomes , Soares Leticia Batista , Rossi Anna Rita
Published: January 2023

Ancistrus Kner, 1854, is the most diverse genus among the Ancistrini (Loricariidae) with 70 valid species showing a wide geographic distribution and great taxonomic and systematic complexity. To date, about 40 Ancistrus taxa have been karyotyped, all from Brazil and Argentina, but the statistic is uncertain because 30 of these reports deal with samples that have not yet been identified at the species level. This study provides the first cytogenetic description of the bristlenose catfish, Ancistrus clementinae Rendahl, 1937, a species endemic to Ecuador, aiming to verify whether a sex chromosome system is identifiable in the species and, if so, which, and if its differentiation is associated with the presence of repetitive sequences reported for other species of the family. We associated the karyotype analysis with the COI molecular identification of the specimens. Karyotype analysis suggested the presence of a ♂ZZ/♀ZW1W2 sex chromosome system, never detected before in Ancistrus, with both W1W2 chromosomes enriched with heterochromatic blocks and 18S rDNA, in addition to GC-rich repeats (W2). No differences were observed between males and females in the distribution of 5S rDNA or telomeric repeats. Cytogenetic data here obtained confirm the huge karyotype diversity of Ancistrus, both in chromosome number and sex-determination systems.
Editorial for Special Issue “Linking Tectonic Setting to Sedimentological and Stratigraphic Variability”
Authors: Maravelis Angelos G.
Published: January 2023

The stratigraphic evolution of sedimentary basins reveals (1) the spatial and temporal development of depositional settings; (2) the geotectonic settings; (3) the climatic conditions [...]
Congruence of Effective Leadership Values between Nurse Leaders and Staff Nurses in a Multicultural Medical City in Saudi Arabia: A Sequential Mixed-Methods Study
Authors: Flores Ian Flor , Dator Wireen Leila T. , Olivar Jennifer Joy , Gaballah Mastoura Khames
Published: January 2023

This study explores the perceived congruence of effective values of nursing leadership between the nurse leaders and the staff nurses in a multicultural tertiary hospital. Methods: This is a descriptive sequential mixed-methods study conducted in a multicultural medical city in Saudi Arabia. Purposive sampling was used in the qualitative phase, while stratified sampling was used for the quantitative part. There were 70 participants in the qualitative phase, including 33 nurse leaders and 37 staff nurses. The quantitative phase had 571 participants, including 105 nurse leaders and 466 staff nurses. Results: Congruent values were categorised into six emerging themes: (1) cascading deference; (2) paragon of probity; (3) professional competence; (4) compassionate presence; (5) team diversity and inclusion; (6) calibrated communication. The quantitative survey confirmed that the values identified from the interviews were considered to be vital by both nurse leaders and staff nurses, and there were no statistically significant differences between staff nurses’ and nurse leaders’ perceptions, regardless of their nationality, as demonstrated by one-way ANOVA, with p-values less than 0.05 deemed to be statistically significant. Conclusion: Both nurse leaders and staff nurses in the multicultural institution have congruent leadership values that are perceived as essential to achieve institutional goals and, ultimately, safe and high-quality patient care.
Integration of Geophysical Survey Data for the Identification of New Archaeological Remains in the Subsoil of the Akrai Greek Site (Sicily, Italy)
Authors: Grassi Sabrina , Morreale Gabriele , Lanteri Rosa , Gilotti Angelo , Latino Federico , Di Raimondo Saro , Imposa Sebastiano
Published: January 2023

For more than a decade now, geophysical prospecting has been considered an integral part of archaeological research; the ability to quickly investigate large areas and locate objects buried in the ground without directly interacting with it is a key feature that makes such surveys essential for identifying and locating, with good accuracy, buried archaeological remains. In this study, two extensive magnetic and electromagnetic surveys were carried out in two different areas of the Akrai archaeological site, where given the distribution of archaeological remains already found at the site, it was likely that additional buried remains were present. The surveys were performed using a proton precession magnetometer and a multifrequency electromagnetic device with a frequency range of 2.5–250 kHz. By processing the data, the vertical magnetic gradient and electrical conductivity maps were obtained. Furthermore, 3D models of electrical conductivity distribution were reconstructed. On comparing the results, it was notable that many anomalies characterized by low vertical gradient values were identified within areas characterized by low electrical conductivity values. These anomalies detected by both surveys can be associated with good probability with buried archaeological remains made up of limestones. In fact, they exhibit shapes and sizes comparable to those of the wall remains already found at the site.
An Evaluation of Factors Influencing the Resilience of Flood-Affected Communities in China
Authors: Xu Wenping , Xie Yingchun , Yu Qimeng , Proverbs David
Published: January 2023

In recent years, the acceleration of urbanization processes coupled with more frequent extreme weather including more severe flood events, have led to an increase in the complexity of managing community flood resilience. This research presents an empirical study to explore the factors influencing community flood resilience in six communities located in the Hubei Province of China. The study presents the development of a flood resilience evaluation index system, comprising the use of the decision-making trial and evaluation laboratory (DEMATEL) and interpretative structural modeling method (ISM) methods. The results show that the three most important factors affecting the flood resilience capacity of the community are (i) the investment in disaster prevention, (ii) disaster relief capacity and (iii) flood control and drainage capacity. The differences between the six communities were analyzed across four dimensions to reveal the strengths and weaknesses of the communities across these dimensions and in terms of their overall resilience. By analyzing the causal hierarchical relationship that affects community flood resilience, this study helps to enhance community resilience to flood disasters and reduce disaster risk. These findings are conducive to enhancing the sustainable development of urban communities and are expected to provide scientific guidance for community risk management and strategic decision-making.