Journal Description
Biology
Biology
is an international, peer-reviewed, open access journal of biological sciences published monthly online by MDPI. The Spanish Society for Nitrogen Fixation (SEFIN) and Federation of European Laboratory Animal Science Associations (FELASA) are affiliated with Biology, and their members receive discounts on the article processing charges.
- Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
- High Visibility: indexed within Scopus, SCIE (Web of Science), PubMed, PMC, PubAg, CAPlus / SciFinder, and other databases.
- Journal Rank: JCR - Q2 (Biology) / CiteScore - Q1 (General Agricultural and Biological Sciences)
- Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 18.7 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the second half of 2023).
- Recognition of Reviewers: reviewers who provide timely, thorough peer-review reports receive vouchers entitling them to a discount on the APC of their next publication in any MDPI journal, in appreciation of the work done.
Impact Factor:
4.2 (2022);
5-Year Impact Factor:
4.4 (2022)
Latest Articles
Phylogenetic Analysis of Rare and Endangered Tulipa Species (Liliaceae) of Kazakhstan Based on Universal Barcoding Markers
Biology 2024, 13(6), 365; https://doi.org/10.3390/biology13060365 (registering DOI) - 22 May 2024
Abstract
In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and
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In Kazakhstan, the genus Tulipa is represented by 35 species, 18 of which are listed in the Red Data Book of Kazakhstan and protected by the state. Recent studies of tulip specimens from regions bordering Kazakhstan emphasize the significance of species inventory and report the discovery of several hybrids. In this study, eight tulip species were identified based on morphological characteristics and using DNA barcoding methods. Molecular genetic markers, including nrDNA (ITS) and cpDNA markers (rbcL, matK), of the studied species were sequenced and analyzed using the Bayesian inference and maximum likelihood phylogenetic analysis methods. Our work demonstrates that DNA barcodes based on the ITS, rbcL, and matK marker regions have successful practical applicability, with ITS being the most informative at the intragenic level. However, for distinguishing closely related taxa, the most effective approach would be to use a combined dataset of sequences from multiple DNA markers. The results showed discrepancies in the placement of several taxa (T. kaufmanniana, T. patens), likely due to introgression and natural spontaneous hybridization. The molecular phylogenetic analysis suggests the existence of a previously undescribed hybrid between T. patens and T. alberti. Further detailed population studies are needed to validate this hypothesis.
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(This article belongs to the Special Issue Feature Papers in 'Conservation Biology and Biodiversity')
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Habitat Enrichment Causes Changes in Fish Behavioural Characteristics: A Case Study of Sparus latus
by
Yu Guo, Zhanlong Chen, Chuanxin Qin, Gang Yu and Jia Zhang
Biology 2024, 13(6), 364; https://doi.org/10.3390/biology13060364 (registering DOI) - 22 May 2024
Abstract
To better understand the habitat preferences and behavioural ecology of Sparus latus, we performed an experiment using box-shaped reefs as habitat enrichment materials, allowing us to determine the behavioural strategies and drivers involved in the response to different enrichment structures. The results
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To better understand the habitat preferences and behavioural ecology of Sparus latus, we performed an experiment using box-shaped reefs as habitat enrichment materials, allowing us to determine the behavioural strategies and drivers involved in the response to different enrichment structures. The results showed that the first contact time of S. latus was negatively correlated (Pearson’s correlation, p < 0.005) with the distribution rate in the artificial reef area. Enrichment structures affected the habitat preferences of S. latus, and there was a significant difference in the average distribution rate between the control and treatment groups (Adonis, p < 0.001). The opening ratio (Adonis, R2 = 0.36) explained the distribution difference of S. latus better than the opening shape (Adonis, R2 = 0.12). In the absence of an enrichment structure, S. latus remained more active during the daytime, exhibiting poor clustering, while in the presence of an enrichment structure, S. latus exhibited clustered movement at night. The opening ratio was negatively correlated with the average interindividual distance (Spearman’s correlation, p < 0.01) and showed a significant positive correlation with the average distribution rate in the reef area (Spearman’s correlation, p< 0.001), indicating that the reef opening ratio significantly affected the reef-tropism and clustering behaviours of S. latus. The light intensity was negatively correlated with the average distance moved, and the average speed (Spearman’s correlation, p < 0.05) was significantly positively correlated with the reef first contact time (Spearman’s correlation, p < 0.001), indicating that the light intensity affected the exploration and activity patterns of S. latus. These results provide a research basis for analysing the pattern and process of fish proliferation induced by artificial reef habitats
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Open AccessArticle
Comparative Analysis of the Gut Microbiota of Bat Species with Different Feeding Habits
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Diego Antonio Mena Canata, Mara Silveira Benfato, Francielly Dias Pereira, María João Ramos Pereira, Fernanda Schäfer Hackenhaar, Michele Bertoni Mann, Ana Paula Guedes Frazzon and Pabulo Henrique Rampelotto
Biology 2024, 13(6), 363; https://doi.org/10.3390/biology13060363 (registering DOI) - 22 May 2024
Abstract
Bats are a diverse and ecologically important group of mammals that exhibit remarkable diversity in their feeding habits. These diverse feeding habits are thought to be reflected in the composition and function of their gut microbiota, which plays important roles in nutrient acquisition,
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Bats are a diverse and ecologically important group of mammals that exhibit remarkable diversity in their feeding habits. These diverse feeding habits are thought to be reflected in the composition and function of their gut microbiota, which plays important roles in nutrient acquisition, immune function, and overall health. Despite the rich biodiversity of bat species in South America, there is a lack of microbiome studies focusing on bats from this region. Such studies could offer major insights into conservation efforts and the preservation of biodiversity in South America. In this work, we aimed to compare the gut microbiota of four bat species with different feeding habits from Southern Brazil, including nectarivorous, frugivorous, insectivorous, and hematophagous bats. Our findings demonstrate that feeding habits can have a significant impact on the diversity and composition of bat gut microbiotas, with each species exhibiting unique metabolic potentials related to their dietary niches. In addition, the identification of potentially pathogenic bacteria suggests that the carriage of microbial pathogens by bats may vary, depending on feeding habits and host-specific factors. These findings provide novel insights into the relationship between bat feeding habits and gut microbiota composition, highlighting the need to promote diverse habitats and food sources to support these ecologically important species.
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(This article belongs to the Collection Feature Papers in Microbial Biology)
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Open AccessReview
Exercise, mTOR Activation, and Potential Impacts on the Liver in Rodents
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Giuliano Moreto Onaka, Marianna Rabelo de Carvalho, Patricia Kubalaki Onaka, Claudiane Maria Barbosa, Paula Felippe Martinez and Silvio Assis de Oliveira-Junior
Biology 2024, 13(6), 362; https://doi.org/10.3390/biology13060362 (registering DOI) - 22 May 2024
Abstract
The literature offers a consensus on the association between exercise training (ET) protocols based on the adequate parameters of intensity and frequency, and several adaptive alterations in the liver. Indeed, regular ET can reverse glucose and lipid metabolism disorders, especially from aerobic modalities,
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The literature offers a consensus on the association between exercise training (ET) protocols based on the adequate parameters of intensity and frequency, and several adaptive alterations in the liver. Indeed, regular ET can reverse glucose and lipid metabolism disorders, especially from aerobic modalities, which can decrease intrahepatic fat formation. In terms of molecular mechanisms, the regulation of hepatic fat formation would be directly related to the modulation of the mechanistic target of rapamycin (mTOR), which would be stimulated by insulin signaling and Akt activation, from the following three different primary signaling pathways: (I) growth factor, (II) energy/ATP-sensitive, and (III) amino acid-sensitive signaling pathways, respectively. Hyperactivation of the Akt/mTORC1 pathway induces lipogenesis by regulating the action of sterol regulatory element binding protein-1 (SREBP-1). Exercise training interventions have been associated with multiple metabolic and tissue benefits. However, it is worth highlighting that the mTOR signaling in the liver in response to exercise interventions remains unclear. Hepatic adaptive alterations seem to be most outstanding when sustained by chronic interventions or high-intensity exercise protocols.
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(This article belongs to the Section Physiology)
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Open AccessArticle
Development of a Target Enrichment Probe Set for Conifer (REMcon)
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Raees Khan, Ed Biffin, Kor-jent van Dijk, Robert S. Hill, Jie Liu and Michelle Waycott
Biology 2024, 13(6), 361; https://doi.org/10.3390/biology13060361 (registering DOI) - 22 May 2024
Abstract
Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as an important approach in evolutionary studies, although there have been relatively few studies of conifers that employ
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Conifers are an ecologically and economically important seed plant group that can provide significant insights into the evolution of land plants. Molecular phylogenetics has developed as an important approach in evolutionary studies, although there have been relatively few studies of conifers that employ large-scale data sourced from multiple nuclear genes. Target enrichment sequencing (target capture, exon capture, or Hyb-Seq) has developed as a key approach in modern phylogenomic studies. However, until now, there has been no bait set that specifically targets the entire conifer clade. REMcon is a target sequence capture probe set intended for family- and species-level phylogenetic studies of conifers that target c. 100 single-copy nuclear loci. We tested the REMcon probe set using 69 species, including 44 conifer genera across six families and four other gymnosperm taxa, to evaluate the efficiency of target capture to efficiently generate comparable DNA sequence data across conifers. The recovery of target loci was high, with, on average, 94% of the targeted regions recovered across samples with high read coverage. A phylogenetic analysis of these data produced a well-supported topology that is consistent with the current understanding of relationships among conifers. The REMcon bait set will be useful in generating relatively large-scale nuclear data sets consistently for any conifer lineage.
Full article
(This article belongs to the Section Genetics and Genomics)
Open AccessArticle
Exogenous Glycinebetaine Regulates the Contrasting Responses in Leaf Physiochemical Attributes and Growth of Maize under Drought and Flooding Stresses
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Guo-Yun Wang, Shakeel Ahmad, Bing-Wei Wang, Li-Bo Shi, Yong Wang, Cheng-Qiao Shi and Xun-Bo Zhou
Biology 2024, 13(6), 360; https://doi.org/10.3390/biology13060360 - 21 May 2024
Abstract
Flooding and drought are the two most devastating natural hazards limiting maize production. Exogenous glycinebetaine (GB), an osmotic adjustment agent, has been extensively used but there is limited research on its role in mitigating the negative effects of different abiotic stresses. This study
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Flooding and drought are the two most devastating natural hazards limiting maize production. Exogenous glycinebetaine (GB), an osmotic adjustment agent, has been extensively used but there is limited research on its role in mitigating the negative effects of different abiotic stresses. This study aims to identify the different roles of GB in regulating the diverse defense regulation of maize against drought and flooding. Hybrids of Yindieyu 9 and Heyu 397 grown in pots in a ventilated greenhouse were subjected to flooding (2–3 cm standing layer) and drought (40–45% field capacity) at the three-leaf stage for 8 d. The effects of different concentrations of foliar GB (0, 0.5, 1.0, 5.0, and 10.0 mM) on the physiochemical attributes and growth of maize were tested. Greater drought than flooding tolerance in both varieties to combat oxidative stress was associated with higher antioxidant activities and proline content. While flooding decreased superoxide dismutase and guaiacol peroxidase (POD) activities and proline content compared to normal water, they all declined with stress duration, leading to a larger reactive oxygen species compared to drought. It was POD under drought stress and ascorbate peroxidase under flooding stress that played crucial roles in tolerating water stress. Foliar GB further enhanced antioxidant ability and contributed more effects to POD to eliminate more hydrogen peroxide than the superoxide anion, promoting growth, especially for leaves under water stress. Furthermore, exogenous GB made a greater increment in Heyu 397 than Yindieyu 9, as well as flooding compared to drought. Overall, a GB concentration of 5.0 mM, with a non-toxic effect on well-watered maize, was determined to be optimal for the effective mitigation of water-stress damage to the physiochemical characteristics and growth of maize.
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(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)
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Open AccessBrief Report
Autoimmunity against Nucleus Ambiguous Is Putatively Possible in Both Long-COVID-19 and Vaccinated Subjects: Scientific Evidence and Working Hypothesis
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Silvestro Ennio D’Anna, Alessandra Maria Vitale, Giuseppa D’Amico, Celeste Caruso Bavisotto, Pasquale Ambrosino, Francesco Cappello, Mauro Maniscalco and Antonella Marino Gammazza
Biology 2024, 13(6), 359; https://doi.org/10.3390/biology13060359 - 21 May 2024
Abstract
As reported by the World Health Organization (WHO), about 10–20% of people have experienced mid- to long-term effects following SARS-CoV-2 infection, collectively referred to as post-COVID-19 condition or long-COVID, including some neurovegetative symptoms. Numerous findings have suggested that the onset of these neurovegetative
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As reported by the World Health Organization (WHO), about 10–20% of people have experienced mid- to long-term effects following SARS-CoV-2 infection, collectively referred to as post-COVID-19 condition or long-COVID, including some neurovegetative symptoms. Numerous findings have suggested that the onset of these neurovegetative symptoms upon viral infection may be caused by the production of autoantibodies through molecular mimicry phenomena. Accordingly, we had previously demonstrated that 22 of the human proteins sharing putatively immunogenic peptides with SARS-CoV-2 proteins are expressed in the dorsal motor nucleus and nucleus ambiguous. Therefore, if molecular mimicry occurs following severe forms of COVID-19, there could be transitory or permanent damage in some vagal structures, resulting in a lower vagal tone and all the related clinical signs. We investigated the presence of autoantibodies against two proteins of vagal nuclei sharing a peptide with SARS-CoV-2 spike glycoprotein using an immunoassay test on blood obtained from patients with cardiorespiratory symptoms in patients affected by ongoing symptomatic COVID-19 (long-COVID), subjects vaccinated without a history of SARS-CoV-2 infection, and subjects not vaccinated without a history of SARS-CoV-2 infection. Interestingly, putative autoantibodies were present in both long-COVID-19 and vaccinated groups, opening interesting questions about pathogenic mechanisms of the disease.
Full article
(This article belongs to the Special Issue Experimental Biology 100 Years after the Foundation of the Italian Society: A Celebratory Special Issue)
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Identification of Insertion/Deletion Markers for Photoperiod Sensitivity in Rice (Oryza sativa L.)
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Nguyen Thanh Tam and Dang Kieu Nhan
Biology 2024, 13(5), 358; https://doi.org/10.3390/biology13050358 - 20 May 2024
Abstract
The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240
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The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies.
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(This article belongs to the Section Plant Science)
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Open AccessArticle
α-Catenin and Piezo1 Mediate Cell Mechanical Communication via Cell Adhesions
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Mingxing Ouyang, Qingyu Zhang, Yiming Zhu, Mingzhi Luo, Bing Bu and Linhong Deng
Biology 2024, 13(5), 357; https://doi.org/10.3390/biology13050357 - 19 May 2024
Abstract
Cell-to-cell distant mechanical communication has been demonstrated using in vitro and in vivo models. However, the molecular mechanisms underlying long-range cell mechanoresponsive interactions remain to be fully elucidated. This study further examined the roles of α-Catenin and Piezo1 in traction force-induced rapid branch
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Cell-to-cell distant mechanical communication has been demonstrated using in vitro and in vivo models. However, the molecular mechanisms underlying long-range cell mechanoresponsive interactions remain to be fully elucidated. This study further examined the roles of α-Catenin and Piezo1 in traction force-induced rapid branch assembly of airway smooth muscle (ASM) cells on a Matrigel hydrogel containing type I collagen. Our findings demonstrated that siRNA-mediated downregulation of α-Catenin or Piezo1 expression or chemical inhibition of Piezo1 activity significantly reduced both directional cell movement and branch assembly. Regarding the role of N-cadherin in regulating branch assembly but not directional migration, our results further confirmed that siRNA-mediated downregulation of α-Catenin expression caused a marked reduction in focal adhesion formation, as assessed by focal Paxillin and Integrin α5 localization. These observations imply that mechanosensitive α-Catenin is involved in both cell–cell and cell-matrix adhesions. Additionally, Piezo1 partially localized to Paxillin in focal adhesions, which was inhibited by siRNA-mediated downregulation of α-Catenin expression. This result provides insights into the Piezo1-mediated mechanosensing of traction force on a hydrogel. Collectively, our findings highlight the significance of α-Catenin in the regulation of cell-matrix interactions and provide a possible interpretation of Piezo1-mediated mechanosensing activity at focal adhesions during cell–cell distant mechanical communication.
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(This article belongs to the Section Cell Biology)
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Carrabiitol®, a Novel Oligosaccharide Polyol Composition, Mitigates the Impact of Flooding, Drought, Salinity, and High Temperature in Tomato
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Femida Yunus Patel, Kaushal Kishore Upreti, Ramanna Hunashikatti Laxman and Neil Jaykumar Shah
Biology 2024, 13(5), 356; https://doi.org/10.3390/biology13050356 - 19 May 2024
Abstract
Abiotic stress results in various physiological and biochemical changes in plants. Osmolytes play a pivotal role in improving the tolerance to abiotic stress in plants. This study evaluated the effectiveness of a commercial formulation, Carrabiitol®, an oligosaccharide polyol composition, in alleviating
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Abiotic stress results in various physiological and biochemical changes in plants. Osmolytes play a pivotal role in improving the tolerance to abiotic stress in plants. This study evaluated the effectiveness of a commercial formulation, Carrabiitol®, an oligosaccharide polyol composition, in alleviating adverse impacts of abiotic stress in tomato (Solanum lycopersicum L. var. Arka Rakshak) plants. Plants were raised from seed and treated with 1 mL/L, 2 mL/L, and 3 mL/L of Carrabiitol®. The foliage of developing plants was treated at the 2–3 leaf stage (T2, T3, and T4) and at pre-flowering stage (T5, T6, and T7). Growth conditions were compared with those of plants developed from untreated seed (T1). Developing tomato plants were then exposed to flooding, salinity (50 mM NaCl), high temperature (41.1 °C), or drought at the flowering stage. Plants were evaluated for their dry weight, leaf water potential, stomatal conductance, transpiration rate, antioxidant potential, chlorophyll, carotenoid, glucose, sucrose, malondialdehyde, and proline contents. Pre-treated seed, which received a booster treatment at the 2–3 leaf stage (T4 = seed treatment and booster at the 2–3 leaf stage with 3 mL/L Carrabiitol®) and pre-flowering stages (T5, T6, and T7 = seed treatment and booster doses at the pre-flowering stage with 1, 2, and 3 mL/L Carrabiitol®, respectively), was effective in mitigating negative impacts on various growth parameters of stressed tomato plants (p < 0.05). Carrabiitol® may be an effective, sustainable, and bio-rational organic osmolyte formulation for reducing the effects of abiotic stress on plant growth and productivity.
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(This article belongs to the Special Issue Uncovering the Mechanisms of Plant Salinity Stress Response and Tolerance)
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Open AccessArticle
Among Other Tissues, Short-Term Garlic Oral Treatment Incrementally Improves Indicants of Only Pancreatic Islets of Langerhans Histology and Insulin mRNA Transcription and Synthesis in Diabetic Rats
by
Amani M. Al-Adsani and Khaled K. Al-Qattan
Biology 2024, 13(5), 355; https://doi.org/10.3390/biology13050355 - 18 May 2024
Abstract
Background: The source, mRNA transcription, and synthesis of insulin in the pancreas, in addition to the bile duct and liver, in streptozotocin (STZ)-induced diabetic rats (DR) in response to garlic oral treatment are not yet clear. Objective: This study investigated the accumulative effects
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Background: The source, mRNA transcription, and synthesis of insulin in the pancreas, in addition to the bile duct and liver, in streptozotocin (STZ)-induced diabetic rats (DR) in response to garlic oral treatment are not yet clear. Objective: This study investigated the accumulative effects of continued garlic oral treatment on changes in the pancreas, bile duct, and liver with regards to: 1—Insulin mRNA transcription, synthesis, and concentration in relation to changes in serum insulin (SI); 2—Insulinogenic cells insulin intensity and distribution, proliferation, and morphology. Method: Fasting blood glucose (FBG) and insulin concentration in serum and pancreas (PI) and sources and mRNA transcription in the pancreas, bile duct, and liver in normal rats given normal saline (NR-NS) and DR given either NS (DR-NS) or garlic extract (DR-GE) before and after 1, 4, and 8 weeks of oral treatment were examined. Results: Compared to NR-NS, DR-NS showed a significant increase in FBG and reductions in SI and PI and deterioration in islets histology, associated pancreatic insulin numerical intensities, and mRNA transcription. However, compared to DR-NS, the targeted biochemical, histological, and genetic variables of DR-GE were significantly and incrementally improved as garlic treatment continued. Insulin or its indicators were not detected either in the bile duct or the liver in DR-GE. Conclusions: 8 weeks of garlic oral treatment is enough to incrementally restore only pancreatic islets of Langerhans insulin intensity and insulinogenic cells proliferation, morphology, and distribution. These indices were associated with enhanced pancreatic insulin mRNA transcription and synthesis. Eight weeks of garlic treatment were not enough to stimulate insulinogenesis in either the bile duct or the liver.
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(This article belongs to the Special Issue Animal Models of Pancreatic Diseases)
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Antibacterial and Antibiofilm Potential of Bacterial Cellulose Hydrogel Containing Vancomycin against Multidrug-Resistant Staphylococcus aureus and Staphylococcus epidermidis
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Ana Alice Venancio Correia, Luís André de Almeida Campos, Hanne Lazla Rafael de Queiroz Macêdo, Davi de Lacerda Coriolano, Maria Anndressa Alves Agreles, Danilo Elias Xavier, Rafaela de Siqueira Ferraz-Carvalho, José Lamartine de Andrade Aguiar and Isabella Macário Ferro Cavalcanti
Biology 2024, 13(5), 354; https://doi.org/10.3390/biology13050354 - 17 May 2024
Abstract
The present study aimed to evaluate the in vitro antibacterial and antibiofilm activity of bacterial cellulose hydrogel produced by Zoogloea sp. (HYDROGEL) containing vancomycin (VAN) against bacterial strains that cause wound infections, such as multidrug-resistant (MDR) Staphylococcus aureus and Staphylococcus epidermidis. Initially,
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The present study aimed to evaluate the in vitro antibacterial and antibiofilm activity of bacterial cellulose hydrogel produced by Zoogloea sp. (HYDROGEL) containing vancomycin (VAN) against bacterial strains that cause wound infections, such as multidrug-resistant (MDR) Staphylococcus aureus and Staphylococcus epidermidis. Initially, HYDROGEL was obtained from sugar cane molasses, and scanning electron microscopy (SEM) was performed to determine morphological characteristics. Then, VAN was incorporated into HYDROGEL (VAN-HYDROGEL). The antibacterial activity of VAN, HYDROGEL, and VAN-HYDROGEL was assessed using the broth microdilution method to determine the minimum inhibitory concentration (MIC) and the minimum bactericidal concentration (MBC) against methicillin-sensitive S. aureus (MSSA) ATCC 25923, methicillin-resistant S. aureus (MRSA) ATCC 33591, S. epidermidis INCQS 00016 (ATCC 12228), five clinical isolates of MRSA, and nine clinical isolates of methicillin-resistant S. epidermidis, following the Clinical and Laboratory Standards Institute (CLSI) guidelines. Additionally, the antibacterial activity of VAN, HYDROGEL, and VAN-HYDROGEL was studied using the time-kill assay. Subsequently, the antibiofilm activity of VAN, HYDROGEL, and VAN-HYDROGEL was evaluated using crystal violet and Congo red methods, as well as SEM analysis. VAN and VAN-HYDROGEL showed bacteriostatic and bactericidal activity against MRSA and methicillin-resistant S. epidermidis strains. HYDROGEL did not show any antibacterial activity. Analysis of the time-kill assay indicated that HYDROGEL maintained the antibacterial efficacy of VAN, highlighting its efficiency as a promising carrier. Regarding antibiofilm activity, VAN and HYDROGEL inhibited biofilm formation but did not demonstrate biofilm eradication activity against methicillin-resistant S. aureus and S. epidermidis strains. However, it was observed that the biofilm eradication potential of VAN was enhanced after incorporation into HYDROGEL, a result also proven through images obtained by SEM. From the methods carried out in this study, it was possible to observe that HYDROGEL preserved the antibacterial activity of vancomycin, aside from exhibiting antibiofilm activity and enhancing the antibiofilm effect of VAN. In conclusion, this study demonstrated the potential of HYDROGEL as a candidate and/or vehicle for antibiotics against MDR bacteria that cause wound infections.
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(This article belongs to the Collection Feature Papers in Microbial Biology)
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Open AccessArticle
Effects of Seed Size and Frequency on Seed Dispersal and Predation by Small Mammals
by
Jiming Cheng, Min Zhang, Xingfu Yan, Chao Zhang, Jinfeng Zhang and Yonghong Luo
Biology 2024, 13(5), 353; https://doi.org/10.3390/biology13050353 - 16 May 2024
Abstract
Frequency-dependent predation is common in predator–prey interactions. Size is an important characteristic of seeds and is crucial in the regeneration stage of plant seeds. However, the frequency dependence of animal predation on seed size has not been reported. In this study, we conducted
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Frequency-dependent predation is common in predator–prey interactions. Size is an important characteristic of seeds and is crucial in the regeneration stage of plant seeds. However, the frequency dependence of animal predation on seed size has not been reported. In this study, we conducted a field experiment and used different sizes of Liaodong oak (Quercus wutaishanica) seeds to test the frequency dependence of intraspecific seed size selection in rodents. We used the number ratio of large to small seeds as the frequency. The results show that the rate of small seeds being eaten in situ was significantly higher than that of large seeds (p < 0.05). The rates of different-sized seeds being eaten after removal decreased with increasing frequencies, and there was no significant difference between frequencies except for 1:9 and 9:1. The rates of large seeds being scatter-hoarded were significantly higher than those of small seeds at different frequencies (p < 0.05). The eating distances after removal of large seeds were significantly longer than those of small seeds at the same frequencies (p < 0.05). Furthermore, the scatter-hoarding distances of large seeds were significantly longer than those of small seeds at three frequencies (1:9, 3:7, and 9:1) (p < 0.05). That is, rodents consumed more small seeds in situ, dispersed and scatter-hoarded more large seeds, and dispersed large seeds over longer distances. Rodents exhibited a negative frequency dependence for small seeds and a positive frequency dependence for large seeds on being eaten in situ. Moreover, rodents exhibited a negative frequency dependence for large seeds and a positive frequency dependence for small seeds on being eaten after removal and scatter-hoarding. These results reveal the frequency dependence of rodent selection on seed size and provide new insights into animal-mediated seed dispersal and the regeneration of plant populations.
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(This article belongs to the Section Ecology)
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Open AccessReview
Associations between “Cancer Risk”, “Inflammation” and “Metabolic Syndrome”: A Scoping Review
by
Elsa Vitale, Alessandro Rizzo, Kazuki Santa and Emilio Jirillo
Biology 2024, 13(5), 352; https://doi.org/10.3390/biology13050352 - 16 May 2024
Abstract
Background: Individuals with metabolic syndrome exhibit simultaneously pro-thrombotic and pro-inflammatory conditions which more probably can lead to cardiovascular diseases progression, type 2 diabetes mellitus, and some types of cancer. The present scoping review is aimed at highlighting the association between cancer risk, inflammation,
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Background: Individuals with metabolic syndrome exhibit simultaneously pro-thrombotic and pro-inflammatory conditions which more probably can lead to cardiovascular diseases progression, type 2 diabetes mellitus, and some types of cancer. The present scoping review is aimed at highlighting the association between cancer risk, inflammation, and metabolic syndrome. Methods: A search strategy was performed, mixing keywords and MeSH terms, such as “Cancer Risk”, “Inflammation”, “Metabolic Syndrome”, “Oncogenesis”, and “Oxidative Stress”, and matching them through Boolean operators. A total of 20 manuscripts were screened for the present study. Among the selected papers, we identified some associations with breast cancer, colorectal cancer, esophageal adenocarcinoma, hepatocellular carcinoma (HCC), and cancer in general. Conclusions: Cancer and its related progression may also depend also on a latent chronic inflammatory condition associated with other concomitant conditions, including type 2 diabetes mellitus, metabolic syndrome, and obesity. Therefore, prevention may potentially help individuals to protect themselves from cancer.
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(This article belongs to the Special Issue Effects of Environmental Stress on the Metabolic Dysfunction and Its Mechanism)
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Open AccessArticle
DExplore: An Online Tool for Detecting Differentially Expressed Genes from mRNA Microarray Experiments
by
Anna D. Katsiki, Pantelis E. Karatzas, Hector-Xavier De Lastic, Alexandros G. Georgakilas, Ourania Tsitsilonis and Constantinos E. Vorgias
Biology 2024, 13(5), 351; https://doi.org/10.3390/biology13050351 - 16 May 2024
Abstract
Microarray experiments, a mainstay in gene expression analysis for nearly two decades, pose challenges due to their complexity. To address this, we introduce DExplore, a user-friendly web application enabling researchers to detect differentially expressed genes using data from NCBI’s GEO. Developed with R,
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Microarray experiments, a mainstay in gene expression analysis for nearly two decades, pose challenges due to their complexity. To address this, we introduce DExplore, a user-friendly web application enabling researchers to detect differentially expressed genes using data from NCBI’s GEO. Developed with R, Shiny, and Bioconductor, DExplore integrates WebGestalt for functional enrichment analysis. It also provides visualization plots for enhanced result interpretation. With a Docker image for local execution, DExplore accommodates unpublished data. To illustrate its utility, we showcase two case studies on cancer cells treated with chemotherapeutic drugs. DExplore streamlines microarray data analysis, empowering molecular biologists to focus on genes of biological significance.
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(This article belongs to the Special Issue Differential Gene Expression and Coexpression 2.0)
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Open AccessArticle
Paired Primary and Recurrent Rhabdoid Meningiomas: Cytogenetic Alterations, BAP1 Gene Expression Profile and Patient Outcome
by
Patricia Alejandra Garrido Ruiz, Álvaro Otero Rodriguez, Luis Antonio Corchete, Victoria Zelaya Huerta, Alejandro Pasco Peña, Cristina Caballero Martínez, Joaquín González-Carreró Fojón, Inmaculada Catalina Fernández, Juan Carlos López Duque, Laura Zaldumbide Dueñas, Lorena Mosteiro González, María Aurora Astudillo, Aurelio Hernández-Laín, Emma Natalia Camacho Urkaray, María Amparo Viguri Diaz, Alberto Orfao and María Dolores Tabernero
Biology 2024, 13(5), 350; https://doi.org/10.3390/biology13050350 - 16 May 2024
Abstract
Rhabdoid meningiomas (RM) are a rare meningioma subtype with a heterogeneous clinical course which is more frequently associated with recurrence, even among tumors undergoing-complete surgical removal. Here, we retrospectively analyzed the clinical-histopathological and cytogenetic features of 29 tumors, from patients with recurrent (seven
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Rhabdoid meningiomas (RM) are a rare meningioma subtype with a heterogeneous clinical course which is more frequently associated with recurrence, even among tumors undergoing-complete surgical removal. Here, we retrospectively analyzed the clinical-histopathological and cytogenetic features of 29 tumors, from patients with recurrent (seven primary and 14 recurrent tumors) vs. non-recurrent RM (n = 8). Recurrent RM showed one (29%), two (29%) or three (42%) recurrences. BAP1 loss of expression was found in one third of all RM at diagnosis and increased to 100% in subsequent tumor recurrences. Despite both recurrent and non-recurrent RM shared chromosome 22 losses, non-recurrent tumors more frequently displayed extensive losses of chromosome 19p (62%) and/or 19q (50%), together with gains of chromosomes 20 and 21 (38%, respectively), whereas recurrent RM (at diagnosis) displayed more complex genotypic profiles with extensive losses of chromosomes 1p, 14q, 18p, 18q (67% each) and 21p (50%), together with focal gains at chromosome 17q22 (67%). Compared to paired primary tumors, recurrent RM samples revealed additional losses at chromosomes 16q and 19p (50% each), together with gains at chromosomes 1q and 17q in most recurrent tumors (67%, each). All deceased recurrent RM patients corresponded to women with chromosome 17q gains, although no statistical significant differences were found vs. the other RM patients.
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(This article belongs to the Special Issue New Sight in Cancer Genetics)
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Open AccessArticle
Transcriptomic Profiles of Long Noncoding RNAs and Their Target Protein-Coding Genes Reveals Speciation Adaptation on the Qinghai-Xizang (Tibet) Plateau in Orinus
by
Qinyue Min, Kaifeng Zheng, Tao Liu, Zitao Wang, Xiuhua Xue, Wanjie Li, Yuping Liu, Yanfen Zhang, Feng Qiao, Jinyuan Chen, Xu Su and Shengcheng Han
Biology 2024, 13(5), 349; https://doi.org/10.3390/biology13050349 - 16 May 2024
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may
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Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nt, which lack the ability to encode proteins and are involved in multifarious growth, development, and regulatory processes in plants and mammals. However, the environmental-regulated expression profiles of lncRNAs in Orinus that may associated with their adaptation on the Qinghai-Xizang (Tibet) Plateau (QTP) have never been characterized. Here, we utilized transcriptomic sequencing data of two Orinus species (O. thoroldii and O. kokonoricus) to identify 1624 lncRNAs, including 1119 intergenic lncRNAs, 200 antisense lncRNAs, five intronic lncRNAs, and 300 sense lncRNAs. In addition, the evolutionary relationships of Orinus lncRNAs showed limited sequence conservation among 39 species, which implied that Orinus-specific lncRNAs contribute to speciation adaptation evolution. Furthermore, considering the cis-regulation mechanism, from 286 differentially expressed lncRNAs (DElncRNAs) and their nearby protein coding genes (PCGs) between O. thoroldii and O. kokonoricus, 128 lncRNA-PCG pairs were obtained in O. thoroldii, whereas 92 lncRNA-PCG pairs were obtained in O. kokonoricus. In addition, a total of 19 lncRNA-PCG pairs in O. thoroldii and 14 lncRNA-PCG pairs in O. kokonoricus were found to participate in different biological processes, indicating that the different expression profiles of DElncRNAs between O. thoroldii and O. kokonoricus were associated with their adaptation at different elevations on the QTP. We also found several pairs of DElncRNA nearby transcription factors (TFs), indicating that these DElncRNAs regulate the expression of TFs to aid O. thoroldii in adapting to the environment. Therefore, this work systematically identified a series of lncRNAs in Orinus, laying the groundwork for further exploration into the biological function of Orinus in environmental adaptation.
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(This article belongs to the Special Issue Biological Response of Plants to Environmental Changes)
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Open AccessArticle
Effects of Bacillus subtilis on Cucumber Seedling Growth and Photosynthetic System under Different Potassium Ion Levels
by
Chun Li, Qingpan Zeng, Yuzhu Han, Xiaofu Zhou and Hongwei Xu
Biology 2024, 13(5), 348; https://doi.org/10.3390/biology13050348 - 15 May 2024
Abstract
Potassium deficiency is one of the important factors restricting cucumber growth and development. This experiment mainly explored the effect of Bacillus subtilis (B. subtilis) on cucumber seedling growth and the photosynthetic system under different potassium levels, and the rhizosphere bacteria (PGPR)
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Potassium deficiency is one of the important factors restricting cucumber growth and development. This experiment mainly explored the effect of Bacillus subtilis (B. subtilis) on cucumber seedling growth and the photosynthetic system under different potassium levels, and the rhizosphere bacteria (PGPR) that promote plant growth were used to solubilize potassium in soil, providing theoretical support for a further investigation of the effect of biological bacteria fertilizer on cucumber growth and potassium absorption. “Xinjin No. 4” was used as the test material for the pot experiment, and a two-factor experiment was designed. The first factor was potassium application treatment, and the second factor was bacterial application treatment. The effects of different treatments on cucumber seedling growth, photosynthetic characteristics, root morphology, and chlorophyll fluorescence parameters were studied. The results showed that potassium and B. subtilis had obvious promotion effects on the cucumber seedling growth and the photosynthesis of leaves. Compared with the blank control, the B. subtilis treatment had obvious effects on the cucumber seedling height, stem diameter, leaf area, total root length, total root surface area, total root volume, branch number, crossing number, gs, WUE, Ci, and A; the dry weight of the shoot and root increased significantly (p ≤ 0.05). Potassium application could significantly promote cucumber growth, and the effect of B. subtilis and potassium application was greater than that of potassium application alone, and the best effect was when 0.2 g/pot and B. subtilis were applied. In conclusion, potassium combined with B. subtilis could enhance the photosynthesis of cucumber leaves and promote the growth of cucumber.
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(This article belongs to the Special Issue Beneficial Microorganisms for Plants)
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Open AccessArticle
New Discovery of Calamitaceae from the Cisuralian in Northwest China: Morphological Evolution of Strobilus
by
Xuelian Wang, Yunfa Miao, Yanzhao Ji and Bainian Sun
Biology 2024, 13(5), 347; https://doi.org/10.3390/biology13050347 - 15 May 2024
Abstract
Calamitaceae was the predominant arborescent element of the Late Paleozoic plant assemblages. However, there is currently controversy surrounding the evolutionary relationships of their four reproductive organs, and there is no unified understanding of the geographical distribution and species richness characteristics. This paper is
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Calamitaceae was the predominant arborescent element of the Late Paleozoic plant assemblages. However, there is currently controversy surrounding the evolutionary relationships of their four reproductive organs, and there is no unified understanding of the geographical distribution and species richness characteristics. This paper is based on the detailed description of the macro- and microstructures of Calamites and Macrostachya discovered in the Shanxi Formation of the Cisuralian in the eastern Hexi Corridor of northwestern China, and it discusses the evolutionary patterns of calamitean reproductive organs. The results indicate that the current specimens can be identified as the Calamites cistii and Macrostachya sp., and the in situ spores should exhibit distinct trilete marks, indicating that they belong to the Punctatisporites punctatus. The abundant fossil records suggest that the “Calamostachys” type should be considered as the ancestral type of strobili. Additionally, Calamitaceae was widely distributed in mid to low latitudes globally from the Pennsylvanian to the Cisuralian and coupled with paleogeographic distribution characteristics.
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(This article belongs to the Section Plant Science)
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Open AccessArticle
1,25-Dihydroxyvitamin D3 Suppresses Prognostic Survival Biomarkers Associated with Cell Cycle and Actin Organization in a Non-Malignant African American Prostate Cell Line
by
Jabril R. Johnson, Rachel N. Martini, Yate-Ching Yuan, Leanne Woods-Burnham, Mya Walker, Greisha L. Ortiz-Hernandez, Firas Kobeissy, Dorothy Galloway, Amani Gaddy, Chidinma Oguejiofor, Blake Allen, Deyana Lewis, Melissa B. Davis, K. Sean Kimbro, Clayton C. Yates, Adam B. Murphy and Rick A. Kittles
Biology 2024, 13(5), 346; https://doi.org/10.3390/biology13050346 - 15 May 2024
Abstract
Vitamin D3 is a steroid hormone that confers anti-tumorigenic properties in prostate cells. Serum vitamin D3 deficiency has been associated with advanced prostate cancer (PCa), particularly affecting African American (AA) men. Therefore, elucidating the pleiotropic effects of vitamin D on signaling
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Vitamin D3 is a steroid hormone that confers anti-tumorigenic properties in prostate cells. Serum vitamin D3 deficiency has been associated with advanced prostate cancer (PCa), particularly affecting African American (AA) men. Therefore, elucidating the pleiotropic effects of vitamin D on signaling pathways, essential to maintaining non-malignancy, may provide additional drug targets to mitigate disparate outcomes for men with PCa, especially AA men. We conducted RNA sequencing on an AA non-malignant prostate cell line, RC-77N/E, comparing untreated cells to those treated with 10 nM of vitamin D3 metabolite, 1α,25(OH)2D3, at 24 h. Differential gene expression analysis revealed 1601 significant genes affected by 1α,25(OH)2D3 treatment. Pathway enrichment analysis predicted 1α,25(OH)2D3- mediated repression of prostate cancer, cell proliferation, actin cytoskeletal, and actin-related signaling pathways (p < 0.05). Prioritizing genes with vitamin D response elements and associating expression levels with overall survival (OS) in The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA PRAD) cohort, we identified ANLN (Anillin) and ECT2 (Epithelial Cell Transforming 2) as potential prognostic PCa biomarkers. Both genes were strongly correlated and significantly downregulated by 1α,25(OH)2D3 treatment, where low expression was statistically associated with better overall survival outcomes in the TCGA PRAD public cohort. Increased ANLN and ECT2 mRNA gene expression was significantly associated with PCa, and Gleason scores using both the TCGA cohort (p < 0.05) and an AA non-malignant/tumor-matched cohort. Our findings suggest 1α,25(OH)2D3 regulation of these biomarkers may be significant for PCa prevention. In addition, 1α,25(OH)2D3 could be used as an adjuvant treatment targeting actin cytoskeleton signaling and actin cytoskeleton-related signaling pathways, particularly among AA men.
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(This article belongs to the Special Issue Cancer and Signalling: Targeting Cellular Pathways)
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