Biology

16 pages, 1491 KiB

Open AccessArticle

Genome-Wide Association Study and Genomic Prediction of Soft Wheat End-Use Quality Traits Under Post-Anthesis Heat-Stressed Conditions

by Dipendra Shahi, Jia Guo, Sumit Pradhan, Muhsin Avci, Guihua Bai, Jahangir Khan, Byung-Kee Baik, Mohamed Mergoum and Md Ali Babar

Biology 2024, 13(12), 962; https://doi.org/10.3390/biology13120962 - 22 Nov 2024

Abstract

Wheat end-use quality is an important component of a wheat breeding program. Heat stress during grain filling impacts wheat quality traits, making it crucial to understand the genetic basis of wheat quality traits under post-anthesis heat stress. This study aimed to identify the [...] Read more.

Wheat end-use quality is an important component of a wheat breeding program. Heat stress during grain filling impacts wheat quality traits, making it crucial to understand the genetic basis of wheat quality traits under post-anthesis heat stress. This study aimed to identify the genomic regions associated with wheat quality traits using genome-wide association studies (GWASs) and evaluate the prediction accuracy of different genomic selection (GS) models. A panel of 236 soft red facultative wheat genotypes was evaluated for end-use quality traits across four heat-stressed environments over three years. Significant phenotypic variation was observed across environments for traits such as grain yield (GY), grain protein (GP), grain hardness (GH), and flour yield (AFY). Heritability estimates ranged from 0.52 (GY) to 0.91 (GH). The GWASs revealed 136 significant marker–trait associations (MTAs) across all 21 chromosomes, with several MTAs located within candidate genes involved in stress responses and quality traits. Genomic selection models showed prediction accuracy values up to 0.60, with within-environment prediction outperforming across-environment prediction. These results suggest that integrating GWAS and GS approaches can enhance the selection of wheat quality traits under heat stress, contributing to the development of heat-tolerant varieties. Full article

(This article belongs to the Section Plant Science)

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19 pages, 687 KiB

Open AccessReview

Exploring Trimethylaminuria: Genetics and Molecular Mechanisms, Epidemiology, and Emerging Therapeutic Strategies

by Antonina Sidoti, Rosalia D’Angelo, Andrea Castagnetti, Elisa Viciani, Concetta Scimone, Simona Alibrandi and Giuseppe Giannini

Biology 2024, 13(12), 961; https://doi.org/10.3390/biology13120961 - 22 Nov 2024

Abstract

Trimethylaminuria (TMAU) is a rare metabolic syndrome caused by the accumulation of trimethylamine in the body, causing odor emissions similar to rotten fish in affected patients. This condition is determined by both genetic and environmental factors, especially gut dysbiosis. The multifactorial nature of [...] Read more.

Trimethylaminuria (TMAU) is a rare metabolic syndrome caused by the accumulation of trimethylamine in the body, causing odor emissions similar to rotten fish in affected patients. This condition is determined by both genetic and environmental factors, especially gut dysbiosis. The multifactorial nature of this syndrome makes for a complex and multi-level diagnosis. To date, many aspects of this disease are still unclear. Recent research revealed the FMO3 haplotypes’ role on the enzyme’s catalytic activity. This could explain why patients showing only combined polymorphisms or heterozygous causative variants also manifest the TMAU phenotype. In addition, another research hypothesized that the behavioral disturbances showed by patients may be linked to gut microbiota alterations. Our review considers current knowledge about TMAU, clarifying its molecular aspects, the therapeutic approaches used to limit this condition, and the new therapies that are under study. Full article

(This article belongs to the Special Issue The Effect of Food- and Nutrient-Derived Molecules on Cells and Tissue)

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13 pages, 1750 KiB

Open AccessArticle

Synthesis of Palladium Nanowires on Flagella Template for Electrochemical Biosensor Detection of microRNA-21

by Kuo Yang, Jueyu Wang, Ying Zhang, Daizong Cui and Min Zhao

Biology 2024, 13(12), 960; https://doi.org/10.3390/biology13120960 - 22 Nov 2024

Abstract

In recent years, the use of bacterial flagella as biomimetic templates has gained increasing attention in nanomaterial synthesis due to their unique structural and functional properties. In this study, we optimized the flagella extraction method and achieved a high concentration of flagella solution. [...] Read more.

In recent years, the use of bacterial flagella as biomimetic templates has gained increasing attention in nanomaterial synthesis due to their unique structural and functional properties. In this study, we optimized the flagella extraction method and achieved a high concentration of flagella solution. Flagella were isolated from Escherichia coli. Surface characterization revealed that the flagella had abundant functional groups, such as amino and carboxyl groups, which can serve as nucleation sites for the controlled nucleation and growth of metal nanomaterials. Using bacterial flagella as a template, we synthesized one-dimensional palladium nanowires (Fla-Pd NWs). The results of morphological and phase analyses showed that the synthesized palladium nanoparticles were uniformly and densely distributed on the surface of the flagella. Moreover, the Fla-Pd nanowires exhibited superior electrocatalytic activity, which was applied to develop an electrochemical biosensor. This biosensor was used to detect the early breast cancer biomarker microRNA-21 and exhibited a linear range of 0.66–1.98 µmol/L and a detection limit of 0.78 µmol/L. The method demonstrated high selectivity and reusability, making it a promising strategy for early cancer diagnosis. Full article

(This article belongs to the Section Biotechnology)

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17 pages, 1817 KiB

Open AccessArticle

Physiological Stress Response and Oxidative Status in Tambaqui (Colossoma macropomum) Fed Diets Supplemented with Selenium

by Celma Maria Ferreira, Valéria Dornelles Gindri Sinhorin, Márcio Aquio Hoshiba and Janessa Sampaio de Abreu

Biology 2024, 13(12), 959; https://doi.org/10.3390/biology13120959 - 22 Nov 2024

Abstract

The present study aimed to evaluate the physiological responses to transport stress in juvenile tambaqui (Colossoma macropomum) fed a diet supplemented with hydroxy-selenomethionine (OH-SeMet; Selisseo^®, Adisseo) and determine through stress biomarkers whether selenium supplementation could reduce the impact of [...] Read more.

The present study aimed to evaluate the physiological responses to transport stress in juvenile tambaqui (Colossoma macropomum) fed a diet supplemented with hydroxy-selenomethionine (OH-SeMet; Selisseo^®, Adisseo) and determine through stress biomarkers whether selenium supplementation could reduce the impact of transport stress on tambaqui resilience. Juvenile fish (15.71 ± 1.90 g) were randomly distributed into five experimental groups; one fed a basal diet without inclusion of OH-SeMet (0.0 mg Se/kg) and four other groups fed supplemented diets with selenium in the form of OH-SeMet at concentrations of 0.3, 0.6, 0.9, and 1.2 mg Se/kg over 75 days. After this period, the fish were transported for 4 h in plastic bags (60 L), and sampling took place before transport (baseline), immediately after transport, and 24 h later. The effects of dietary OH-SeMet in tambaqui challenged by transport were studied in terms of antioxidative status (superoxide dismutase, catalase, glutathione peroxidase, glutathione s-transferase, and reduced glutathione); stress markers (serum cortisol, blood glucose, ionic and hematological parameters), and immunological status (respiratory burst activity and total protein, A/G ratio). Following transport, we observed an elevation in cortisol and blood glucose concentrations, accompanied by hemoconcentration, as evidenced by elevated hematocrit, erythrocyte count, hemoglobin concentration, and mean corpuscular hemoglobin concentration (MCHC). Additionally, there was a decrease in immune response, indicated by reduced respiratory activity of leukocytes and an osmotic imbalance, which culminated in hypochloremia, increased plasma protein concentration, and a rise in red blood cell volume, all of which were measured 24 h after the stressor was applied. Twenty-four hours after transport, the antioxidant defense system was activated, and no recovery of homeostasis was observed for most of the parameters analyzed. The dietary inclusion of selenium did not alleviate the hormonal, metabolic, hematological, and ionic changes caused by transport, but at a concentration of 0.9 mg Se/kg, it was able to increase the activity of enzymes related to oxidative stress (catalase and superoxide dismutase, mainly) in tambaqui juveniles submitted to this challenge. Full article

(This article belongs to the Special Issue Aquatic Animal Nutrition and Feed)

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15 pages, 328 KiB

Open AccessReview

Circadian Regulation in Diurnal Mammals: Neural Mechanisms and Implications in Translational Research

by Yirun Jiang, Jiaming Shi, Jun Tai and Lily Yan

Biology 2024, 13(12), 958; https://doi.org/10.3390/biology13120958 - 22 Nov 2024

Abstract

Diurnal and nocturnal mammals have evolved unique behavioral and physiological adaptations to optimize survival for their day- or night-active lifestyle. The mechanisms underlying the opposite activity patterns are not fully understood but likely involve the interplay between the circadian time-keeping system and various [...] Read more.

Diurnal and nocturnal mammals have evolved unique behavioral and physiological adaptations to optimize survival for their day- or night-active lifestyle. The mechanisms underlying the opposite activity patterns are not fully understood but likely involve the interplay between the circadian time-keeping system and various arousal- or sleep-promoting factors, e.g., light or melatonin. Although the circadian systems between the two chronotypes share considerable similarities, the phase relationships between the principal and subordinate oscillators are chronotype-specific. While light promotes arousal and wakefulness in diurnal species like us, it induces sleep in nocturnal ones. Similarly, melatonin, the hormone of darkness, is commonly used as a hypnotic in humans but is secreted in the active phase of nocturnal animals. Thus, the difference between the two chronotypes is more complex than a simple reversal, as the physiological and neurological processes in diurnal mammals during the day are not equivalent to that of nocturnal ones at night. Such chronotype differences could present a significant translational gap when applying research findings obtained from nocturnal rodents to diurnal humans. The potential advantages of diurnal models are being discussed in a few sleep-related conditions including familial natural short sleep (FNSS), obstructive sleep apnea (OSA), and Smith–Magenis syndrome (SMS). Considering the difference in chronotype, a diurnal model will be more adequate for revealing the physiology and physiopathology pertaining to human health and disease, especially in conditions in which circadian rhythm disruption, altered photic response, or melatonin secretion is involved. We hope the recent advances in gene editing in diurnal rodents will promote greater utility of the diurnal models in basic and translational research. Full article

(This article belongs to the Special Issue Discovering the Physiological Significance and Regulatory Mechanisms of Circadian Rhythm Generation)

17 pages, 3192 KiB

Open AccessReview

Biobank Digitalization: From Data Acquisition to Efficient Use

by Anastasiia S. Bukreeva, Kristina A. Malsagova, Denis V. Petrovskiy, Tatiana V. Butkova, Valeriya I. Nakhod, Vladimir R. Rudnev, Alexander A. Izotov and Anna L. Kaysheva

Biology 2024, 13(12), 957; https://doi.org/10.3390/biology13120957 - 22 Nov 2024

Abstract

Biobanks are involved in a broad range of studies, including both basic and clinical research, so their functions and roles are evolving. Digital biobanks have emerged due to digitalization in this field; however, it also entails an increasing number of ethical and legal [...] Read more.

Biobanks are involved in a broad range of studies, including both basic and clinical research, so their functions and roles are evolving. Digital biobanks have emerged due to digitalization in this field; however, it also entails an increasing number of ethical and legal issues, in particular those related to the protection of donor data and potential commercial applications. The development of biobanks and the size of stored datasets lay the groundwork for proceeding to digital biobanks that intensely employ artificial intelligence tools. Digital biobanks can simplify the search for and access to biological specimens, thus contributing to the conduction of research and creating new collaborations. They are becoming an increasingly important tool for personalized medicine and an individualized approach to disease treatment, contributing to the elaboration of more accurate diagnostic methods and the development of innovative therapeutic strategies. Full article

(This article belongs to the Section Bioinformatics)

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13 pages, 1775 KiB

Open AccessArticle

Convergent Evolution of Armor: Thermal Resistance in Deep-Sea Hydrothermal Vent Crustaceans

by Boongho Cho, Sook-Jin Jang, Hee-seung Hwang and Taewon Kim

Biology 2024, 13(12), 956; https://doi.org/10.3390/biology13120956 - 21 Nov 2024

Abstract

Organisms occupy diverse ecological niches worldwide, each with characteristics finely evolved for their environments. Crustaceans residing in deep-sea hydrothermal vents, recognized as one of Earth’s extreme environments, may have adapted to withstand severe conditions, including elevated temperatures and pressure. This study compares the [...] Read more.

Organisms occupy diverse ecological niches worldwide, each with characteristics finely evolved for their environments. Crustaceans residing in deep-sea hydrothermal vents, recognized as one of Earth’s extreme environments, may have adapted to withstand severe conditions, including elevated temperatures and pressure. This study compares the exoskeletons of two vent crustaceans (bythograeid crab Austinograea sp. and squat lobster Munidopsis lauensis) with four coastal species (Asian paddle crabs, blue crab, hermit crab, and mantis shrimp) to identify traits influenced by vent environments. The goal was to identify distinctive exoskeletal characteristics commonly observed in vent crustaceans, resulting from their exposure to severe abiotic factors, including elevated temperatures and pressures, found in vent environments. Results show that the exoskeletons of vent crustaceans demonstrated significantly enhanced thermal stability compared to coastal species. These vent crustaceans consistently featured exoskeletons characterized by a reduced proportion of volatile components, such as water, and an increased proportion of CaCO₃, compared with coastal crustaceans. Furthermore, vent crustaceans lacked carotenoid pigments that had low heat resistance. However, no apparent differences were observed in the mechanical properties. Our findings suggest that the similar composition of exoskeletons in vent crustaceans evolved convergently to withstand high temperatures. Full article

(This article belongs to the Special Issue The Biodiversity and Ecosystem Dynamics of Deep-Sea Hydrothermal Vents)

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Graphical abstract

15 pages, 6895 KiB

Open AccessArticle

Curcumin Mitigates Gut Dysbiosis and Enhances Gut Barrier Function to Alleviate Metabolic Dysfunction in Obese, Aged Mice

by Gopal Lamichhane, Femi Olawale, Jing Liu, Da-Yeon Lee, Su-Jeong Lee, Nathan Chaffin, Sanmi Alake, Edralin A. Lucas, Guolong Zhang, Josephine M. Egan and Yoo Kim

Biology 2024, 13(12), 955; https://doi.org/10.3390/biology13120955 - 21 Nov 2024

Abstract

The gut microbiome plays a critical role in maintaining gut and metabolic health, and its composition is often altered by aging and obesity. This study aimed to investigate the protective effects of curcumin on gut dysbiosis, gut barrier integrity, and bile acid homeostasis [...] Read more.

The gut microbiome plays a critical role in maintaining gut and metabolic health, and its composition is often altered by aging and obesity. This study aimed to investigate the protective effects of curcumin on gut dysbiosis, gut barrier integrity, and bile acid homeostasis in aged mice fed a high-fat, high-sugar diet (HFHSD). Eighteen- to twenty-one-month-old male C57BL/6 mice were divided into groups fed a normal chow diet or HFHSD, with or without curcumin supplementation (0.4% w/w) for 8 and 15 weeks. We assessed body weight, food intake, insulin sensitivity, gut microbiota composition, and gene expression in the gut and liver and performed histological analysis of gut tissues. Curcumin supplementation prevented HFHSD-induced weight gain and metabolic disturbances. In the gut, curcumin-treated mice showed a higher abundance of beneficial bacterial genera, such as Lachnospiraceae, Akkermansia, Mucispirillum, and Verrucomicrobiota, alongside a lower abundance of harmful bacterial genera like Desulfobacteria, Alistipes, and Muribaculaceae compared to control. This shift in gut microbiota was associated with improved gut integrity, as demonstrated by increased expression of the tight junction protein occludin and reduced levels of the pro-inflammatory marker interleukin-1β in the ileum. Additionally, curcumin modulated hepatic gene expression involved in bile acid homeostasis, suggesting a positive effect on liver health. Curcumin supplementation can alleviate the negative effects of aging and an HFHSD on the gut microbiome, improve gut barrier integrity, and maintain bile acid homeostasis. These findings highlight curcumin’s potential as a dietary intervention for managing obesity- and age-associated gut health issues. Full article

(This article belongs to the Special Issue Gut Microbiome in Health and Disease (2nd Edition))

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15 pages, 1265 KiB

Open AccessArticle

Polygenic Risk Score Improves Melanoma Risk Assessment in a Patient Cohort from the Veneto Region of Italy

by Stefania Pellegrini, Thomas P. Potjer, Paola Del Bianco, Antonella Vecchiato, Alessio Fabozzi, Luisa Piccin, Debora Tonello, Nienke van der Stoep, Emily Tinsley, Maria Teresa Landi, Mark M. Iles and Chiara Menin

Biology 2024, 13(11), 954; https://doi.org/10.3390/biology13110954 - 20 Nov 2024

Abstract

Recent genome-wide association studies (GWASs) have identified many single nucleotide polymorphisms (SNPs) that alone weakly affect melanoma risk, but their combined effect on a polygenic risk score (PRS) can have a far bigger impact on estimating risk. However, the PRS is not yet [...] Read more.

Recent genome-wide association studies (GWASs) have identified many single nucleotide polymorphisms (SNPs) that alone weakly affect melanoma risk, but their combined effect on a polygenic risk score (PRS) can have a far bigger impact on estimating risk. However, the PRS is not yet at the stage of being utilized in clinical practice, and further evidence is needed. In this study, 270 melanoma patients fulfilling the criteria for a suspected genetic predisposition but with a negative genetic test for high/medium-penetrance genes were genotyped for 57 SNPs selected in previous GWASs to construct a PRS model. We found a significantly higher mean PRS₅₇ in all melanoma cases than in controls (0.58 vs. 0.00, p < 0.001), and the mean PRS₅₇ in multiple primary melanoma cases was twice that in single melanoma cases (0.689 vs. 0.362, p = 0.025). Interestingly, our results confirm the association of the PRS₅₇ not only with other melanoma risk factors but also with a younger age at diagnosis. This evidence supports the potentially powerful discriminative role of PRS in the selection of high-risk patients who should undergo stricter surveillance protocols. Full article

(This article belongs to the Special Issue New Sight in Cancer Genetics)

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18 pages, 25417 KiB

Open AccessArticle

Combination of Adult Mesenchymal Stem Cell Therapy and Immunomodulation with Dimethyl Fumarate Following Spinal Cord Ventral Root Repair

by Paula Regina Gelinski Kempe, Mateus Vidigal de Castro, Lilian de Oliveira Coser, Luciana Politti Cartarozzi, Benedito Barraviera, Rui Seabra Ferreira, Jr. and Alexandre Leite Rodrigues de Oliveira

Biology 2024, 13(11), 953; https://doi.org/10.3390/biology13110953 - 20 Nov 2024

Abstract

Spinal cord injury results in significant motor and sensory loss. In the experimental ventral root avulsion (VRA) model, the ventral (motor) roots are disconnected from the spinal cord surface, disrupting contact between spinal motoneurons and muscle fibers. Axotomized motoneurons typically degenerate within two [...] Read more.

Spinal cord injury results in significant motor and sensory loss. In the experimental ventral root avulsion (VRA) model, the ventral (motor) roots are disconnected from the spinal cord surface, disrupting contact between spinal motoneurons and muscle fibers. Axotomized motoneurons typically degenerate within two to three weeks after avulsion, the situation being exacerbated by an increased glial response and chronic inflammation. Nevertheless, root reimplantation has been observed to stimulate regenerative potential in some motoneurons, serving as a model for CNS/PNS regeneration. We hypothesized that a combination of neuroprotective and immunomodulatory therapies is capable of enhancing regenerative responses following nerve root injury and repair. A heterologous fibrin biopolymer (HFB) was used for surgical repair; dimethyl fumarate (DMF) was used for neuroprotection and immunomodulation; and adipose tissue-derived mesenchymal stem cells (AT-MSCs) were used as a source of trophic factors and cytokines that may further enhance neuronal survival. Thus, adult female Lewis rats underwent unilateral VRA of the L4–L6 roots, followed by reimplantation with HFB, AT-MSCs transplantation, and daily DMF treatment for four weeks, with a 12-week postoperative survival period. An evaluation of the results focused on light microscopy, qRT-PCR, and the Catwalk motor function recovery system. Data were analyzed using one-way or two-way ANOVA (p < 0.05). The results indicate that the combined therapy resulted in a reduced glial response and a 70% improvement in behavioral motor recovery. Overall, the data support the potential of combined regenerative approaches after spinal cord root injury. Full article

(This article belongs to the Section Neuroscience)

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19 pages, 2564 KiB

Open AccessArticle

Genome Structure, Evolution, and Host Shift of Nosema

by Xiao Xiong, Christopher J. Geden, Yongjun Tan, Ying Zhang, Dapeng Zhang, John H. Werren and Xu Wang

Biology 2024, 13(11), 952; https://doi.org/10.3390/biology13110952 - 19 Nov 2024

Abstract

Nosema is a diverse fungal genus of unicellular, obligate symbionts infecting various arthropods. We performed comparative genomic analyses of seven Nosema species that infect bees, wasps, moths, butterflies, and amphipods. As intracellular parasites, these species exhibit significant genome reduction, retaining only about half [...] Read more.

Nosema is a diverse fungal genus of unicellular, obligate symbionts infecting various arthropods. We performed comparative genomic analyses of seven Nosema species that infect bees, wasps, moths, butterflies, and amphipods. As intracellular parasites, these species exhibit significant genome reduction, retaining only about half of the genes found in free-living yeast genomes. Notably, genes related to oxidative phosphorylation are entirely absent (p < 0.001), and those associated with endocytosis are significantly diminished compared to other pathways (p < 0.05). All seven Nosema genomes display significantly lower G-C content compared to their microsporidian outgroup. Species-specific 5~12 bp motifs were identified immediately upstream of start codons for coding genes in all species (p ≤ 1.6 × 10⁻⁷²). Our RNA-seq data from Nosema muscidifuracis showed that this motif is enriched in highly expressed genes but depleted in lowly expressed ones (p < 0.05), suggesting it functions as a cis-regulatory element in gene expression. We also discovered diverse telomeric repeats within the genus. Phylogenomic analyses revealed two major Nosema clades and incongruency between the Nosema species tree and their hosts’ phylogeny, indicating potential host switch events (100% bootstrap values). This study advances the understanding of genomic architecture, gene regulation, and evolution of Nosema, offering valuable insights for developing strategies to control these microbial pathogens. Full article

(This article belongs to the Special Issue Advances in Evolutionary Ecology of Host–Parasite Interactions)

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18 pages, 5502 KiB

Open AccessArticle

Biodiversity Patterns and DNA Barcode Gap Analysis of COI in Coastal Lagoons of Albania

by Mariola Ismailaj, Francesco Zangaro, Valeria Specchia, Franca Sangiorgio, Francesca Marcucci, Hajdar Kiçaj, Alberto Basset and Maurizio Pinna

Biology 2024, 13(11), 951; https://doi.org/10.3390/biology13110951 - 19 Nov 2024

Abstract

Aquatic biodiversity includes a variety of unique species, their habitats, and their interactions with each other. Albania has a large hydrographic network including rivers, lakes, wetlands and coastal marine areas, contributing to a high level of aquatic biodiversity. Currently, evaluating aquatic biodiversity relies [...] Read more.

Aquatic biodiversity includes a variety of unique species, their habitats, and their interactions with each other. Albania has a large hydrographic network including rivers, lakes, wetlands and coastal marine areas, contributing to a high level of aquatic biodiversity. Currently, evaluating aquatic biodiversity relies on morphological species identification methods, but DNA-based taxonomic identification could improve the monitoring and assessment of aquatic ecosystems. This study aims to evaluate the coverage of COI DNA barcodes in the reference libraries for the known aquatic animal species present in the coastal lagoons of Albania. In this study, the six most studied coastal lagoons of Albania were selected. Species data were gathered from the scientific literature and publicly available sites and studies. The collected species lists were taxonomically standardised using global public taxonomic databases like WORMS. The standardised lists were used to analyse the barcode gap of COI based on two public DNA barcode libraries: Barcode of Life Data Systems (BOLD) and NCBI GenBank. The results show that the COI DNA barcode gap in the coastal lagoons of Albania ranges from 7% (Lagoon of Patok) to 33% (Karavasta Lagoon). Fishes and Amphibia represent the groups with the lowest barcode gap (8% each), while Annelida shows the highest (47%). In conclusion, the COI gene marker for DNA-based biodiversity assessments is reliable for the coastal lagoons of Albania. Full article

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17 pages, 6158 KiB

Open AccessArticle

Transcriptome Responses of the Soil-Dwelling Collembolan (Entomobrya proxima Folsom) to Fertilizer Type and Concentration

by Xinyue Yang, Gang Li and Weiming Xiu

Biology 2024, 13(11), 950; https://doi.org/10.3390/biology13110950 - 19 Nov 2024

Abstract

Soil collembolans have been regarded as the effective bioindicator of environmental changes. However, the physiological mechanisms through which collembolans respond to agricultural activities are largely unknown. Given the plasticity and sensitivity to environmental changes, even subtle responses can be quantified via transcriptomics. Therefore, [...] Read more.

Soil collembolans have been regarded as the effective bioindicator of environmental changes. However, the physiological mechanisms through which collembolans respond to agricultural activities are largely unknown. Given the plasticity and sensitivity to environmental changes, even subtle responses can be quantified via transcriptomics. Therefore, the relevant in situ soil ecosystem and numerically dominant collembolan species Entomobrya proxima Folsom was selected to explore the dynamic responses to fertilizer type and concentration using transcriptome sequencing over three periods (6 h, 24 h and 10 d). The results showed that exposure duration caused significant alterations in gene expression profiles. At day 10 after exposure, gene expression patterns differed remarkably between the two fertilizer types and the control. Relative to organic fertilizer, the number of DEGs was increased by 114.31% under inorganic fertilizer, which declined with increasing inorganic fertilizer concentrations. Functional enrichment analysis was indicative of enhanced fatty acid and carbohydrate metabolism and reduced disease occurrence by organic fertilizer; however, an inhibited lipid synthesis process promoted susceptibility to infection, triggered oxidative stress, etc. by inorganic fertilizer. Overall, fertilizer addition changed the transcriptional pattern of the collembolan, potentially causing shifts in pathways related to metabolism, immunity, etc. In comparison to inorganic fertilizer, organic fertilizer impacted less on the gene expression patterns, implying that organic fertilizer application may be more beneficial to soil animal health. Full article

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15 pages, 6950 KiB

Open AccessArticle

Etomoxir Sodium Salt Promotes Imidazole Ketone Erastin-Induced Myeloid-Derived Suppressor Cell Ferroptosis and Enhances Cancer Therapy

by Nada Mohamady Farouk Abdalsalam, Zihao Liang, Hafiza Kashaf Tariq, Abdulrahman Ibrahim, Rong Li, Xiaochun Wan and Dehong Yan

Biology 2024, 13(11), 949; https://doi.org/10.3390/biology13110949 - 19 Nov 2024

Abstract

Although ferroptosis inducers trigger ferroptotic tumor cells and immune cells in the tumor microenvironment (TME), imidazole ketone erastin (IKE)’s induction of ferroptosis shows no effect on tumor growth in immunocompetent tumor-bearing mice due to the presence of myeloid-derived suppressor cells (MDSCs). Treatment of [...] Read more.

Although ferroptosis inducers trigger ferroptotic tumor cells and immune cells in the tumor microenvironment (TME), imidazole ketone erastin (IKE)’s induction of ferroptosis shows no effect on tumor growth in immunocompetent tumor-bearing mice due to the presence of myeloid-derived suppressor cells (MDSCs). Treatment of the carnitine palmitoyltransferase 1a (CPT1A)-specific inhibitor decreases the immunosuppressive function of MDSCs and enhances ferroptotic inducer-initiated tumor cell ferroptosis. However, whether blocking CPT1A could enhance IKE-induced MDSC ferroptosis and thereby inhibit tumor growth is still unclear. Here, we report that a CPT1A-specific inhibitor, etomoxir sodium salt (Eto), and IKE combined treatment increased MDSC ferroptosis. Interestingly, the combination treatment of Eto and IKE blocked MDSCs’ immunosuppressive function and accumulation by downregulating the expression of SLC7A11, GPX4, and ARG1 while promoting T-cell proliferation and infiltration into tumor tissues to enhance cancer therapy. These data provide a rationale for the combination therapy of a specific CPT1A inhibitor, Eto, with IKE in clinical settings. Full article

(This article belongs to the Special Issue Cell Self-Destruction (Programmed Cell Death), Immunonutrition and Metabolism)

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13 pages, 2223 KiB

Open AccessArticle

Red Blood Cell Morphology Is Associated with Altered Hemorheological Properties and Fatigue in Patients with Long COVID

by Marijke Grau, Alena Presche, Anna-Lena Krüger, Wilhelm Bloch and Björn Haiduk

Biology 2024, 13(11), 948; https://doi.org/10.3390/biology13110948 - 19 Nov 2024

Abstract

Background: SARS-CoV-2 infection adversely affects rheological parameters, particularly red blood cell (RBC) aggregation and deformability, but whether these changes persist in patients suffering from Long-COVID (LC) and whether these changes are related to RBC morphology remain unknown. Methods: Venous blood was collected from [...] Read more.

Background: SARS-CoV-2 infection adversely affects rheological parameters, particularly red blood cell (RBC) aggregation and deformability, but whether these changes persist in patients suffering from Long-COVID (LC) and whether these changes are related to RBC morphology remain unknown. Methods: Venous blood was collected from n = 30 diagnosed LC patients and n = 30 non-LC controls and RBC deformability, RBC aggregation, and hematological parameters were measured. In addition, RBCs were examined microscopically for morphological abnormalities. The mechanical sensitivity index (MS) was assessed in n = 15 LC and n = 15 non-LC samples. Results: Hematological parameters did not differ between the groups. However, LC showed higher aggregation-related parameters. Although RBC deformability was higher in LC, MS, reflecting the functional capacity to deform, was limited in this group. RBCs from LC showed significantly more morphological abnormalities. The extent of morphological abnormalities correlated with MS and the FACIT-Fatigue score of the LC patients. Conclusion: RBCs from LC show a high degree of morphological abnormalities, which might limit the blood flow determining RBC properties and also be related to fatigue symptomatology in LC. Approaches are now needed to understand the underlying cause of these alterations and to ameliorate these permanent changes. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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18 pages, 11437 KiB

Open AccessArticle

Anatomical Tool as Additional Approach for Identifying Pharmaceutically Important Ephedra Species (Ephedraceae) at Gender Identity Level in Egypt

by Maha H. Khalaf, Wafaa M. Amer, Najla A. Al Shaye, Mahmoud O. Hassan and Nasr H. Gomaa

Biology 2024, 13(11), 947; https://doi.org/10.3390/biology13110947 - 18 Nov 2024

Abstract

The genus Ephedra Tourn. ex L. (Ephedraceae) is an important source with pharmacological and environmental potential. Conversely, Ephedra spp. still exhibit taxonomic complexity, especially for the specimens lacking reproductive cones. This complexity is attributed to its xeromorphic features, notably the reduced leaves and [...] Read more.

The genus Ephedra Tourn. ex L. (Ephedraceae) is an important source with pharmacological and environmental potential. Conversely, Ephedra spp. still exhibit taxonomic complexity, especially for the specimens lacking reproductive cones. This complexity is attributed to its xeromorphic features, notably the reduced leaves and analogous assimilating branches, which make the species identification a real challenge. The current study provides a pioneering approach to distinguish fragments of Ephedra species at the gender level. This study was based on the stem anatomy and stem epidermal features using a light microscope for five species (E. alata Decne., E. aphylla Forssk., E. ciliata Fisch. & C.A.Mey., E. foeminea Forssk. and E. Ephedra pachyclada Boiss.) represented by ten genders collected from S. Sinai, Egypt. Anomocytic and brachyparacytic stomata, tanniniferous idioblasts, annual rings, a terete and furrowed outline, the number and width of tracheids, patches of cortical fibers, unicellular trichomes, druses, solitary crystals, and the activity of interfascicular cambium were among the distinguishing features that were found. Different statistical analyses were applied to explore the diversity at interspecific and intra-generic levels. This study revealed that the stem anatomy was not only an efficient tool for identifying the investigated five Ephedra species at the species level but also presented a differential key to distinguish between genders and species. In addition, our results indicated that the epidermal features played a critical role in differentiating the studied Ephedra species at the gender level. This study confirms the efficacy of stem anatomy as an identification approach for the Ephedra species at the gender level and recommends this approach to identify the fragmented Ephedra for taxonomical, pharmaceutical, and medical applications. Full article

(This article belongs to the Section Plant Science)

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25 pages, 723 KiB

Open AccessReview

Can IMTA System Improve the Productivity and Quality Traits of Aquatic Organisms Produced at Different Trophic Levels? The Benefits of IMTA—Not Only for the Ecosystem

by Giusy Rusco, Alessandra Roncarati, Michele Di Iorio, Michela Cariglia, Caterina Longo and Nicolaia Iaffaldano

Biology 2024, 13(11), 946; https://doi.org/10.3390/biology13110946 - 18 Nov 2024

Abstract

IMTA is one of the most innovative and sustainable farming systems, exhibiting the best technique available in rearing aquatic organisms belonging to different positions along the trophic levels. In the literature and in legislation, the environmental benefits of IMTA protocols have been extensively [...] Read more.

IMTA is one of the most innovative and sustainable farming systems, exhibiting the best technique available in rearing aquatic organisms belonging to different positions along the trophic levels. In the literature and in legislation, the environmental benefits of IMTA protocols have been extensively recognized, mainly for its capability to reduce the ecological footprint of intensive aquaculture systems and concretely address the Sustainable Development Goal no. 14 (SDG 14). However, lesser attention is given to the assessments of its role in enhancing the zootechnical performance, animal welfare, and flesh quality of the species involved. To the best of our knowledge, this is the first review that aims to offer a systematic analysis of the existing literature on the main commercial motivations that could draw the attention of stakeholders, including consumers and fish farmers, towards a greater social acceptability and implementation of the IMTA system on a large scale. The findings suggest that, beyond its environmental advantages, IMTA systems can positively influence the productivity, growth, survival, feed efficiency, and animal health and welfare (AH&W), as well as the nutritional quality of the harvested species, thus offering significant economic and market value both in terms of Environmental, Societal and Governance (ESG) parameters and One Health. Full article

(This article belongs to the Special Issue Nutrition, Environment, and Fish Physiology)

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20 pages, 3121 KiB

Open AccessReview

Understanding the Role of NLRP3 Inflammasome in Acute Pancreatitis

by Konstantinos Papantoniou, Ioanna Aggeletopoulou, Christos Michailides, Ploutarchos Pastras and Christos Triantos

Biology 2024, 13(11), 945; https://doi.org/10.3390/biology13110945 - 18 Nov 2024

Abstract

Acute pancreatitis (AP) remains a serious clinical condition, with current treatment options being largely supportive. The discovery of inflammasomes, particularly the NOD-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome, has significantly advanced our knowledge regarding many inflammatory diseases’ pathogenesis, including AP. The NLRP3 [...] Read more.

Acute pancreatitis (AP) remains a serious clinical condition, with current treatment options being largely supportive. The discovery of inflammasomes, particularly the NOD-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome, has significantly advanced our knowledge regarding many inflammatory diseases’ pathogenesis, including AP. The NLRP3 inflammasome is central in mediating the inflammatory process in AP through its diverse activation mechanisms and its involvement in multiple signal transduction pathways. This has made NLRP3 an appealing target for novel therapeutic strategies aimed at modulating inflammation in AP. Despite the growing interest in NLRP3 as a therapeutic target, there remains a notable gap in clinical research, with few clinical trials exploring the efficacy of NLRP3 inhibitors in AP. Results of several preclinical studies and animal models are promising and suggest that the use of NLRP3 inhibitors could result in reduced inflammation and improved patient outcomes in AP. Further research is urgently needed to assess their potential benefits, safety, and applicability in human patients and address the underlying inflammatory processes driving AP. Full article

(This article belongs to the Special Issue Biology and Function of Inflammasomes)

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17 pages, 4026 KiB

Open AccessArticle

The Isolation and Characterization of Perlucin in Pacific Abalone, Haliotis discus hannai: A Shell Morphogenic Protein with Potential Responses to Thermal Stress and Starvation

by Yusin Cho, Md Abu Hanif, Shaharior Hossen, Soo Cheol Kim, Ji Do Han, Doo Hyun Cho and Kang Hee Kho

Biology 2024, 13(11), 944; https://doi.org/10.3390/biology13110944 - 18 Nov 2024

Abstract

Perlucin is a shell matrix protein that plays a significant role in regulating shell biomineralization. This study aimed to isolate and characterize the perlucin gene and analyze its expression to explore its role in shell formation, regeneration, and responses to thermal stress and [...] Read more.

Perlucin is a shell matrix protein that plays a significant role in regulating shell biomineralization. This study aimed to isolate and characterize the perlucin gene and analyze its expression to explore its role in shell formation, regeneration, and responses to thermal stress and starvation in Pacific abalone. The isolated full-length cDNA sequence of Hdh-Perlucin is 1002 bp long, encoding a 163-amino-acid polypeptide with a signal peptide. The mature peptide of Hdh-Perlucin contains a C-type lectin domain with signature motif and six conserved cysteine residues. Gene Ontology analysis suggests that Hdh-Perlucin exhibits carbohydrate-binding activity. Significantly higher expression of Hdh-Perlucin was observed during the juvenile, veliger, and trochophore stages, compared with cell division stage during early development. Upregulated expression was recorded from slow to rapid growth phases and during shell biomineralization, while downregulated expression was noted during starvation. Under thermal stress, expression peaked at 30 °C and 25 °C for 6 and 12 h, respectively, while consistently higher levels were observed at 15 °C throughout the experiment. This study provides the first comprehensive structural and expression analysis of Hdh-Perlucin, highlighting its roles in metamorphosis, shell formation and regeneration, and responses to heat stress and starvation in abalone. Full article

(This article belongs to the Section Marine Biology)

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