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Biology, Vol. 14, Pages 34: Changes in Antioxidant and Photosynthetic Capacity in Rice Under Different Substrates

Biology doi: 10.3390/biology14010034

Authors: Hang Zhou Liming Zhao Yiwen Song Xiaole Du Jingxin Huo Wanqi Mei Xi Wang Naijie Feng Dianfeng Zheng Zhaohui Wu

Against the backdrop of a changing global climate, the soil environment may undergo significant changes, directly affecting agricultural productivity and exacerbating global food security issues. Three different substrates were set up in this study, namely, S (high sand and low nutrient content), T (medium sand and medium nutrient content), and TT (low sand and high nutrient content). The results showed that the root/shoot ratio increased as the sand content increased (nutrient content decreased). Rice in different substrates had various degrees of dependence on antioxidant enzymes and antioxidants. For example, seedlings in TT treatment may depend more on ascorbic acid (AsA) compared to T. In addition, compared with S and T, the photosynthetic activity of rice in the optimized substrate (TT) was the highest; the net photosynthetic rate (Pn) of TT seedlings was significantly higher than that of T. This study also detected that the change in substrates affected the gas exchange parameters of rice leaves. The transpiration rate (Tr) and stomatal conductance (Gs) of the TT treatment were higher than those of the T treatment. The results of this study may provide a scientific basis for formulating agricultural management strategies.

Biology, Vol. 14, Pages 35: Comparative Analysis of Prediction Models for Trawling Grounds of the Argentine Shortfin Squid Illex argentinus in the Southwest Atlantic High Seas Based on Vessel Position and Fishing Log Data

Biology doi: 10.3390/biology14010035

Authors: Delong Xiang Yuyan Sun Hanji Zhu Jianhua Wang Sisi Huang Shengmao Zhang Famou Zhang Heng Zhang

To evaluate and compare the effectiveness of prediction models for Argentine squid Illex argentinus trawling grounds in the Southwest Atlantic high seas based on vessel position and fishing log data, this study used AIS datasets and fishing log datasets from fishing seasons spanning 2019–2024 (December to June each year). Using a spatial resolution of 0.1° × 0.1° and a monthly temporal resolution, we constructed two datasets—one based on vessel positions and the other on fishing logs. Fishing ground levels were defined according to the density of fishing locations, and combined with oceanographic data (sea surface temperature, 50 m water temperature, sea surface salinity, sea surface height, and mixed layer depth). A CNN-Attention deep learning model was applied to each dataset to develop Illex argentinus trawling ground prediction models. Model accuracy was then compared and potential causes for differences were analyzed. Results showed that the vessel position-based model had a higher accuracy (Accuracy = 0.813) and lower loss rate (Loss = 0.407) than the fishing log-based model (Accuracy = 0.727, Loss = 0.513). The vessel-based model achieved a prediction accuracy of 0.763 on the 2024 test set, while the fishing log-based model reached an accuracy of 0.712, slightly lower than the former, indicating the high accuracy and unique advantages of the vessel position-based model in predicting fishing grounds. Using CPUE from fishing logs as a reference, we found that the vessel position-based model performed well from January to April, whereas the CPUE-based model consistently maintained good accuracy across all months. The 2024 fishing season predictions indicated the formation of primary fishing grounds as early as January 2023, initially near the 46° S line of the Argentine Exclusive Economic Zone, with grounds shifting southeastward from March onward and reaching around 42° S by May and June. This study confirms the reliability of vessel position data in identifying fishing ground information and levels, with higher accuracy in some months compared to the fishing log-based model, thereby reducing the data lag associated with fishing logs, which are typically available a year later. Additionally, national-level fishing log data are often confidential, limiting the ability to fully consider fishing activities across the entire fishing ground region, a limitation effectively addressed by AIS vessel position data. While vessel data reflects daily catch volumes across vessels without distinguishing CPUE by species, log data provide a detailed daily CPUE breakdown by species (e.g., Illex argentinus). This distinction resulted in lower accuracy for vessel-based predictions in December 2023 and May–June 2024, suggesting the need to incorporate fishing log data for more precise assessments of fishing ground levels or resource abundance during those months. Given the near-real-time nature of vessel position data, fishing ground dynamics can be monitored in near real time. The successful development of vessel position-based prediction models aids enterprises in reducing fuel and time costs associated with indiscriminate squid searches, enhancing trawling efficiency. Additionally, such models support quota management in global fisheries by optimizing resource use, reducing fishing time, and consequently lowering carbon emissions and environmental impact, while promoting marine environmental protection in the Southwest Atlantic high seas.

Biology, Vol. 14, Pages 36: ITS2 rRNA Gene Sequence–Structure Phylogeny of the Chytridiomycota (Opisthokonta, Fungi)

Biology doi: 10.3390/biology14010036

Authors: Yuveantheni Kalaiventhan Kensuke Seto Matthias Wolf

To date, standard rRNA marker genes have had limited success in resolving the phylogeny of the phylum Chytridiomycota. Whereas the conserved and easily alignable ribosomal small subunit 18S rRNA gene had problems resolving nodes relating orders, the internal transcribed spacer 2 (ITS2) has been claimed to not be alignable for this group of organisms. Although the ITS2 is a fast-evolving locus, its secondary structure is well conserved. To improve the accuracy and robustness of Chytridiomycota phylogeny, in this study, we attempt, for the first, time to reconstruct an ITS2 sequence–structure phylogeny using the primary sequence and the secondary structure information simultaneously in inferring alignments and trees. Although currently only possible for a fraction of the available data, we show a well-supported ITS2 tree for selected organisms. The results are promising for further exploration of the large number of available ITS2 sequences.

Biology, Vol. 14, Pages 37: Bird Richness and Abundance in Urban Areas: Simulation-Based Conservation Strategies for an Italian Town

Biology doi: 10.3390/biology14010037

Authors: Alessandro Ferrarini Luca Bagni Marco Gustin

In this study, we (a) inventoried the breeding bird community of a town located in Northern Italy using quadrat sampling, (b) quantified bird richness and abundance, (c) measured sample completeness, (d) tested whether the bird community assembly was driven by environmental filtering (i.e., local properties of every single quadrat), e) explained bird richness and abundance in light of the land cover types present in each quadrat, (f) disentangled the marginal effects of every land cover type, and (g) simulated the effects on birds of different planning decisions. We recorded 36 breeding bird species, of which 17 were resident, 10 were mid-range migrants, and 9 were trans-Saharan migrators. The sampling completeness estimated ranged from 82.73% to 99.66% depending on the estimator procedure. Environmental filtering affected significantly (p < 0.10) the bird community assembly. Generalized Additive Models (GAMs) explained both bird richness (R2 = 91.7%) and abundance (R2 = 87.4%) satisfactorily in light of the land cover types. Simulations based on GAMs showed that local planners can largely influence bird richness in the study area, with both positive (urban greening) and negative (urban densification and sprawl) strategies.

Biology, Vol. 14, Pages 38: Exploring Brain Size Asymmetry and Its Relationship with Predation Risk Among Chinese Anurans

Biology doi: 10.3390/biology14010038

Authors: Chuan Chen Ying Jiang Yiming Wu Lingsen Cao Wenbo Liao

Brain size asymmetry differs considerably across species, including humans, vertebrates, and invertebrates. The subtle structural, functional, or size differences between the two brain sides are associated with processing specific cognitive tasks. To evaluate the differences between the sizes of the left and right sides of the whole brain and brain regions and the effect of predation risk (i.e., snake density) on brain size asymmetry among Chinese anurans, we compared the differences between the left and right hemisphere sizes of the whole brain and brain regions among anuran species and analyzed the correlations between the predation risk and size asymmetry index of the brain and brain regions. We found that when one side of the brain was consistently larger than the other, there was a significant difference between the sizes of the left and right sides of the brain and brain regions, displaying directional asymmetry of the whole brain and brain regions. We also found that total brain size was positively correlated with the size asymmetry index of the olfactory bulb and optic tecta when the left hemispheres of the whole brain and brain regions were larger than the right ones. Meanwhile, the index of telencephalon size asymmetry was positively correlated with predation risk when the right hemispheres of the brain and brain regions were larger than the left ones. However, there were non-significant differences between the sizes of the left and right sides of the brain and brain regions across 99 species of anurans. Our findings suggest that an increased predation risk linked to sociality is likely to drive an increase in right telencephalon size.

Biology, Vol. 14, Pages 39: The Role of Aquaculture in Shaping the Morphology of Babylonia areolata: A Comparative Study of Cultured and Wild Populations

Biology doi: 10.3390/biology14010039

Authors: Haishan Wang Zhi Chen Yuhe Tong Le Ye Youming Li

Background: With the rapid expansion of aquaculture, the impact of rearing environments on the morphological characteristics of marine species has become a critical research focus. This study investigates the morphological differences between wild and cultured populations of B. areolata, a commercially valuable marine mollusk, to understand how aquaculture environments influence morphological traits. Objective: The study aims to evaluate the morphological variance between wild and cultured populations using multivariate statistical techniques and to analyze the ecological implications of these differences. Methods: A total of 120 specimens (56 cultured, 64 wild) were collected from 2 habitats in Hainan, China, and analyzed for 9 morphological traits. Statistical methods, including Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA), were used to assess morphological differences. Results: The study revealed significant morphological differences between wild and cultured populations of B. areolata. Cultured populations exhibited greater morphological uniformity, particularly in traits such as shell height, shell length, and total weight. In contrast, wild populations showed higher variability in traits like shell thickness and shell aperture width, driven by resource heterogeneity and natural selection pressures in their environment. Conclusion: The findings suggest that aquaculture environments significantly influence the development of morphological traits, potentially affecting mollusk adaptability and survival in natural habitats. These results provide valuable insights into aquaculture management and strategies for conserving wild populations.

Biology, Vol. 14, Pages 40: Genome-Wide Scans for Selection Signatures in Haimen Goats Reveal Candidate Genes Associated with Growth Traits

Biology doi: 10.3390/biology14010040

Authors: Zhen Zhang Jiafeng Lu Yifei Wang Zhipeng Liu Dongxu Li Kaiping Deng Guomin Zhang Bingru Zhao Peihua You Yixuan Fan Feng Wang Ziyu Wang

Understanding the genetic characteristics of indigenous goat breeds is vital for their conservation and breeding. Haimen goats, native to China’s Yangtze River Delta, possess distinctive traits such as white hair, moderate growth rate, high-quality meat, and small body size. However, knowledge regarding the genetic structure and germplasm characteristics of Haimen goats remains limited. In this study, we performed 20× whole-genome resequencing of 90 goats (60 Haimen goats and 30 Boer goats) to identify single-nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) associated with growth traits. Here, we analyzed population genetic structure and genome-wide selection signatures between the Haimen and Boer goats based on whole-genome resequencing data. The principal component analysis (PCA) and neighbor-joining (N-J) tree results demonstrated significant genetic differentiation between the Haimen and Boer goats. The nucleotide diversity (Pi) and linkage disequilibrium (LD) decay results indicated higher genomic diversity in the Haimen goat population. Furthermore, selective sweep analysis identified candidate genes associated with growth traits. These genes exhibited strong selection signatures and were related to body size (DONSON, BMPR1B, and EPHA5), muscle development (GART, VGLL3, MYH15), and fat metabolism (ADAMTS5, LRP6, XDH, CPT1A, and GPD1). We also identified growth-related candidate genes (NCOR1, DPP6, NOTCH2, and FGGY) specific to Haimen goats. Among these genes, pancreatic lipase-related protein 1 (PNLIPRP1) emerged as the primary candidate gene influencing growth phenotypes. Further analysis revealed that a 26 bp Indel in PNLIPRP1 increased its gene expression, suggesting that this Indel could serve as a molecular marker for early marker-assisted selection, potentially enhancing early growth in goats. These findings provide valuable molecular markers and candidate genes for improving growth traits in Haimen goat breeding.

Biology, Vol. 14, Pages 41: Proline Promotes Drought Tolerance in Maize

Biology doi: 10.3390/biology14010041

Authors: Pirzada Khan Ashraf M. M. Abdelbacki Mohammed Albaqami Rahmatullah Jan Kyung-Min Kim

Drought stress significantly affects maize (Zea mays L.) growth by disrupting vital physiological and biochemical processes. This study investigates the potential of proline supplementation to alleviate drought-induced stress in maize plants. The results show that proline supplementation enhanced shoot and root growth under normal conditions and alleviated drought-induced reductions in growth parameters. Under drought stress, proline increased shoot length by 40%, root length by 36%, shoot fresh weight by 97%, root fresh weight by 247%, shoot dry weight by 77%, and root dry weight by 154% compared to the untreated plants. While drought stress induced electrolyte leakage and reduced the relative water content (RWC) and leaf area, proline treatment mitigated these effects by improving membrane stability, water retention, and chlorophyll content. Moreover, proline supplementation reduced hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels by 38% and 67%, respectively, in the drought-stressed plants compared to the untreated controls. It also enhanced catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD) activities by 14%, 69%, and 144%, respectively, under drought stress, indicating a strengthened antioxidative defense. Proline also increased the protein content and improved N, P, and K retention by 30%, 40%, and 28%, respectively, in the drought-stressed plants, supporting metabolic and osmotic balance. Additionally, proline improved endogenous proline and sugar levels, facilitating osmotic adjustment and providing energy reserves. These findings suggest that proline supplementation effectively enhances maize resilience under drought stress, improving growth, reducing oxidative stress, and enhancing osmoprotection.

Biology, Vol. 14, Pages 42: Epigenetic Mechanisms in the Transcriptional Regulation of Circadian Rhythm in Mammals

Biology doi: 10.3390/biology14010042

Authors: Wei Mao Xingnan Ge Qianping Chen Jia-Da Li

Almost all organisms, from the simplest bacteria to advanced mammals, havea near 24 h circadian rhythm. Circadian rhythms are highly conserved across different life forms and are regulated by circadian genes as well as by related transcription factors. Transcription factors are fundamental to circadian rhythms, influencing gene expression, behavior in plants and animals, and human diseases. This review examines the foundational research on transcriptional regulation of circadian rhythms, emphasizing histone modifications, chromatin remodeling, and Pol II pausing control. These studies have enhanced our understanding of transcriptional regulation within biological circadian rhythms and the importance of circadian biology in human health. Finally, we summarize the progress and challenges in these three areas of regulation to move the field forward.

Biology, Vol. 14, Pages 43: Integrated Analysis of microRNA Targets Reveals New Insights into Transcriptional–Post-Transcriptional Regulatory Cross-Talk

Biology doi: 10.3390/biology14010043

Authors: Simona Panni Roberto Pizzolotto

It is becoming increasingly clear that microRNAs are key players in gene regulatory networks, modulating gene expression at post-transcriptional level. Their involvement in almost all cellular processes predicts their role in diseases, and several microRNA-based therapeutics are currently undergoing clinical testing. Despite their undeniable relevance and the substantial body of literature demonstrating their role in cancer and other pathologies, the identification of functional interactions is still challenging. To address this issue, several resources have been developed to collect information from the literature, according to different criteria and reliability scores. In the present study, we have constructed a network of verified microRNA-mRNA interactions by integrating strong-evidence couples from different resources. Our analysis of the resulting network reveals that only one-fifth of the human genes exhibits experimental validated regulation by microRNAs. A very small subset of them is controlled by more than 20 microRNAs, and these hubs are highly enriched of pivotal transcription factors and regulatory proteins, strongly suggesting a complex interplay and a combinatorial effect between transcriptional and post-transcriptional gene control. Data analysis also reveals that several microRNAs control multiple targets involved in the same pathway or biological process, likely contributing to the coordinated control of the protein levels.

Biology, Vol. 14, Pages 44: Community Composition of Epibiont Hydroids of the Naturalized Alien Macroalga Acanthophora spicifera in Pichilingue, Mexico

Biology doi: 10.3390/biology14010044

Authors: Jessica Licona Angeles Francisco Rubén Castañeda Rivero María A. Mendoza-Becerril

This study provides a detailed analysis of the community of hydrozoan epibionts of Acanthophora spicifera in La Paz Bay, Baja California Sur. The investigation was carried out in two season periods, corresponding to the warm and cold seasons on the pier of the Autonomous University of Baja California Sur (UABCS) Pichilingue research station. The percentage of epibiont coverage was calculated and analyzed. The average length of the thalli was 7.8 ± 4.6 cm. Eleven taxa of hydrozoans were recorded; the hydrozoan Obelia cf. dichotoma had the highest coverage percentage, and in summer, there was a higher taxa richness. It is recommended to monitor this macroalga and its epibionts for its wide distribution in the bay, although in UABCS, Pichilingue Pier has not seen epibionts that threaten biological diversity.

Biology, Vol. 14, Pages 45: FAM98 Family Proteins Play Distinct Roles in Osteoclastogenesis and Bone Resorption

Biology doi: 10.3390/biology14010045

Authors: Lei Wang Tarun Minocha Bhaba K. Das Mikaela D. Kunika Aarthi Kannan Ling Gao Subburaman Mohan Weirong Xing Kottayil I. Varughese Haibo Zhao

There are three FAM98 family proteins (FAM98A/B/C) in humans and mice. Their physiological functions remain largely unknown. We have previously reported that Fam98a interacts with Plekhm1 in murine osteoclasts and functions in lysosome trafficking/secretion and bone resorption in osteoclasts in vitro. In this study, we found that all three Fam98 genes were expressed in precursor and mature osteoclasts. While the knockdown of Fam98c by a specific short-hairpin RNA (shRNA) in osteoclast precursors attenuated osteoclastogenesis, depletion of Fam98b by an shRNA specifically disrupted osteoclast lysosome trafficking and bone resorption with phenotypes similar to Fam98a shRNA-knockdown in our previous study. Loss of Fam98a in myeloid osteoclast precursors was dispensable for trabecular and cortical bone mass in mice, as well as osteoclastogenesis/bone resorption in vitro, possibly due to compensation by increased Fam98b expression in Fam98a-null osteoclasts. These findings indicate that the three Fam98 proteins play distinct roles in osteoclastogenesis and osteoclast function and need further investigation in future studies.