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Biology, Volume 13, Issue 3 (March 2024) – 69 articles

Cover Story (view full-size image): The COVID-19 pandemic showcases the impact of global mitigation efforts, including that of vaccine development. Nevertheless, rapid viral mutations present a challenge to disease control strategies worldwide. The experimental acquisition of mutant structures cannot match the rate at which the virus evolves. Here, we use AlphaFold2 to model SARS-CoV-2 spike protein structures for various haplotypes that remain unexplored. This AI tool delivers near-experimental resolution models in only a few hours. We compare major Variants of Concern (Alpha, Delta, and Omicron) and latitude-delimited haplotypes to the Wuhan strain. Structural changes from seasonal haplotype diversification aid in predicting virus evolution, understanding seasonal behavior, and enhancing vaccine and drug development strategies. View this paper
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14 pages, 4112 KiB  
Article
Amorphous Calcium Carbonate from Plants Can Promote Bone Growth in Growing Rats
by Chun-Kai Chen, Yu-Shan Lee, Zwe-Ling Kong and Yi-Wen Chien
Biology 2024, 13(3), 201; https://doi.org/10.3390/biology13030201 - 21 Mar 2024
Viewed by 691
Abstract
Objectives: This study aimed to investigate the effect of amorphous calcium carbonate (ACC) supplementation on bone growth in growing rats. Methods: We used 3-week-old male Wistar rats to simulate childhood and adolescent growth stages. Rats were divided into four groups as follows: a [...] Read more.
Objectives: This study aimed to investigate the effect of amorphous calcium carbonate (ACC) supplementation on bone growth in growing rats. Methods: We used 3-week-old male Wistar rats to simulate childhood and adolescent growth stages. Rats were divided into four groups as follows: a control group (C), a low-dose group (L, 20.65 mg/kg body weight (BW) ACC), a medium-dose group (M, 206.5 mg/kg BW ACC), and a high-dose group (H, 413 mg/kg BW ACC) administered by gavage. Body length (BL) and BW were measured weekly. The bone mineral density (BMD) of two lumbar vertebrae (L3 and L4) and the left femur were analyzed by micro-computed tomography (μCT) at 0, 4, 8, and 12 weeks. At the end of 12 weeks, the rats were sacrificed. After that, blood samples were collected from the abdominal aorta. Femurs and tibias were collected and weighed, and their lengths were measured. Then, bone samples were used to perform histopathological and histomorphometric analyses. Results: It showed that ACC supplementation in growing rats increased the trabecular bone thickness and serum bone formation biomarkers. Furthermore, high-dose ACC decreased serum bone resorption biomarkers and increased BMD. Conclusions: ACC supplementation can enhance osteoblast metabolism and inhibit osteoclast metabolism, resulting in a higher bone formation rate compared to bone resorption. This led to increased trabecular bone thickness, a higher BMD, and supported bone growth. Full article
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21 pages, 3418 KiB  
Review
The Role of Cerebellar Intrinsic Neuronal Excitability, Synaptic Plasticity, and Perineuronal Nets in Eyeblink Conditioning
by Bernard G. Schreurs, Deidre E. O’Dell and Desheng Wang
Biology 2024, 13(3), 200; https://doi.org/10.3390/biology13030200 - 21 Mar 2024
Viewed by 861
Abstract
Evidence is strong that, in addition to fine motor control, there is an important role for the cerebellum in cognition and emotion. The deep nuclei of the mammalian cerebellum also contain the highest density of perineural nets—mesh-like structures that surround neurons—in the brain, [...] Read more.
Evidence is strong that, in addition to fine motor control, there is an important role for the cerebellum in cognition and emotion. The deep nuclei of the mammalian cerebellum also contain the highest density of perineural nets—mesh-like structures that surround neurons—in the brain, and it appears there may be a connection between these nets and cognitive processes, particularly learning and memory. Here, we review how the cerebellum is involved in eyeblink conditioning—a particularly well-understood form of learning and memory—and focus on the role of perineuronal nets in intrinsic membrane excitability and synaptic plasticity that underlie eyeblink conditioning. We explore the development and role of perineuronal nets and the in vivo and in vitro evidence that manipulations of the perineuronal net in the deep cerebellar nuclei affect eyeblink conditioning. Together, these findings provide evidence of an important role for perineuronal net in learning and memory. Full article
(This article belongs to the Special Issue Plasticity and Computation in Cerebellar Neurons and Microcircuits)
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19 pages, 2627 KiB  
Review
Advances in the Development of Biofertilizers and Biostimulants from Microalgae
by Alejandra M. Miranda, Fabian Hernandez-Tenorio, Fabian Villalta, Gabriel J. Vargas and Alex A. Sáez
Biology 2024, 13(3), 199; https://doi.org/10.3390/biology13030199 - 21 Mar 2024
Viewed by 1217
Abstract
Microalgae have commercial potential in different sectors of the industry. Specifically in modern agriculture, they can be used because they have the ability to supply nutrients to the soil and produce plant growth hormones, polysaccharides, antimicrobial compounds, and other metabolites that improve agricultural [...] Read more.
Microalgae have commercial potential in different sectors of the industry. Specifically in modern agriculture, they can be used because they have the ability to supply nutrients to the soil and produce plant growth hormones, polysaccharides, antimicrobial compounds, and other metabolites that improve agricultural productivity. Therefore, products formulated from microalgae as biofertilizers and biostimulants turn out to be beneficial for agriculture and are positioned as a novel and environmentally friendly strategy. However, these bioproducts present challenges in preparation that affect their shelf life due to the rapid degradation of bioformulated products. Therefore, this work aimed to provide a comprehensive review of biofertilizers and biostimulants from microalgae, for which a bibliometric analysis was carried out to establish trends using scientometric indicators, technological advances were identified in terms of formulation methods, and the global market for these bioproducts was analyzed. Full article
(This article belongs to the Section Biotechnology)
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17 pages, 16421 KiB  
Article
Distribution Model Reveals Rapid Decline in Habitat Extent for Endangered Hispid Hare: Implications for Wildlife Management and Conservation Planning in Future Climate Change Scenarios
by Imon Abedin, Tanoy Mukherjee, Ah Ran Kim, Hyun-Woo Kim, Hye-Eun Kang and Shantanu Kundu
Biology 2024, 13(3), 198; https://doi.org/10.3390/biology13030198 - 20 Mar 2024
Viewed by 897
Abstract
The hispid hare, Caprolagus hispidus, belonging to the family Leporidae is a small grassland mammal found in the southern foothills of the Himalayas, in India, Nepal, and Bhutan. Despite having an endangered status according to the IUCN Red List, it lacks studies [...] Read more.
The hispid hare, Caprolagus hispidus, belonging to the family Leporidae is a small grassland mammal found in the southern foothills of the Himalayas, in India, Nepal, and Bhutan. Despite having an endangered status according to the IUCN Red List, it lacks studies on its distribution and is threatened by habitat loss and land cover changes. Thus, the present study attempted to assess the habitat suitability using the species distribution model approach for the first time and projected its future in response to climate change, habitat, and urbanization factors. The results revealed that out of the total geographical extent of 188,316 km2, only 11,374 km2 (6.03%) were identified as suitable habitat for this species. The results also revealed that habitat significantly declined across its range (>60%) under certain climate change scenarios. Moreover, in the present climate scenario protected areas such as Shuklaphanta National Park (0.837) in Nepal exhibited the highest mean extent of habitat whereas, in India, Dibru-Saikhowa National Park (0.631) is found to be the most suitable habitat. Notably, two protected areas in Uttarakhand, India, specifically Corbett National Park (0.530) and Sonanandi Wildlife Sanctuary (0.423), have also demonstrated suitable habitats for C. hispidus. Given that protected areas showing a future rise in habitat suitability might also be regarded as potential sites for species translocation, this study underscores the importance of implementing proactive conservation strategies to mitigate the adverse impacts of climate change on this species. It is essential to prioritize habitat restoration, focused protection measures, and further species-level ecological exploration to address these challenges effectively. Furthermore, fostering transboundary collaboration and coordinated conservation actions between nations is crucial to safeguarding the long-term survival of the species throughout its distribution range. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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17 pages, 4404 KiB  
Article
Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress
by Tingting Cheng, Xia Zhou, Juan Lin, Xianjian Zhou, Hongsu Wang and Tiezhu Chen
Biology 2024, 13(3), 197; https://doi.org/10.3390/biology13030197 - 20 Mar 2024
Viewed by 835
Abstract
Ophiopogon japonicus, a plant that thrives in river alluvial dams, often faces waterlogging stress due to sustained rainfall and flood seasons, which significantly impacts its growth and development. Currently, the mechanisms of waterlogging tolerance in Ophiopogon japonicus are still unclear. This study [...] Read more.
Ophiopogon japonicus, a plant that thrives in river alluvial dams, often faces waterlogging stress due to sustained rainfall and flood seasons, which significantly impacts its growth and development. Currently, the mechanisms of waterlogging tolerance in Ophiopogon japonicus are still unclear. This study analyzed the transcriptome and metabolome data for Ophiopogon japonicus in the Sichuan region (referred to as CMD) under varying degrees of waterlogging stress: mild, moderate, and severe. The results indicate that the group exposed to flooding stress exhibited a higher number of differentially expressed genes (DEGs) compared to the control group. Notably, most DEGs were downregulated and primarily enriched in phenylpropanoid biosynthesis, starch and sucrose metabolism, and plant hormone signal transduction pathways. A total of 5151 differentially accumulated metabolites (DAMs) were identified, with significantly upregulated DAMs annotated to two clusters, namely flavonoids such as apiin, pelargonin, and others. Furthermore, our study revealed significant upregulation in the expression of C2H2 (C2H2 zinc finger proteins) and AP2/ERF-ERF (the subfamily ERF proteins of APETALA2/ethylene-responsive element binding factors) transcription factors in CMD under flooding stress, suggesting their critical roles in enabling CMD to adapt to these conditions. In conclusion, this research provides insights into the intricate molecular mechanisms underlying CMD’s response to flooding stress and reports valuable genetic data for the development of transgenic plants with improved waterlogging tolerance. Full article
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13 pages, 3102 KiB  
Article
Engineering a Dual Specificity γδ T-Cell Receptor for Cancer Immunotherapy
by David M. Davies, Giuseppe Pugliese, Ana C. Parente Pereira, Lynsey M. Whilding, Daniel Larcombe-Young and John Maher
Biology 2024, 13(3), 196; https://doi.org/10.3390/biology13030196 - 20 Mar 2024
Viewed by 1066
Abstract
γδ T-cells provide immune surveillance against cancer, straddling both innate and adaptive immunity. G115 is a clonal γδ T-cell receptor (TCR) of the Vγ9Vδ2 subtype which can confer responsiveness to phosphoantigens (PAgs) when genetically introduced into conventional αβ T-cells. Cancer immunotherapy using γδ [...] Read more.
γδ T-cells provide immune surveillance against cancer, straddling both innate and adaptive immunity. G115 is a clonal γδ T-cell receptor (TCR) of the Vγ9Vδ2 subtype which can confer responsiveness to phosphoantigens (PAgs) when genetically introduced into conventional αβ T-cells. Cancer immunotherapy using γδ TCR-engineered T-cells is currently under clinical evaluation. In this study, we sought to broaden the cancer specificity of the G115 γδ TCR by insertion of a tumour-binding peptide into the complementarity-determining region (CDR) three regions of the TCR δ2 chain. Peptides were selected from the foot and mouth disease virus A20 peptide which binds with high affinity and selectivity to αvβ6, an epithelial-selective integrin that is expressed by a range of solid tumours. Insertion of an A20-derived 12mer peptide achieved the best results, enabling the resulting G115 + A12 T-cells to kill both PAg and αvβ6-expressing tumour cells. Cytolytic activity of G115 + A12 T-cells against PAg-presenting K562 target cells was enhanced compared to G115 control cells, in keeping with the critical role of CDR3 δ2 length for optimal PAg recognition. Activation was accompanied by interferon (IFN)-γ release in the presence of either target antigen, providing a novel dual-specificity approach for cancer immunotherapy. Full article
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14 pages, 6290 KiB  
Review
Bibliometric Overview on T-Cell Intracellular Antigens and Their Pathological Implications
by Beatriz Ramos-Velasco, Rocío Naranjo and José M. Izquierdo
Biology 2024, 13(3), 195; https://doi.org/10.3390/biology13030195 - 19 Mar 2024
Viewed by 799
Abstract
T-cell intracellular antigen 1 (TIA1) and TIA1-like/related protein (TIAL1/TIAR) are two members of the classical family of RNA binding proteins. Through their selective interactions with distinct RNAs and proteins, these multifunctional regulators are involved in chromatin remodeling, RNA splicing and processing and translation [...] Read more.
T-cell intracellular antigen 1 (TIA1) and TIA1-like/related protein (TIAL1/TIAR) are two members of the classical family of RNA binding proteins. Through their selective interactions with distinct RNAs and proteins, these multifunctional regulators are involved in chromatin remodeling, RNA splicing and processing and translation regulation, linking them to a wide range of diseases including neuronal disorders, cancer and other pathologies. From their discovery to the present day, many studies have focused on the behavior of these proteins in order to understand their impact on molecular and cellular processes and to understand their relationship to human pathologies. The volume of research on these proteins in various fields, including molecular biology, biochemistry, cell biology, immunology and cancer, has steadily increased, indicating a growing interest in these gene expression regulators among researchers. This information can be used to know the most productive institutions working in the field, understand the focus of research, identify key areas of involvement, delve deeper into their relationship and impact on different diseases, and to establish the level of study associated with them. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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16 pages, 2508 KiB  
Article
The Response of Endogenous ABA and Soluble Sugars of Platycladus orientalis to Drought and Post-Drought Rehydration
by Na Zhao, Jiahui Zhao, Shaoning Li, Bin Li, Jiankui Lv, Xin Gao, Xiaotian Xu and Shaowei Lu
Biology 2024, 13(3), 194; https://doi.org/10.3390/biology13030194 - 19 Mar 2024
Viewed by 672
Abstract
To uncover the internal mechanisms of various drought stress intensities affecting the soluble sugar content in organs and its regulation by endogenous abscisic acid (ABA), we selected the saplings of Platycladus orientalis, a typical tree species in the Beijing area, as our [...] Read more.
To uncover the internal mechanisms of various drought stress intensities affecting the soluble sugar content in organs and its regulation by endogenous abscisic acid (ABA), we selected the saplings of Platycladus orientalis, a typical tree species in the Beijing area, as our research subject. We investigated the correlation between tree soluble sugars and endogenous ABA in the organs (comprised of leaf, branch, stem, coarse root, and fine root) under two water treatments. One water treatment was defined as T1, which stopped watering until the potted soil volumetric water content (SWC) reached the wilting coefficient and then rewatered the sapling. The other water treatment, named T2, replenished 95% of the total water loss of one potted sapling every day and irrigated the above-mentioned sapling after its SWC reached the wilt coefficients. The results revealed that (1) the photosynthetic physiological parameters of P. orientalis were significantly reduced (p < 0.05) under fast and slow drought processes. The photosynthetic physiological parameters of P. orientalis in the fast drought–rehydration treatment group recovered faster relative to the slow drought–rehydration treatment group. (2) The fast and slow drought treatments significantly (p < 0.05) increased the ABA and soluble sugar contents in all organs. The roots of the P. orientalis exhibited higher sensitivity in ABA and soluble sugar content to changes in soil moisture dynamics compared to other organs. (3) ABA and soluble sugar content of P. orientalis showed a significant positive correlation (p < 0.05) under fast and slow drought conditions. During the rehydration stage, the two were significantly correlated in the T2 treatment (p < 0.05). In summary, soil drought rhythms significantly affected the photosynthetic parameters, organ ABA, and soluble sugar content of P. orientalis. This study elucidates the adaptive mechanisms of P. orientalis plants to drought and rehydration under the above-mentioned two water drought treatments, offering theoretical insights for selecting and cultivating drought-tolerant tree species. Full article
(This article belongs to the Collection Abiotic Stress in Plants and Resilience: Recent Advances)
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14 pages, 410 KiB  
Article
Reducing Epistasis and Pleiotropy Can Avoid the Survival of the Flattest Tragedy
by Priyanka Mehra and Arend Hintze
Biology 2024, 13(3), 193; https://doi.org/10.3390/biology13030193 - 17 Mar 2024
Viewed by 738
Abstract
This study investigates whether reducing epistasis and pleiotropy enhances mutational robustness in evolutionary adaptation, utilizing an indirect encoded model within the “survival of the flattest” (SoF) fitness landscape. By simulating genetic variations and their phenotypic consequences, we explore organisms’ adaptive mechanisms to maintain [...] Read more.
This study investigates whether reducing epistasis and pleiotropy enhances mutational robustness in evolutionary adaptation, utilizing an indirect encoded model within the “survival of the flattest” (SoF) fitness landscape. By simulating genetic variations and their phenotypic consequences, we explore organisms’ adaptive mechanisms to maintain positions on higher, narrower evolutionary peaks amidst environmental and genetic pressures. Our results reveal that organisms can indeed sustain their advantageous positions by minimizing the complexity of genetic interactions—specifically, by reducing the levels of epistasis and pleiotropy. This finding suggests a counterintuitive strategy for evolutionary stability: simpler genetic architectures, characterized by fewer gene interactions and multifunctional genes, confer a survival advantage by enhancing mutational robustness. This study contributes to our understanding of the genetic underpinnings of adaptability and robustness, challenging traditional views that equate complexity with fitness in dynamic environments. Full article
(This article belongs to the Section Evolutionary Biology)
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14 pages, 3304 KiB  
Article
Estrogen and Progesterone Receptors Are Dysregulated at the BPH/5 Mouse Preeclamptic-Like Maternal–Fetal Interface
by Viviane C. L. Gomes, Bryce M. Gilbert, Carolina Bernal, Kassandra R. Crissman and Jenny L. Sones
Biology 2024, 13(3), 192; https://doi.org/10.3390/biology13030192 - 16 Mar 2024
Viewed by 1174
Abstract
The etiopathogenesis of preeclampsia, a leading hypertensive disorder of pregnancy, has been proposed to involve an abnormal circulating sex hormone profile and misexpression of placental estrogen and progesterone receptors (ER and PR, respectively). However, existing research is vastly confined to third trimester preeclamptic [...] Read more.
The etiopathogenesis of preeclampsia, a leading hypertensive disorder of pregnancy, has been proposed to involve an abnormal circulating sex hormone profile and misexpression of placental estrogen and progesterone receptors (ER and PR, respectively). However, existing research is vastly confined to third trimester preeclamptic placentas. Consequently, the placental–uterine molecular crosstalk and the dynamic ER and PR expression pattern in the peri-conception period remain overlooked. Herein, our goal was to use the BPH/5 mouse to elucidate pre-pregnancy and early gestation Er and Pr dynamics in a preeclamptic-like uterus. BPH/5 females display low circulating estrogen concentration during proestrus, followed by early gestation hypoestrogenemia, hyperprogesteronemia, and a spontaneous preeclamptic-like phenotype. Preceding pregnancy, the gene encoding Er alpha (Erα, Esr1) is upregulated in the diestrual BPH/5 uterus. At the peak of decidualization, Esr1, Er beta (Erβ, Esr2), and Pr isoform B (Pr-B) were upregulated in the BPH/5 maternal–fetal interface. At the protein level, BPH/5 females display higher percentage of decidual cells with nuclear Erα expression, as well as Pr downregulation in the decidua, luminal and glandular epithelium. In conclusion, we provide evidence of disrupted sex hormone signaling in the peri-conception period of preeclamptic-like pregnancies, potentially shedding some light onto the intricate role of sex hormone signaling at unexplored timepoints of human preeclampsia. Full article
(This article belongs to the Section Reproductive Biology)
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15 pages, 687 KiB  
Article
PTCH1 Gene Variants, mRNA Expression, and Bioinformatics Insights in Mexican Cutaneous Squamous Cell Carcinoma Patients
by Marianela Zambrano-Román, Jorge R. Padilla-Gutiérrez, Yeminia Valle, José Francisco Muñoz-Valle, Elizabeth Guevara-Gutiérrez, Patricia Aidé López-Olmos, Laura Cristina Sepúlveda-Loza, Luis Alberto Bautista-Herrera and Emmanuel Valdés-Alvarado
Biology 2024, 13(3), 191; https://doi.org/10.3390/biology13030191 - 16 Mar 2024
Viewed by 812
Abstract
Background: Skin cancer is one of the most frequent types of cancer, and cutaneous squamous cell carcinoma (cSCC) constitutes 20% of non-melanoma skin cancer (NMSC) cases. PTCH1, a tumor suppressor gene involved in the Sonic hedgehog signaling pathway, plays a crucial role [...] Read more.
Background: Skin cancer is one of the most frequent types of cancer, and cutaneous squamous cell carcinoma (cSCC) constitutes 20% of non-melanoma skin cancer (NMSC) cases. PTCH1, a tumor suppressor gene involved in the Sonic hedgehog signaling pathway, plays a crucial role in neoplastic processes. Methods: An analytical cross-sectional study, encompassing 211 cSCC patients and 290 individuals in a control group (CG), was performed. A subgroup of samples was considered for the relative expression analysis, and the results were obtained using quantitative real-time PCR (qPCR) with TaqMan® probes. The functional, splicing, and disease-causing effects of the proposed variants were explored via bioinformatics. Results: cSCC was predominant in men, especially in sun-exposed areas such as the head and neck. No statistically significant differences were found regarding the rs357564, rs2236405, rs2297086, and rs41313327 variants of PTCH1, or in the risk of cSCC, nor in the mRNA expression between the cSCC group and CG. A functional effect of rs357564 and a disease-causing relation to rs41313327 was identified. Conclusion: The proposed variants were not associated with cSCC risk in this Mexican population, but we recognize the need for analyzing larger population groups to elucidate the disease-causing role of rare variants. Full article
(This article belongs to the Section Genetics and Genomics)
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12 pages, 1860 KiB  
Article
The Effects of Salinity and Genotype on the Rhizospheric Mycobiomes in Date Palm Seedlings
by Mahmoud W. Yaish, Aya Al-Busaidi, Bernard R. Glick, Talaat Ahmed and Juha M. Alatalo
Biology 2024, 13(3), 190; https://doi.org/10.3390/biology13030190 - 15 Mar 2024
Viewed by 954
Abstract
Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the [...] Read more.
Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, ‘Zabad’, and the tolerant cultivar, ‘Umsila’. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms. Full article
(This article belongs to the Collection Plant Growth-Promoting Bacteria: Mechanisms and Applications)
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17 pages, 2899 KiB  
Article
Heart Rate and Acceleration Dynamics during Swim-Fitness and Stress Challenge Tests in Yellowtail Kingfish (Seriola lalandi)
by Arjan P. Palstra, Wout Abbink, Wisdom E. K. Agbeti, Leo Kruijt, Pauline Jéhannet and Martin J. Lankheet
Biology 2024, 13(3), 189; https://doi.org/10.3390/biology13030189 - 15 Mar 2024
Viewed by 1139
Abstract
The yellowtail kingfish is a highly active and fast-growing marine fish with promising potential for aquaculture. In this study, essential insights were gained into the energy economy of this species by heart rate and acceleration logging during a swim-fitness test and a subsequent [...] Read more.
The yellowtail kingfish is a highly active and fast-growing marine fish with promising potential for aquaculture. In this study, essential insights were gained into the energy economy of this species by heart rate and acceleration logging during a swim-fitness test and a subsequent stress challenge test. Oxygen consumption values of the 600–800 g fish, when swimming in the range of 0.2 up to 1 m·s−1, were high—between 550 and 800 mg·kg−1·h−1—and the heart rate values—up to 228 bpm—were even among the highest ever measured for fishes. When swimming at these increasing speeds, their heart rate increased from 126 up to 162 bpm, and acceleration increased from 11 up to 26 milli-g. When exposed to four sequential steps of increasing stress load, the decreasing peaks of acceleration (baseline values of 12 to peaks of 26, 19 and 15 milli-g) indicated anticipatory behavior, but the heart rate increases (110 up to 138–144 bpm) remained similar. During the fourth step, when fish were also chased, peaking values of 186 bpm and 44 milli-g were measured. Oxygen consumption and heart rate increased with swimming speed and was well reflected by increases in tail beat and head width frequencies. Only when swimming steadily near the optimal swimming speed were these parameters strongly correlated. Full article
(This article belongs to the Special Issue Sensor Applications to Study the Biology of Fish Movement)
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17 pages, 375 KiB  
Review
Artificial Feeding Systems for Vector-Borne Disease Studies
by Olayinka M. Olajiga, Samuel B. Jameson, Brendan H. Carter, Dawn M. Wesson, Dana Mitzel and Berlin Londono-Renteria
Biology 2024, 13(3), 188; https://doi.org/10.3390/biology13030188 - 15 Mar 2024
Viewed by 1180
Abstract
This review examines the advancements and methodologies of artificial feeding systems for the study of vector-borne diseases, offering a critical assessment of their development, advantages, and limitations relative to traditional live host models. It underscores the ethical considerations and practical benefits of such [...] Read more.
This review examines the advancements and methodologies of artificial feeding systems for the study of vector-borne diseases, offering a critical assessment of their development, advantages, and limitations relative to traditional live host models. It underscores the ethical considerations and practical benefits of such systems, including minimizing the use of live animals and enhancing experimental consistency. Various artificial feeding techniques are detailed, including membrane feeding, capillary feeding, and the utilization of engineered biocompatible materials, with their respective applications, efficacy, and the challenges encountered with their use also being outlined. This review also forecasts the integration of cutting-edge technologies like biomimicry, microfluidics, nanotechnology, and artificial intelligence to refine and expand the capabilities of artificial feeding systems. These innovations aim to more accurately simulate natural feeding conditions, thereby improving the reliability of studies on the transmission dynamics of vector-borne diseases. This comprehensive review serves as a foundational reference for researchers in the field, proposing a forward-looking perspective on the potential of artificial feeding systems to revolutionize vector-borne disease research. Full article
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11 pages, 1600 KiB  
Article
How Mitochondrial Signaling Games May Shape and Stabilize the Nuclear-Mitochondrial Symbiosis
by Will Casey, Thiviya Kumaran, Steven E. Massey and Bud Mishra
Biology 2024, 13(3), 187; https://doi.org/10.3390/biology13030187 - 15 Mar 2024
Viewed by 851
Abstract
The eukaryotic lineage has enjoyed a long-term “stable” mutualism between nucleus and mitochondrion, since mitochondrial endosymbiosis began about 2 billion years ago. This mostly cooperative interaction has provided the basis for eukaryotic expansion and diversification, which has profoundly altered the forms of life [...] Read more.
The eukaryotic lineage has enjoyed a long-term “stable” mutualism between nucleus and mitochondrion, since mitochondrial endosymbiosis began about 2 billion years ago. This mostly cooperative interaction has provided the basis for eukaryotic expansion and diversification, which has profoundly altered the forms of life on Earth. While we ignore the exact biochemical details of how the alpha-proteobacterial ancestor of mitochondria entered into endosymbiosis with a proto-eukaryote, in more general terms, we present a signaling games perspective of how the cooperative relationship became established, and has been maintained. While games are used to understand organismal evolution, information-asymmetric games at the molecular level promise novel insights into endosymbiosis. Using a previously devised biomolecular signaling games approach, we model a sender–receiver information asymmetric game, in which the informed mitochondrial sender signals and the uninformed nuclear receiver may take actions (involving for example apoptosis, senescence, regeneration and autophagy/mitophagy). The simulation shows that cellularization is a stabilizing mechanism for Pareto efficient sender/receiver strategic interaction. In stark contrast, the extracellular environment struggles to maintain efficient outcomes, as senders are indifferent to the effects of their signals upon the receiver. Our hypothesis has translational implications, such as in cellular therapy, as mitochondrial medicine matures. It also inspires speculative conjectures about how an analogous human–AI endosymbiosis may be engineered. Full article
(This article belongs to the Section Reproductive Biology)
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16 pages, 3210 KiB  
Article
Integrative Transcriptome Analysis of mRNA and miRNA in Pepper’s Response to Phytophthora capsici Infection
by Yuan Li, Nan Wang, Jianwen Guo, Xianjun Zhou, Xueyi Bai, Muhammad Azeem, Liyun Zhu, Lin Chen, Moli Chu, Hui Wang and Wei Cheng
Biology 2024, 13(3), 186; https://doi.org/10.3390/biology13030186 - 14 Mar 2024
Viewed by 958
Abstract
Phytophthora blight of pepper is a notorious disease caused by the oomycete pathogen Phytophthora capsici, which poses a great threat to global pepper production. MicroRNA (miRNA) is a class of non-coding small RNAs that regulate gene expressions by altering the translation efficiency [...] Read more.
Phytophthora blight of pepper is a notorious disease caused by the oomycete pathogen Phytophthora capsici, which poses a great threat to global pepper production. MicroRNA (miRNA) is a class of non-coding small RNAs that regulate gene expressions by altering the translation efficiency or stability of targeted mRNAs, which play important roles in the regulation of a plant’s response to pathogens. Herein, time-series mRNA-seq libraries and small RNA-seq libraries were constructed using pepper roots from the resistant line CM334 and the susceptible line EC01 inoculated with P. capsici at 0, 6, 24, and 48 h post-inoculation, respectively. For mRNA-seq analysis, a total of 2159 and 2971 differentially expressed genes (DEGs) were identified in CM334 and EC01, respectively. For miRNA-seq analysis, 491 pepper miRNAs were identified, including 330 known miRNAs and 161 novel miRNAs. Among them, 69 and 88 differentially expressed miRNAs (DEMs) were identified in CM334 and EC01, respectively. Examination of DEMs and their targets revealed 22 regulatory networks, predominantly featuring up-regulated miRNAs corresponding to down-regulated target genes. Notably, these DEM-DEG regulatory networks exhibited significant overlap between CM334 and EC01, suggesting that they might contribute to pepper’s basal defense against P. capsici. Furthermore, five selected DEMs (miR166, miR1171, miR395, miR530 and miRN2) and their target genes underwent qRT-PCR validation, confirming a consistent negative correlation in the expression patterns of miRNAs and their targets. This comprehensive analysis provides novel insights into the regulatory networks of miRNAs and their targets, offering valuable contributions to our understanding of pepper’s defense mechanisms against P. capsici. Full article
(This article belongs to the Special Issue Advances in Research on Diseases of Plants)
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41 pages, 1405 KiB  
Review
Putative Molecular Mechanisms Underpinning the Inverse Roles of Mitochondrial Respiration and Heme Function in Lung Cancer and Alzheimer’s Disease
by Atefeh Afsar and Li Zhang
Biology 2024, 13(3), 185; https://doi.org/10.3390/biology13030185 - 14 Mar 2024
Viewed by 1615
Abstract
Mitochondria are the powerhouse of the cell. Mitochondria serve as the major source of oxidative stress. Impaired mitochondria produce less adenosine triphosphate (ATP) but generate more reactive oxygen species (ROS), which could be a major factor in the oxidative imbalance observed in Alzheimer’s [...] Read more.
Mitochondria are the powerhouse of the cell. Mitochondria serve as the major source of oxidative stress. Impaired mitochondria produce less adenosine triphosphate (ATP) but generate more reactive oxygen species (ROS), which could be a major factor in the oxidative imbalance observed in Alzheimer’s disease (AD). Well-balanced mitochondrial respiration is important for the proper functioning of cells and human health. Indeed, recent research has shown that elevated mitochondrial respiration underlies the development and therapy resistance of many types of cancer, whereas diminished mitochondrial respiration is linked to the pathogenesis of AD. Mitochondria govern several activities that are known to be changed in lung cancer, the largest cause of cancer-related mortality worldwide. Because of the significant dependence of lung cancer cells on mitochondrial respiration, numerous studies demonstrated that blocking mitochondrial activity is a potent strategy to treat lung cancer. Heme is a central factor in mitochondrial respiration/oxidative phosphorylation (OXPHOS), and its association with cancer is the subject of increased research in recent years. In neural cells, heme is a key component in mitochondrial respiration and the production of ATP. Here, we review the role of impaired heme metabolism in the etiology of AD. We discuss the numerous mitochondrial effects that may contribute to AD and cancer. In addition to emphasizing the significance of heme in the development of both AD and cancer, this review also identifies some possible biological connections between the development of the two diseases. This review explores shared biological mechanisms (Pin1, Wnt, and p53 signaling) in cancer and AD. In cancer, these mechanisms drive cell proliferation and tumorigenic functions, while in AD, they lead to cell death. Understanding these mechanisms may help advance treatments for both conditions. This review discusses precise information regarding common risk factors, such as aging, obesity, diabetes, and tobacco usage. Full article
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16 pages, 2998 KiB  
Article
Personalized Driver Gene Prediction Using Graph Convolutional Networks with Conditional Random Fields
by Pi-Jing Wei, An-Dong Zhu, Ruifen Cao and Chunhou Zheng
Biology 2024, 13(3), 184; https://doi.org/10.3390/biology13030184 - 14 Mar 2024
Viewed by 848
Abstract
Cancer is a complex and evolutionary disease mainly driven by the accumulation of genetic variations in genes. Identifying cancer driver genes is important. However, most related studies have focused on the population level. Cancer is a disease with high heterogeneity. Thus, the discovery [...] Read more.
Cancer is a complex and evolutionary disease mainly driven by the accumulation of genetic variations in genes. Identifying cancer driver genes is important. However, most related studies have focused on the population level. Cancer is a disease with high heterogeneity. Thus, the discovery of driver genes at the individual level is becoming more valuable but is a great challenge. Although there have been some computational methods proposed to tackle this challenge, few can cover all patient samples well, and there is still room for performance improvement. In this study, to identify individual-level driver genes more efficiently, we propose the PDGCN method. PDGCN integrates multiple types of data features, including mutation, expression, methylation, copy number data, and system-level gene features, along with network structural features extracted using Node2vec in order to construct a sample–gene interaction network. Prediction is performed using a graphical convolutional neural network model with a conditional random field layer, which is able to better combine the network structural features with biological attribute features. Experiments on the ACC (Adrenocortical Cancer) and KICH (Kidney Chromophobe) datasets from TCGA (The Cancer Genome Atlas) demonstrated that the method performs better compared to other similar methods. It can identify not only frequently mutated driver genes, but also rare candidate driver genes and novel biomarker genes. The results of the survival and enrichment analyses of these detected genes demonstrate that the method can identify important driver genes at the individual level. Full article
(This article belongs to the Special Issue 3rd Edition of Intelligent Computing in Biology and Medicine)
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14 pages, 2903 KiB  
Article
Identification and Characterisation of the CircRNAs Involved in the Regulation of Leaf Colour in Quercus mongolica
by Yangchen Yuan, Xinbo Pang, Jiushuai Pang, Qian Wang, Miaomiao Zhou, Yan Lu, Chenyang Xu and Dazhuang Huang
Biology 2024, 13(3), 183; https://doi.org/10.3390/biology13030183 - 14 Mar 2024
Viewed by 762
Abstract
Circular RNAs (circRNAs) are important regulatory molecules involved in various biological processes. However, the potential function of circRNAs in the turning red process of Quercus mongolica leaves is unclear. This study used RNA-seq data to identify 6228 circRNAs in leaf samples from four [...] Read more.
Circular RNAs (circRNAs) are important regulatory molecules involved in various biological processes. However, the potential function of circRNAs in the turning red process of Quercus mongolica leaves is unclear. This study used RNA-seq data to identify 6228 circRNAs in leaf samples from four different developmental stages and showed that 88 circRNAs were differentially expressed. A correlation analysis was performed between anthocyanins and the circRNAs. A total of 16 circRNAs that may be involved in regulating the colour of Mongolian oak leaves were identified. CircRNAs may affect the colour of Q. mongolica leaves by regulating auxin, cytokinin, gibberellin, ethylene, and abscisic acid. This study revealed the potential role of circRNAs in the colour change of Q. mongolica leaves. Full article
(This article belongs to the Special Issue Recent Advances in Biosynthesis and Degradation of Plant Anthocyanin)
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30 pages, 1478 KiB  
Review
The Perpetual Vector Mosquito Threat and Its Eco-Friendly Nemeses
by Leticia Silva Miranda, Sarah Renee Rudd, Oscar Mena, Piper Eden Hudspeth, José E. Barboza-Corona, Hyun-Woo Park and Dennis Ken Bideshi
Biology 2024, 13(3), 182; https://doi.org/10.3390/biology13030182 - 12 Mar 2024
Viewed by 1767
Abstract
Mosquitoes are the most notorious arthropod vectors of viral and parasitic diseases for which approximately half the world’s population, ~4,000,000,000, is at risk. Integrated pest management programs (IPMPs) have achieved some success in mitigating the regional transmission and persistence of these diseases. However, [...] Read more.
Mosquitoes are the most notorious arthropod vectors of viral and parasitic diseases for which approximately half the world’s population, ~4,000,000,000, is at risk. Integrated pest management programs (IPMPs) have achieved some success in mitigating the regional transmission and persistence of these diseases. However, as many vector-borne diseases remain pervasive, it is obvious that IPMP successes have not been absolute in eradicating the threat imposed by mosquitoes. Moreover, the expanding mosquito geographic ranges caused by factors related to climate change and globalization (travel, trade, and migration), and the evolution of resistance to synthetic pesticides, present ongoing challenges to reducing or eliminating the local and global burden of these diseases, especially in economically and medically disadvantaged societies. Abatement strategies include the control of vector populations with synthetic pesticides and eco-friendly technologies. These “green” technologies include SIT, IIT, RIDL, CRISPR/Cas9 gene drive, and biological control that specifically targets the aquatic larval stages of mosquitoes. Regarding the latter, the most effective continues to be the widespread use of Lysinibacillus sphaericus (Ls) and Bacillus thuringiensis subsp. israelensis (Bti). Here, we present a review of the health issues elicited by vector mosquitoes, control strategies, and lastly, focus on the biology of Ls and Bti, with an emphasis on the latter, to which no resistance has been observed in the field. Full article
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2 pages, 470 KiB  
Correction
Correction: Sundaram et al. Effects of Intermediate Frequency (150 kHz) Electromagnetic Radiation on the Vital Organs of Female Sprague Dawley Rats. Biology 2023, 12, 310
by Venkatesan Sundaram, Stephanie Mohammed, Brian N. Cockburn, M. R. Srinivasan, Chalapathi R. Adidam Venkata, Jenelle Johnson, Lester Gilkes, Kegan Romelle Jones and Nikolay Zyuzikov
Biology 2024, 13(3), 181; https://doi.org/10.3390/biology13030181 - 12 Mar 2024
Viewed by 603
Abstract
In the original publication [...] Full article
(This article belongs to the Special Issue Infection, Inflammation and Cancer)
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20 pages, 1950 KiB  
Review
Insights into the Multifaceted Roles of Thioredoxin-1 System: Exploring Knockout Murine Models
by Tetiana Shcholok and Eftekhar Eftekharpour
Biology 2024, 13(3), 180; https://doi.org/10.3390/biology13030180 - 12 Mar 2024
Viewed by 840
Abstract
Redox balance is increasingly identified as a major player in cellular signaling. A fundamentally simple reaction of oxidation and reduction of cysteine residues in cellular proteins is the central concept in this complex regulatory mode of protein function. Oxidation of key cysteine residues [...] Read more.
Redox balance is increasingly identified as a major player in cellular signaling. A fundamentally simple reaction of oxidation and reduction of cysteine residues in cellular proteins is the central concept in this complex regulatory mode of protein function. Oxidation of key cysteine residues occurs at the physiological levels of reactive oxygen species (ROS), but they are reduced by a supply of thiol antioxidant molecules including glutathione, glutaredoxin, and thioredoxin. While these molecules show complex compensatory roles in experimental conditions, transgenic animal models provide a comprehensive picture to pinpoint the role of each antioxidant. In this review, we have specifically focused on the available literature on thioredoxin-1 system transgenic models that include thioredoxin and thioredoxin reductase proteins. As the identification of thioredoxin protein targets is technically challenging, the true contribution of this system in maintaining cellular balance remains unidentified, including the role of this system in the brain. Full article
(This article belongs to the Section Cell Biology)
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10 pages, 899 KiB  
Commentary
Quantification of Thermal Acclimation in Immune Functions in Ectothermic Animals
by Franziska C. Sandmeier
Biology 2024, 13(3), 179; https://doi.org/10.3390/biology13030179 - 09 Mar 2024
Viewed by 884
Abstract
This short review focuses on current experimental designs to quantify immune acclimation in animals. Especially in the face of rapidly changing thermal regimes, thermal acclimation of immune function has the potential to impact host–pathogen relationships and the fitness of hosts. While much of [...] Read more.
This short review focuses on current experimental designs to quantify immune acclimation in animals. Especially in the face of rapidly changing thermal regimes, thermal acclimation of immune function has the potential to impact host–pathogen relationships and the fitness of hosts. While much of the field of ecoimmunology has focused on vertebrates and insects, broad interest in how animals can acclimate to temperatures spans taxa. The literature shows a recent increase in thermal acclimation studies in the past six years. I categorized studies as focusing on (1) natural thermal variation in the environment (e.g., seasonal), (2) in vivo manipulation of animals in captive conditions, and (3) in vitro assays using biological samples taken from wild or captive animals. I detail the strengths and weaknesses of these approaches, with an emphasis on mechanisms of acclimation at different levels of organization (organismal and cellular). These two mechanisms are not mutually exclusive, and a greater combination of the three techniques listed above will increase our knowledge of the diversity of mechanisms used by animals to acclimate to changing thermal regimes. Finally, I suggest that functional assays of immune system cells (such as quantification of phagocytosis) are an accessible and non-taxa-specific way to tease apart the effects of animals upregulating quantities of immune effectors (cells) and changes in the function of immune effectors (cellular performance) due to structural changes in cells such as those of membranes and enzymes. Full article
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14 pages, 1951 KiB  
Article
Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa
by Seth Duwor, Daniela Brites and Pascal Mäser
Biology 2024, 13(3), 178; https://doi.org/10.3390/biology13030178 - 09 Mar 2024
Viewed by 1048
Abstract
The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the [...] Read more.
The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance the adaptation of protozoa in hostile environments. Comparative genomics of Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, identified eleven candidate genes for HGT involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide more validated evidence to support the horizontal transfer of pfor from bacteria. Full article
(This article belongs to the Section Infection Biology)
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14 pages, 7538 KiB  
Article
Projecting the Global Potential Geographical Distribution of Ceratitis capitata (Diptera: Tephritidae) under Current and Future Climates
by Jiawei Rao, Yu Zhang, Haoxiang Zhao, Jianyang Guo, Fanghao Wan, Xiaoqing Xian, Nianwan Yang and Wanxue Liu
Biology 2024, 13(3), 177; https://doi.org/10.3390/biology13030177 - 08 Mar 2024
Viewed by 890
Abstract
The Mediterranean fruit fly, Ceratitis capitata (Wiedemann), which is native to tropical Africa, has invaded more than 100 countries and constitutes a risk to the citrus sector. Studying its potential geographical distribution (PGD) in the context of global climate change is important for [...] Read more.
The Mediterranean fruit fly, Ceratitis capitata (Wiedemann), which is native to tropical Africa, has invaded more than 100 countries and constitutes a risk to the citrus sector. Studying its potential geographical distribution (PGD) in the context of global climate change is important for prevention and control efforts worldwide. Therefore, we used the CLIMEX model to project and assess the risk of global invasion by C. capitata under current (1981–2010) and future (2040–2059) climates. In the prevailing climatic conditions, the area of PGD for C. capitata was approximately 664.8 × 105 km2 and was concentrated in South America, southern Africa, southern North America, eastern Asia, and southern Europe. Under future climate conditions, the area of PGD for C. capitata is projected to decrease to approximately 544.1 × 105 km2 and shift to higher latitudes. Cold stress was shown to affect distribution at high latitudes, and heat stress was the main factor affecting distribution under current and future climates. According to the predicted results, countries with highly suitable habitats for C. capitata that have not yet been invaded, such as China, Myanmar, and Vietnam, must strengthen quarantine measures to prevent the introduction of this pest. Full article
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25 pages, 6188 KiB  
Article
First European Erwinia amylovora Lytic Bacteriophage Cocktails Effective in the Host: Characterization and Prospects for Fire Blight Biocontrol
by Elena G. Biosca, Ricardo Delgado Santander, Félix Morán, Àngela Figàs-Segura, Rosa Vázquez, José Francisco Català-Senent and Belén Álvarez
Biology 2024, 13(3), 176; https://doi.org/10.3390/biology13030176 - 08 Mar 2024
Viewed by 1182
Abstract
Fire blight, caused by the plant-pathogenic bacterium Erwinia amylovora, is a highly contagious and difficult-to-control disease due to its efficient dissemination and survival and the scarcity of effective control methods. Copper and antibiotics are the most used treatments but pose environmental and [...] Read more.
Fire blight, caused by the plant-pathogenic bacterium Erwinia amylovora, is a highly contagious and difficult-to-control disease due to its efficient dissemination and survival and the scarcity of effective control methods. Copper and antibiotics are the most used treatments but pose environmental and human health risks. Bacteriophages (phages) constitute an ecological, safe, and sustainable fire blight control alternative. The goal of this study was to search for specific E. amylovora phages from plant material, soil, and water samples in Mediterranean environments. A collection of phages able to specifically infect and lyse E. amylovora strains was generated from former fire blight-affected orchards in Eastern Spain. Following in vitro characterization, assays in immature fruit revealed that preventively applying some of the phages or their combinations delayed the onset of fire blight symptoms and reduced the disease’s severity, suggesting their biocontrol potential in Spain and other countries. The morphological and molecular characterization of the selected E. amylovora phages classified them as members of the class Caudoviricetes (former Myoviridae family) and genus Kolesnikvirus. This study reveals Mediterranean settings as plausible sources of E. amylovora-specific bacteriophages and provides the first effective European phage cocktails in plant material for the development of sustainable fire blight management measures. Full article
(This article belongs to the Special Issue Advances in Research on Diseases of Plants)
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13 pages, 2211 KiB  
Article
A Cyclic Permutation Approach to Removing Spatial Dependency between Clustered Gene Ontology Terms
by Rachel Rapoport, Avraham Greenberg, Zohar Yakhini and Itamar Simon
Biology 2024, 13(3), 175; https://doi.org/10.3390/biology13030175 - 08 Mar 2024
Viewed by 805
Abstract
Traditional gene set enrichment analysis falters when applied to large genomic domains, where neighboring genes often share functions. This spatial dependency creates misleading enrichments, mistaking mere physical proximity for genuine biological connections. Here we present Spatial Adjusted Gene Ontology (SAGO), a novel cyclic [...] Read more.
Traditional gene set enrichment analysis falters when applied to large genomic domains, where neighboring genes often share functions. This spatial dependency creates misleading enrichments, mistaking mere physical proximity for genuine biological connections. Here we present Spatial Adjusted Gene Ontology (SAGO), a novel cyclic permutation-based approach, to tackle this challenge. SAGO separates enrichments due to spatial proximity from genuine biological links by incorporating the genes’ spatial arrangement into the analysis. We applied SAGO to various datasets in which the identified genomic intervals are large, including replication timing domains, large H3K9me3 and H3K27me3 domains, HiC compartments and lamina-associated domains (LADs). Intriguingly, applying SAGO to prostate cancer samples with large copy number alteration (CNA) domains eliminated most of the enriched GO terms, thus helping to accurately identify biologically relevant gene sets linked to oncogenic processes, free from spatial bias. Full article
(This article belongs to the Special Issue Understanding the Genomic Mechanisms of Oncology)
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13 pages, 4100 KiB  
Article
Molecular Cloning, Characterization, and Expression of a Receptor for Activated Protein Kinase C1 (RACK1) Gene in Exopalaemon carinicauda Zoea Larvae under Aroclor 1254 Stress
by Yuefeng Cai, Jie Hu, Yepeng Guo and Xin Shen
Biology 2024, 13(3), 174; https://doi.org/10.3390/biology13030174 - 08 Mar 2024
Viewed by 755
Abstract
The receptor for activated protein kinase C1 (RACK1) belongs to the typical WD repeat family, which is extremely conservative and important in multiple signal transduction pathways related to growth and development that coordinate the intracellular role of various life activities. As a novel [...] Read more.
The receptor for activated protein kinase C1 (RACK1) belongs to the typical WD repeat family, which is extremely conservative and important in multiple signal transduction pathways related to growth and development that coordinate the intracellular role of various life activities. As a novel protein with versatile functions, it was found in a variety of organisms. In a previous study, we identified the RACK1 sequence of white shrimp from transcriptome data. In this study, we employed specialized bioinformatics software to conduct an in-depth analysis of EcRACK1 and compare its amino acid sequence homology with other crustaceans. Furthermore, we investigated the expression patterns of RACK1 at different developmental stages and tissues, as well as at various time points after exposure to Aroclor 1245, aiming to elucidate its function and potential response towards Aroclor 1245 exposure. The length of EcRACK1 is 957 nucleotides, which encodes 318 amino acids. Moreover, there were seven typical WD repeats in EcRACK1, which have more than a 96% sequence identity with the RACK1 proteins of Penaeus. The results of tissue expression and spatiotemporal expression showed that it was significantly increased in the II and IV stages, but had a significant tissue specificity in the hepatopancreas, spermary, and muscle tissues of E. carinicauda, adult stage. Compared to the control, EcRACK1 was significantly induced in E. carinicauda zoea larvae exposed to Aroclor 1254 for 6, 10, 20, and 30 d (p < 0.05). These results suggested that EcRACK1 may play an important role in the larval development and environmental defense of E. carinicauda. Full article
(This article belongs to the Special Issue Crustacean Immunology and Pathology)
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12 pages, 7273 KiB  
Brief Report
New Genetic Variants of RUNX2 in Mexican Families Cause Cleidocranial Dysplasia
by Jaime Toral López, Sandra Gómez Martinez, María del Refugio Rivera Vega, Edgar Hernández-Zamora, Sergio Cuevas Covarrubias, Belem Arely Ibarra Castrejón and Luz María González Huerta
Biology 2024, 13(3), 173; https://doi.org/10.3390/biology13030173 - 08 Mar 2024
Viewed by 943
Abstract
Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia characterized by persistent open skull sutures with bulging calvaria, hypoplasia, or aplasia of clavicles permitting abnormal opposition of the shoulders; wide public symphysis; short middle phalanx of the fifth fingers; and vertebral, craniofacial, and [...] Read more.
Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia characterized by persistent open skull sutures with bulging calvaria, hypoplasia, or aplasia of clavicles permitting abnormal opposition of the shoulders; wide public symphysis; short middle phalanx of the fifth fingers; and vertebral, craniofacial, and dental anomalies. It is a rare disease, with a prevalence of 1–9/1,000,000, high penetrance, and variable expression. The gene responsible for CCD is the Runt-related transcription factor 2 (RUNX2) gene. We characterize the clinical, genetic, and bioinformatic results of four CCD cases: two cases within Mexican families with six affected members, nine asymptomatic individuals, and two sporadic cases with CCD, with one hundred healthy controls. Genomic DNA analyses of the RUNX2 gene were performed for Sanger sequencing. Bioinformatics tools were used to predict the function, stability, and structural changes of the mutated RUNX2 proteins. Three novel heterozygous mutations (c.651_652delTA; c.538_539delinsCA; c.662T>A) and a previously reported mutation (c.674G>A) were detected. In silico analysis showed that all mutations had functional, stability-related, and structural alterations in the RUNX2 protein. Our results show novel mutations that enrich the pool of RUNX2 gene mutations with CCD. Moreover, the proband 1 presented clinical data not previously reported that could represent an expanded phenotype of severe expression. Full article
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15 pages, 20759 KiB  
Article
Deletion of Interleukin-1β Converting Enzyme Alters Mouse Cardiac Structure and Function
by Gohar Azhar, Koichiro Nagano, Pankaj Patyal, Xiaomin Zhang, Ambika Verma and Jeanne Y. Wei
Biology 2024, 13(3), 172; https://doi.org/10.3390/biology13030172 - 07 Mar 2024
Viewed by 971
Abstract
Interleukin-1β converting enzyme (ICE, caspase-1) is a thiol protease that cleaves the pro-inflammatory cytokine precursors of IL-1β and IL-18 into active forms. Given the association between caspase-1 and cardiovascular pathology, we analyzed the hearts of ICE knockout (ICE KO) mice to test the [...] Read more.
Interleukin-1β converting enzyme (ICE, caspase-1) is a thiol protease that cleaves the pro-inflammatory cytokine precursors of IL-1β and IL-18 into active forms. Given the association between caspase-1 and cardiovascular pathology, we analyzed the hearts of ICE knockout (ICE KO) mice to test the hypothesis that caspase-1 plays a significant role in cardiac morphology and function. We characterized the histological and functional changes in the hearts of ICE KO mice compared to the Wild type. The cardiomyocytes from the neonatal ICE KO mice showed an impaired response to oxidative stress. Subsequently, the hearts from the ICE KO mice were hypertrophied, with a significant increase in the left ventricular and septal wall thickness and a greater LV mass/body weight ratio. The ICE KO mice hearts exhibited irregular myofibril arrangements and disruption of the cristae in the mitochondrial structure. Proapoptotic proteins that were significantly increased in the hearts of ICE KO versus the Wild type included pErk, pJNK, p53, Fas, Bax, and caspase 3. Further, the antiapoptotic proteins Bag-1 and Bcl-2 are activated in ICE KO hearts. Functionally, there was an increase in the left ventricular epicardial diameter and volume in ICE KO. In conclusion, our findings support the important role of caspase-1 in maintaining cardiac health; specifically, a significant decrease in caspase-1 is detrimental to the cardiovascular system. Full article
(This article belongs to the Special Issue Molecular Sciences in Cardiology and Vascular Disorders)
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