Biology

19 pages, 3946 KiB

Open AccessArticle

Analysis of the Interrelation and Seasonal Variation Characteristics of the Spatial Niche of Dominant Fishery Species—A Case Study of the East China Sea

by Yong Liu and Jiahua Cheng

Biology 2024, 13(9), 751; https://doi.org/10.3390/biology13090751 - 23 Sep 2024

Viewed by 711

Abstract

The spatial niche has garnered significant attention in ecological research, particularly regarding species distribution patterns. The East China Sea, known for its favorable natural conditions and abundant fishery resources, exhibits diverse spatial distribution patterns among species, shaped by their seasonal physiological needs. This [...] Read more.

The spatial niche has garnered significant attention in ecological research, particularly regarding species distribution patterns. The East China Sea, known for its favorable natural conditions and abundant fishery resources, exhibits diverse spatial distribution patterns among species, shaped by their seasonal physiological needs. This study utilized a habitat suitability index model to explore the spatial distribution patterns of key fishery resources in the East China Sea across four seasons and their interactions. Two methodologies were employed to identify key environmental factors and assess the ecological niche overlap among different species and seasons. Results indicated that the initial method identified water temperature as the critical factor for hairtail, while the subsequent method emphasized water temperature and salinity for hairtail, salinity for small yellow croaker, and water depth for Bombay duck. The main spatial habitat overlap was observed between paired species, likely driven by predator-prey interactions. During summer and autumn, increased overlap among multiple species was primarily influenced by synchronized life cycles. An overlap index formula quantified the seasonal species overlap, showing an increase from spring to winter, reflecting changes in convergent habitat preferences. The peak overlap occurred in winter, driven by overwintering, reduced food competition, and enhanced coexistence potential, while the lowest overlap was noted in spring as overwintering ended and predation and competition intensified. Full article

(This article belongs to the Section Ecology)

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18 pages, 5528 KiB

Open AccessArticle

The Effect of Calcium Ions on Resting Membrane Potential

by Elizabeth R. Elliott and Robin L. Cooper

Biology 2024, 13(9), 750; https://doi.org/10.3390/biology13090750 - 23 Sep 2024

Viewed by 1197

Abstract

Regulating membrane potential is key to cellular function. For many animal cells, resting membrane potential is predominantly driven by a family of K2P (two-pore domain) potassium channels. These channels are commonly referred to as leak channels, as their presence results in the membrane [...] Read more.

Regulating membrane potential is key to cellular function. For many animal cells, resting membrane potential is predominantly driven by a family of K2P (two-pore domain) potassium channels. These channels are commonly referred to as leak channels, as their presence results in the membrane being permeable to K⁺ ions. These channels, along with various pumps and exchangers, keep the cell resting membrane potential (Rp) relatively close to potassium’s equilibrium potential (E_K); however, in many cells, the resting membrane potential is more depolarized than the E_K due to a small Na⁺ ion leak. Raising [Ca²⁺]_O (extracellular Ca²⁺ concentration) can result in hyperpolarization of the membrane potential from the resting state. The mechanism for this hyperpolarization likely lies in the blockage of a Na⁺ leak channel (NALCN) and/or voltage-gated Na⁺ channels. The effects may also be connected to calcium-activated potassium channels. Using Drosophila melanogaster, we here illustrate that changing [Ca²⁺]_O from 0.5 to 3 mM hyperpolarizes the muscle. Replacing NaCl with LiCl or choline chloride still led to hyperpolarization when increasing [Ca²⁺]_O. Replacing CaCl₂ with BaCl₂ results in depolarization. K2P channel overexpression in the larval muscle greatly reduces the effects of [Ca²⁺]_O on cell membrane potential, likely because potential is heavily driven by the E_K in these muscles. These experiments provide an understanding of the mechanisms behind neuronal hypo-excitability during hypercalcemia, as well as the effects of altered expression of K2P channels on membrane potential. Full article

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11 pages, 3227 KiB

Open AccessArticle

Effect of Different Opening Diet on the Growth, the Structure of the Digestive Tract and Digestive Enzyme Activity of Larval and Juvenile Mystus macropterus

by Xiaoli Li, Xingbing Wu, Xuemei Li, Nian Wei, Ming Jiang, Yongjiu Zhu and Tingbing Zhu

Biology 2024, 13(9), 749; https://doi.org/10.3390/biology13090749 - 23 Sep 2024

Viewed by 610

Abstract

One of the crucial factors influencing the growth and viability of larvae and juveniles is their opening diets. The objective of this study was to identify suitable initial feed options for M. macropterus larvae and juveniles. A total of 1200 newly hatched M. [...] Read more.

One of the crucial factors influencing the growth and viability of larvae and juveniles is their opening diets. The objective of this study was to identify suitable initial feed options for M. macropterus larvae and juveniles. A total of 1200 newly hatched M. macropterus with an average weight of 18.3 mg and an average length of 11.58 mm were selected and randomly divided into four groups. The fish were fed with different opening diets, including rotifer, Artemia nauplii, Tubifex, and micro-diet from six days after hatching (dahs), respectively. Growth indices and activities of digestive enzymes were assessed at 10, 15, 20, 25, 30, 35, and 40 dahs. Histological examination of the structure of the digestive tract was performed at 40 dahs, while survival rates were also documented. The results demonstrated that different diets had no effect on the survival rate of larvae and juveniles of M. macropterus. The growth performance indices were ranked as follows: Tubifex group > Artemia nauplii group > micro-diet group > rotifer group. Remarkably, the Tubifex group exhibited superior growth performance, which was also reflected in the structure of the digestive tract and digestive enzyme activity. Therefore, it is recommended to include Tubifex in the diet of M. macropterus larvae and juvenile during the standardized farming process. Full article

(This article belongs to the Special Issue Aquatic Economic Animal Breeding and Healthy Farming)

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11 pages, 4894 KiB

Open AccessArticle

Exploring the Causal Relationship between Ibuprofen Use and Osteoarthritis Risk: A Mendelian Randomization Study

by Yongzhi Jian, Yanmin Lyu and Said Hashemolhosseini

Biology 2024, 13(9), 748; https://doi.org/10.3390/biology13090748 - 23 Sep 2024

Viewed by 868

Abstract

This study explored the potential causal relationship between ibuprofen (IBU) use and the risk of developing osteoarthritis, a prevalent joint disorder characterized by pain and stiffness. We conducted a two-sample MR analysis using four distinct OA GWAS datasets as outcomes and single-nucleotide polymorphisms [...] Read more.

This study explored the potential causal relationship between ibuprofen (IBU) use and the risk of developing osteoarthritis, a prevalent joint disorder characterized by pain and stiffness. We conducted a two-sample MR analysis using four distinct OA GWAS datasets as outcomes and single-nucleotide polymorphisms (SNPs) associated with IBU metabolism as exposures. The inverse variance weighted (IVW) and weighted median methods were utilized to assess the causal association by meta-analysis, while pleiotropy and heterogeneity were evaluated using MR–Egger regression and Cochran’s Q statistics. The MR analysis provided strong evidence for a causal association between IBU use and an increased risk of OA. A meta-analysis of the IVW and weighted median results across all datasets demonstrated an OR = 1.116 (95% CI = 1.063–1.170) and an OR = 1.110 (95% CI = 1.041–1.184). The consistency of the results obtained from different methods enhanced the reliability of the findings. Low pleiotropy and minimal heterogeneity were observed, further validating the results. The study supports a causal link between IBU use and an increased risk of OA, suggesting that IBU may accelerate the progression of OA while relieving symptoms. These findings highlight the importance of cautious use of IBU in clinical practice, especially considering its potential impact on long-term joint health. Full article

(This article belongs to the Section Medical Biology)

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13 pages, 1439 KiB

Open AccessArticle

Response of Seed Germination and Seedling Growth of Six Desert Shrubs to Different Moisture Levels under Greenhouse Conditions

by Yonghong Luo, Hui Yang, Xingfu Yan, Yongrui Ma, Shuhua Wei, Jiazhi Wang, Ziyu Cao, Zhong Zuo, Chunhui Yang and Jiming Cheng

Biology 2024, 13(9), 747; https://doi.org/10.3390/biology13090747 - 23 Sep 2024

Viewed by 1086

Abstract

Moisture is the most important environmental factor limiting seed regeneration of shrubs in desert areas. Therefore, understanding the effects of moisture changes on seed germination, morphological and physiological traits of shrubs is essential for vegetation restoration in desert areas. In March to June [...] Read more.

Moisture is the most important environmental factor limiting seed regeneration of shrubs in desert areas. Therefore, understanding the effects of moisture changes on seed germination, morphological and physiological traits of shrubs is essential for vegetation restoration in desert areas. In March to June 2023, in a greenhouse using the potting method, we tested the effects of soil moisture changes (5%, 10%, 15%, 20% and 25%) on seed germination and seedling growth of six desert shrubs (Zygophyllum xanthoxylum, Nitraria sibirica, Calligonum mongolicum, Corethrodendron scoparium, Caragana korshinskii, and Corethrodendron fruticosu). Results showed that (1) seed germination percent and vigor index were significantly higher at 15 and 20% soil moisture content than at 5 and 10%; (2) shoot length, primary root length, specific leaf area and biomass of seedlings were significantly higher in the 15% and 20% soil moisture content treatments than in the 5% and 10% treatments; (3) superoxide dismutase activity (SOD) and soluble protein content (SP) decreased with decreasing soil water content, while peroxidase activity (POD) and catalase activity (CAT) showed a decreasing and then increasing trend with increasing soil water content; (4) the six seeds and seedling of shrubs were ranked in order of their survivability in response to changes in soil moisture: Caragana korshinskii > Zygophyllum xanthoxylum > Calligonum mongolicum > Corethrodendron scoparium > Corethrodendron fruticosu > Nitraria sibirica. Our study shows that shrub seedlings respond to water changes by regulating morphological and physiological traits together. More importantly, we found that C. korshinskii, Z. xanthoxylum and C. mongolicum were more survivable when coping with water deficit or extreme precipitation. The results of the study may provide a reference for the selection and cultivation of similar shrubs in desert areas under frequent extreme droughts in the future. Full article

(This article belongs to the Special Issue Dendrochronology in Arid and Semiarid Regions)

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21 pages, 1698 KiB

Open AccessReview

Mitochondrial Dynamics and mRNA Translation: A Local Synaptic Tale

by Marta Zaninello, Pedro Baptista and Filipe V. Duarte

Biology 2024, 13(9), 746; https://doi.org/10.3390/biology13090746 - 23 Sep 2024

Viewed by 1355

Abstract

Mitochondria are dynamic organelles that can adjust and respond to different stimuli within a cell. This plastic ability allows them to effectively coordinate several cellular functions in cells and becomes particularly relevant in highly complex cells such as neurons. An imbalance in mitochondrial [...] Read more.

Mitochondria are dynamic organelles that can adjust and respond to different stimuli within a cell. This plastic ability allows them to effectively coordinate several cellular functions in cells and becomes particularly relevant in highly complex cells such as neurons. An imbalance in mitochondrial dynamics can disrupt mitochondrial function, leading to abnormal cellular function and ultimately to a range of diseases, including neurodegenerative disorders. Regulation of mRNA transport and local translation inside neurons is crucial for maintaining the proteome of distal mitochondria, which is vital for energy production and synaptic function. A significant portion of the axonal transcriptome is dedicated to mRNAs for mitochondrial proteins, emphasizing the importance of local translation in sustaining mitochondrial function in areas far from the cell body. In neurons, local translation and the regulation of mRNAs encoding mitochondrial-shaping proteins could be essential for synaptic plasticity and neuronal health. The dynamics of these mRNAs, including their transport and local translation, may influence the morphology and function of mitochondria, thereby affecting the overall energy status and responsiveness of synapses. Comprehending the mitochondria-related mRNA regulation and local translation, as well as its influence on mitochondrial morphology near the synapses will help to better understand neuronal physiology and neurological diseases where mitochondrial dysfunction and impaired synaptic plasticity play a central role. Full article

(This article belongs to the Special Issue The Emerging Role of Mitochondria in Neurobiology)

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14 pages, 5489 KiB

Open AccessArticle

MaxEnt Modeling for Predicting the Potential Geographical Distribution of Hydrocera triflora since the Last Interglacial and under Future Climate Scenarios

by Qitao Su, Zhixuan Du, Yi Luo, Bing Zhou, Yi’an Xiao and Zhengrong Zou

Biology 2024, 13(9), 745; https://doi.org/10.3390/biology13090745 - 22 Sep 2024

Viewed by 824

Abstract

Hydrocera triflora is a perennial herb found in southeastern and southern Asia. In China, it is only found in Hainan Province. With global climate change, studying the impact of climate change on the distribution of H. triflora can provide a theoretical basis for [...] Read more.

Hydrocera triflora is a perennial herb found in southeastern and southern Asia. In China, it is only found in Hainan Province. With global climate change, studying the impact of climate change on the distribution of H. triflora can provide a theoretical basis for the scientific protection of this species. In this study, the MaxEnt model was used to predict the potential distribution area of H. triflora in China under historical, current, and future periods based on 66 distribution points and 12 environmental variables. The results were as follows: (i) The main environmental variables affecting the distribution of H. triflora were precipitation in the coldest month and in the wettest quarter, with elevation also being a significant factor. (ii) Over the past three periods, the last interglacial, last glacial maximum, and mid-Holocene, the suitable area for H. triflora initially decreased and then increased. The suitable area reached the lowest value in the last glacial maximum period, at only 27.03 × 10⁴ km². (iii) The current potential distribution area is 67.81 × 10⁴ km², and the optimal area is mainly distributed in the Guangxi, Guangdong, and Hainan provinces. (iv) Under future climate scenarios, the potential distribution area of H. triflora is projected to increase by 11.27~90.83 × 10⁴ km². It is expected to reach a maximum value (158.64 × 10⁴ km²) in 2081~2100 under the SSP-585 climate scenario, with the distribution centroid shifting to higher latitudes. The newly gained optimal habitats will provide potential areas for introduction and ex situ conservation of this species. Full article

(This article belongs to the Section Conservation Biology and Biodiversity)

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13 pages, 1258 KiB

Open AccessReview

Peronema canescens as a Source of Immunomodulatory Agents: A New Opportunity and Perspective

by Ahmad Hafidul Ahkam, Yasmiwar Susilawati and Sri Adi Sumiwi

Biology 2024, 13(9), 744; https://doi.org/10.3390/biology13090744 - 22 Sep 2024

Viewed by 794

Abstract

Immunomodulators are pivotal in managing various health conditions by regulating the immune response by either enhancing or suppressing it to maintain homeostasis. The growing interest in natural sources of immunomodulatory agents has spurred the investigation of numerous medicinal plants, including Peronema canescens, [...] Read more.

Immunomodulators are pivotal in managing various health conditions by regulating the immune response by either enhancing or suppressing it to maintain homeostasis. The growing interest in natural sources of immunomodulatory agents has spurred the investigation of numerous medicinal plants, including Peronema canescens, commonly known in Asia as sungkai. Traditionally used for its medicinal properties in Southeast Asia, Peronema canescens belongs to the Verbenaceae family and has garnered significant attention. This review discusses the immunomodulatory activity of the active compounds in Peronema canescens and explores the potential directions for future research. Full article

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13 pages, 1266 KiB

Open AccessArticle

MiRNAs in Extracellular Vesicles as Biomarkers in Plasma of Papillary Thyroid Cancer Patients: A Proof-of-Concept Study

by Giuseppa D’Amico, Radha Santonocito, Godfrey Grech, Giuseppa Graceffa, Calogero Cipolla, Federica Scalia, Samuele Raccosta, Mauro Manno, Everly Conway de Macario, Alberto J. L. Macario, Francesco Cappello, Francesca Rappa, Celeste Caruso Bavisotto and Claudia Campanella

Biology 2024, 13(9), 743; https://doi.org/10.3390/biology13090743 - 22 Sep 2024

Viewed by 1162

Abstract

Background: The incidence of various types of cancer, for example, papillary thyroid carcinoma (PTC), is on the rise. Since therapeutic success depends greatly on early diagnosis, reliable diagnostic biomarkers must be identified, and easy-to-apply tools for detecting them must urgently be standardized. Here, [...] Read more.

Background: The incidence of various types of cancer, for example, papillary thyroid carcinoma (PTC), is on the rise. Since therapeutic success depends greatly on early diagnosis, reliable diagnostic biomarkers must be identified, and easy-to-apply tools for detecting them must urgently be standardized. Here, we contribute to solving this medical challenge by assessing miRNAs suspected of promoting carcinogenesis in extracellular vesicles (EVs) that can be routinely obtained via liquid biopsy. We profit from current progress in cancerology that provides innovations in liquid biopsy and EVs analysis, along with the identification of miRNAs and chaperone system (CS) components implicated in carcinogenesis. Methods: We measured in EVs obtained from circulating blood plasma from PTC patients the levels of three miRNAs implicated in thyroid cancer, hsa-miR-1-3p, hsa-miR-206, and hsa-miR-221-3p, and most likely involved in the regulation of two members of the CS, Hsp60 and CCT. EVs were isolated from the plasma of patients with PTC and controls with benign goiter (BG) and from the culture medium of a PTC cell line (MDAT32) and were appropriately characterized. Results: The levels of miRNAs determined by RT-qPCR were consistently higher in PTC patients and decreased down to control levels after thyroidectomy. Bioinformatics showed that the miRNAs target genes are associated with the molecular pathogenesis of PTC. Conclusions: Our exploratory study reaffirms the potential in clinics of the selected miRNAs in EVs as useful biomarkers of PTC easily accessible via liquid biopsy, which is minimally invasive and amenable to periodic repetition, an improvement compared to the established fine-needle aspirate biopsy. Full article

(This article belongs to the Special Issue Role of Extracellular Vesicles in Cancer Development, Metastasis and Treatment)

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14 pages, 1523 KiB

Open AccessArticle

Bifunctional Phenylalanine/Tyrosine Ammonia-Lyase (PTAL) Enhances Lignin Biosynthesis: Implications in Carbon Fixation in Plants by Genetic Engineering

by Ye Yuan, Chao-Lei Sheng, Li-Hao Pang and Bao-Rong Lu

Biology 2024, 13(9), 742; https://doi.org/10.3390/biology13090742 - 22 Sep 2024

Viewed by 777

Abstract

Lignin is a key metabolite for terrestrial plants. Two types of aromatic amino acids, phenylalanine (Phe) and tyrosine (Tyr), serve as the precursors for lignin biosynthesis. In most plant species, Phe is deaminated by Phe ammonia-lyase (PAL) to initiate lignin biosynthesis, but in [...] Read more.

Lignin is a key metabolite for terrestrial plants. Two types of aromatic amino acids, phenylalanine (Phe) and tyrosine (Tyr), serve as the precursors for lignin biosynthesis. In most plant species, Phe is deaminated by Phe ammonia-lyase (PAL) to initiate lignin biosynthesis, but in grass species, Phe and Tyr are deaminated by Phe/Tyr ammonia-lyase (PTAL). To understand the efficiency of PAL and PTAL, we used transgenic and non-transgenic Arabidopsis with PAL and crop-weedy rice hybrids (CWRH) with PTAL to analyze lignin-biosynthesis-associated metabolites. The transgenic plants overexpressed the exogenous 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, whereas the non-transgenic plants normally expressed the endogenous EPSPS gene. Our results show significantly increased Phe/Tyr contents in transgenic Arabidopsis and CWRH plants, leading to substantially increased lignin and biomass. In addition, the PTAL pathway promotes a much greater proportion of increased lignin and biomass in transgenic CWRH than in transgenic Arabidopsis lineages. Evidently, more efficient lignin biosynthesis characterized the grass species possessing the PTAL pathway. These findings are important for a better understanding of the PAL and PTAL’s functions in the phenylpropanoid metabolic pathways in the evolution of plant species. These findings also have great value for implications such as effective carbon fixation by enhancing lignin biosynthesis through genetic engineering of their key genes in appropriately selected plant species. Full article

(This article belongs to the Section Plant Science)

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4 pages, 197 KiB

Open AccessEditorial

Improvement and Innovation of Cryopreservation and In Vitro Methods in Plant Resource Protection

by Haeng-Hoon Kim and Elena Popova

Biology 2024, 13(9), 741; https://doi.org/10.3390/biology13090741 - 21 Sep 2024

Viewed by 857

Abstract

Plant genetic resources (PGRs) are perhaps the most precious gift of nature to humanity: they provide food, shelter, medicines, and many goods of high economic value, not to mention their key importance for healthy ecosystems and their aesthetic value [...] Full article

(This article belongs to the Special Issue Improvement and Innovation of Cryopreservation and In Vitro Methods in Plant Resources Protection)

19 pages, 2459 KiB

Open AccessArticle

Taxonomic Diversity and Interannual Variation of Fish in the Lagoon of Meiji Reef (Mischief Reef), South China Sea

by Yuyan Gong, Jun Zhang, Zuozhi Chen, Yancong Cai and Yutao Yang

Biology 2024, 13(9), 740; https://doi.org/10.3390/biology13090740 - 21 Sep 2024

Viewed by 619

Abstract

Coral reef fish are important groups of coral reefs, which have great economic and ecological value. Meiji Reef is a representative tropical semi-enclosed atoll in the South China Sea, with rich fish resources. Based on the data from hand-fishing, line-fishing, and gillnet surveys [...] Read more.

Coral reef fish are important groups of coral reefs, which have great economic and ecological value. Meiji Reef is a representative tropical semi-enclosed atoll in the South China Sea, with rich fish resources. Based on the data from hand-fishing, line-fishing, and gillnet surveys of fish in Meiji Reef from 1998 to 2018, this study summarized the fish species list of Meiji Reef and analyzed the species composition, inclusion index at the taxonomic level (TINCL), genus–family diversity index (G–F index), average taxonomic distinctness index (Δ⁺), and variation in taxonomic distinctness (Λ⁺) and their changes. The results revealed that from 1998 to 2018, there were 166 reef-dwelling fish species on Meiji Reef, belonging to 69 genera, 33 families, and 11 orders, of which 128 species were from 20 families of Perciformes, accounting for 77.10% of the total cataloged species. Regarding the dependence of fish on coral reefs, there were 155 reef-dependent species or resident species (accounting for 93.37%) and 11 reef-independent species or wandering species (accounting for 6.63%). The TINCL of the order, families, and genus of fish in Meiji Reef were very high. The genus diversity index (G index), family diversity index (F index), and G–F index of fish in Meiji Reef were very high, and the G index of fish in Meiji Reef in 1998–1999 was higher than that in 2016–2018. The Δ⁺ and Λ⁺ values of fish in Meiji Reef from 1998 to 2018 were 56.1 and 148.5, respectively. Compared with 1998–1999, Δ⁺ and Λ⁺ of fish increased during 2016–2018, reflecting that the relatives of fish in Meiji Reef became further distant, and the uniformity of taxonomic relationships among species decreased. The research findings indicated that fish exhibited a high taxonomic diversity in Meiji Reef; however, it also revealed significant fluctuations in the fish diversity of Meiji Reef over an extended period, emphasizing the urgent need for timely protection measures. This investigation significantly contributes to our comprehension of the intricate dynamics governing fish species within Meiji Reef and holds broader implications for biodiversity conservation in tropical marine ecosystems. Full article

(This article belongs to the Section Conservation Biology and Biodiversity)

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15 pages, 7306 KiB

Open AccessArticle

Effects of Nitrogen and Phosphorus in Sediment on the Occurrence of Cladophora sp. (Cladophoraceae) in Aquaculture Ponds

by Yuanyuan Zhang, Kaifang Liu, Jun Lv, Xinliang Peng, Yongtao Tang, Liangjie Zhao, Yongxu Cheng and Qigen Liu

Biology 2024, 13(9), 739; https://doi.org/10.3390/biology13090739 - 21 Sep 2024

Viewed by 3569

Abstract

To explore the impact of sedimentary nitrogen and phosphorus on Cladophora occurrence, we conducted a microecosystem experiment simulating different nitrogen and phosphorus content as well as nitrogen-to-phosphorus ratios in the sediment. Subsequently, to further explore the specific mechanism of influence that epiphytic algae [...] Read more.

To explore the impact of sedimentary nitrogen and phosphorus on Cladophora occurrence, we conducted a microecosystem experiment simulating different nitrogen and phosphorus content as well as nitrogen-to-phosphorus ratios in the sediment. Subsequently, to further explore the specific mechanism of influence that epiphytic algae have on Cladophora, we designed various microsystem culture experiments. These results revealed that an N/P ratio of 40:1 was relatively unfavorable for Cladophora growth. Additionally, there was an extremely significant negative correlation between the benthic cyanobacteria coverage on the sediment surface and the wet weight of Cladophora (p < 0.01), indicating that benthic cyanobacteria could inhibit the growth of Cladophora. Total nitrogen levels in the water column showed a significant positive correlation with phytoplankton biomass (p < 0.05), while benthic cyanobacteria coverage exhibited an extremely significant positive correlation with phytoplankton biomass through phosphorus absorption and nitrogen release (p < 0.01). Metabolite analysis of benthic cyanobacteria identified annotations for 313 metabolites; among them cis,cis-muconic acid (32.48‰), erucamide (9.52‰), phosphoric acid (6.97‰), fenpropidin (6.53‰), and propionic acid (5.16‰) accounted for proportions exceeding 5‰. However, none of these metabolites have been recognized as allelochemicals or toxins at present. This study provides novel insights into controlling Cladophora occurrence by considering sediment nutrients, including nitrogen and phosphorus, along with allelochemicals. Full article

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18 pages, 3661 KiB

Open AccessArticle

Targeting Polyprotein to Design Potential Multiepitope Vaccine against Omsk Hemorrhagic Fever Virus (OHFV) by Evaluating Allergenicity, Antigenicity, and Toxicity Using Immunoinformatic Approaches

by Abdullah M. Alnuqaydan and Alaa Abdulaziz Eisa

Biology 2024, 13(9), 738; https://doi.org/10.3390/biology13090738 - 20 Sep 2024

Viewed by 836

Abstract

Omsk Hemorrhagic Fever Virus (OHFV) is an RNA virus with a single-stranded, positive-sense genome. It is classified under the Flaviviridae family. The genome of this virus is 98% similar to the Alkhurma hemorrhagic fever virus (AHFV), which belongs to the same family. Cases [...] Read more.

Omsk Hemorrhagic Fever Virus (OHFV) is an RNA virus with a single-stranded, positive-sense genome. It is classified under the Flaviviridae family. The genome of this virus is 98% similar to the Alkhurma hemorrhagic fever virus (AHFV), which belongs to the same family. Cases of the virus have been reported in various regions of Saudi Arabia. Both OHFV and AHFV have similarities in pathogenic polyprotein targets. No effective and licensed vaccines are available to manage OHFV infections. Therefore, an effective and safe vaccine is required that can activate protective immunity against OHFV. The current study aimed to design a multiepitope subunit vaccine against the OHFV utilizing several immunoinformatic tools. The polyprotein of OHFV was selected and potent antigenic, non-allergenic, and nontoxic cytotoxic T-lymphocyte (CTL), helper T-lymphocyte (HTL), and linear B-lymphocyte (LBL) epitopes were chosen. After screening, eight (8) CTL, five (5) HTL, and six (6) B cell epitopes were joined with each other using different linkers. Adjuvant human beta defensin-2 was also linked to the epitopes to increase vaccine antigenic and immunogenic efficiency. The designed vaccine was docked with Toll-like receptor 4 (TLR4) as it activates and induces primary and secondary immune responses against OHFV. Codon optimization was carried out, which resulted in a CAI value of 0.99 and 53.4% GC contents. In addition, the construct was blindly docked to the TLR4 immune receptor and subjected to conformational dynamics simulation analysis to interpret the intricate affinity and comprehend the time-dependent behavior. Moreover, it was predicted that immune responses to the developed vaccine construct reported formation of strong humoral and cellular immune cells. Therefore, the proposed vaccine may be considered in experimental assays to combat OHFV infections. Laboratory experiments for the above predictions are essential in order to evaluate the effectiveness, safety, and protective properties of the subject in question. Full article

(This article belongs to the Special Issue Human Leukocyte Antigen (HLA)—Antigen Interactions in Vaccine Development)

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13 pages, 2454 KiB

Open AccessArticle

The Protection and Management of Wapiti in Desert Oases: Bare Land Poses a Limitation to Wapiti Conservation

by Fujie Qiao, Hairong Du, Xia Zhang, Caiping Feng, Zhihua Tan, Yanqin Yu and Zhensheng Liu

Biology 2024, 13(9), 737; https://doi.org/10.3390/biology13090737 - 20 Sep 2024

Viewed by 537

Abstract

The Helan Mountains, situated in the heart of the desert, act as a dividing line between China’s arid and semi-arid zones. Often referred to as a “desert oasis”, they create an ecological island with a uniquely distinctive geographical location, making this area a [...] Read more.

The Helan Mountains, situated in the heart of the desert, act as a dividing line between China’s arid and semi-arid zones. Often referred to as a “desert oasis”, they create an ecological island with a uniquely distinctive geographical location, making this area a focal point of contemporary research. Ungulates play a critical role in this ecosystem. The Alashan wapiti (Cervus canadensis alashanicus), an isolated population of China’s smallest wapiti (Cervus canadensis) subspecies, is found exclusively within the Helan Mountains Nature Reserve. The conservation of this isolated population is fraught with challenges, particularly during winter, the harshest season for northern ungulates. Winter habitats are crucial for ensuring population stability. Therefore, we used certain methods, such as factor screening and model parameter optimization to assess habitat suitability using multi-scale species distribution models. The optimized results show that suitable habitats overlap with areas of high vegetation coverage in the Helan Mountains, covering just 588.32 km², which is less than a quarter of the reserve’s total area. The bare land area and winter NDVI are the two primary factors influencing habitat suitability, with other factors having minimal impact, underscoring the critical importance of food resources for the Alashan wapiti. The limited availability of these resources poses significant conservation challenges. Our findings provide a more precise foundation for targeted habitat protection and restoration efforts. We recommend enhancing the protection and restoration of food resources, effectively conserving vegetated areas, and preventing desertification. Full article

(This article belongs to the Section Ecology)

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12 pages, 2330 KiB

Open AccessArticle

The Natural HASPIN Inhibitor Coumestrol Suppresses Intestinal Polyp Development, Cachexia, and Hypogonadism in a Mouse Model of Familial Adenomatous Polyposis (Apc^Min/+)

by Hiromitsu Tanaka, Shunsuke Matsuyama, Tomoe Ohta, Keisuke Kakazu, Kazutoshi Fujita, Shinichiro Fukuhara, Tetsuji Soda, Yasushi Miyagawa and Akira Tsujimura

Biology 2024, 13(9), 736; https://doi.org/10.3390/biology13090736 - 20 Sep 2024

Viewed by 1009

Abstract

(1) Background: HASPIN kinase is involved in regulating spindle function and chromosome segregation, as well as phosphorylating histone H3 at Thr3 in mitotic cells. Several HASPIN inhibitors suppress cancer cell proliferation. It was recently reported that coumestrol from bean sprouts inhibits HASPIN, and [...] Read more.

(1) Background: HASPIN kinase is involved in regulating spindle function and chromosome segregation, as well as phosphorylating histone H3 at Thr3 in mitotic cells. Several HASPIN inhibitors suppress cancer cell proliferation. It was recently reported that coumestrol from bean sprouts inhibits HASPIN, and a cultivation method for bean sprouts containing large amounts of coumestrol has been established. Here, we showed the effects of bean sprout ingestion on intestinal polyp development, cachexia, and hypogonadism in a mouse model of familial adenomatous polyposis (Apc^Min/+). (2) Methods: Apc^Min/+ mice were randomized into control and treatment groups. Mice in the control group were given the standard diet, while those in the treatment group were given the same standard diet with the addition of 15% bean sprouts. Treatments were commenced at 7 weeks old and analyses were performed at 12 weeks old. (3) Results: ingesting bean sprouts suppressed the development of intestinal polyps, cachexia, and hypogonadism, and also increased serum levels of testosterone in male wild-type and Apc^Min/+ mice. (4) Conclusions: ingesting bean sprouts helps prevent cancer and increases serum levels of testosterone in a mouse model. These results are expected to be applicable to humans. Full article

(This article belongs to the Section Cancer Biology)

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4 pages, 193 KiB

Open AccessEditorial

Phytoplasmas: Molecular Characterization and Host–Pathogen Interactions

by Wei Wei, Yan Zhao and Fabio Quaglino

Biology 2024, 13(9), 735; https://doi.org/10.3390/biology13090735 - 20 Sep 2024

Viewed by 892

Abstract

Phytoplasmas are small, wall-less bacteria that infect many plant species and multiply within phloem-feeding insects of the Hemiptera order [...] Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host-Pathogen Interactions)

37 pages, 4357 KiB

Open AccessArticle

Low Magnetic Field Exposure Alters Prostate Cancer Cell Properties

by Sigrun Lange, Jameel M. Inal, Igor Kraev, Dafydd Alwyn Dart and Pinar Uysal-Onganer

Biology 2024, 13(9), 734; https://doi.org/10.3390/biology13090734 - 19 Sep 2024

Viewed by 1700

Abstract

Prostate cancer is the second most common neoplasia and fifth-leading cause of cancer death in men worldwide. Electromagnetic and magnetic fields have been classified as possible human carcinogens, but current understanding of molecular and cellular pathways involved is very limited. Effects due to [...] Read more.

Prostate cancer is the second most common neoplasia and fifth-leading cause of cancer death in men worldwide. Electromagnetic and magnetic fields have been classified as possible human carcinogens, but current understanding of molecular and cellular pathways involved is very limited. Effects due to extremely low magnetic/hypomagnetic fields (LMF) are furthermore poorly understood. Extracellular vesicles (EVs) are crucial mediators of cellular communication with multifaceted roles in cancer progression, including via transport and uptake of various protein and microRNA (miRNA) EV-cargoes. miRNAs regulate gene expression and are implicated in cancer-related processes such as proliferation, metastasis, and chemoresistance. This study investigated the effects of LMF exposure (20 nT) by magnetic shielding on the prostate cancer cell line PC3 compared to the prostate epithelial cell line PNT2 under short-term (4 h) conditions. We examined EV profiles following a 4 h LMF exposure alongside associated functional enrichment KEGG and GO pathways for the EV proteomes. The 4 h LMF exposure significantly reduced cellular EV release and modified PC3 EV cargoes to a more inflammatory and metastatic profile, with 16 Disease Pathways and 95 Human Phenotypes associated specifically with the LMF-treated PC3 EV proteomes. These included cancerous, metabolic, blood, skin, cardiac and skeletal Disease Pathways, as well as pain and developmental disorders. In the normal PNT2 cells, less EV protein cargo was observed following LMF exposure compared with cells not exposed to LMF, and fewer associated functional enrichment pathways were identified. This pointed to some differences in various cellular functions, ageing, defence responses, oxidative stress, and disease phenotypes, including respiratory, digestive, immune, and developmental pathways. Furthermore, we analysed alterations in matrix metalloproteinases (MMPs) and miRNAs linked to metastasis, as this is crucial in cancer aggressiveness. The 4 h LMF exposure caused a significant increase in MMP2 and MMP9, as well as in onco-miRs miR-155, miR-210, miR-21, but a significant reduction in tumour-suppressor miRs (miR-200c and miR-126) in the metastatic PC3 cells, compared with normal PNT2 cells. In addition, 4 h LMF exposure significantly induced cellular invasion of PC3 cells. Overall, our findings suggest that changes in magnetic field exposures modulate EV-mediated and miR-regulatory processes in PCa metastasis, providing a basis for exploring novel therapeutic strategies. Full article

(This article belongs to the Special Issue The Rules of Life Rethought: Latest Progress in Quantum Biology)

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21 pages, 4373 KiB

Open AccessArticle

Stomata Are Driving the Direction of CO₂-Induced Water-Use Efficiency Gain in Selected Tropical Trees in Fiji

by Wuu Kuang Soh, Charilaos Yiotis, Michelle Murray, Sarah Pene, Alivereti Naikatini, Johan A. Dornschneider-Elkink, Joseph D. White, Marika Tuiwawa and Jennifer C. McElwain

Biology 2024, 13(9), 733; https://doi.org/10.3390/biology13090733 - 19 Sep 2024

Viewed by 825

Abstract

Understanding plant physiological response to a rising atmospheric CO₂ concentration (c_a) is key in predicting Earth system plant–climate feedbacks; however, the effects of long-term rising c_a on plant gas-exchange characteristics in the tropics are largely unknown. Studying this [...] Read more.

Understanding plant physiological response to a rising atmospheric CO₂ concentration (c_a) is key in predicting Earth system plant–climate feedbacks; however, the effects of long-term rising c_a on plant gas-exchange characteristics in the tropics are largely unknown. Studying this long-term trend using herbarium records is challenging due to specimen trait variation. We assessed the impact of a c_a rise of ~95 ppm (1927–2015) on the intrinsic water-use efficiency (iWUE) and maximum stomatal conductance (g_smax) of five tropical tree species in Fiji using the isotopic composition and stomatal traits of herbarium leaves. Empirical results were compared with simulated values using models that uniquely incorporated the variation in the empirical g_smax responses and species-specific parameterisation. The magnitude of the empirical iWUE and g_smax response was species-specific, ranging from strong to negligible. Stomatal density was more influential than the pore size in determining the g_smax response to c_a. While our simulation results indicated that photosynthesis is the main factor contributing to the iWUE gain, stomata were driving the iWUE trend across the tree species. Generally, a stronger increase in the iWUE was accompanied by a stronger decline in stomatal response. This study demonstrates that the incorporation of variation in the g_smax in simulations is necessary for assessing an individual species’ iWUE response to changing c_a. Full article

(This article belongs to the Special Issue Biological Response of Plants to Environmental Changes)

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27 pages, 6095 KiB

Open AccessArticle

Forecasting the Pharmacological Mechanisms of Plumbago zeylanica and Solanum xanthocarpum in Diabetic Retinopathy Treatment: A Network Pharmacology, Molecular Docking, and Molecular Dynamics Simulation Study

by Nilanchala Sahu, Rama Tyagi, Neeraj Kumar, Mohd. Mujeeb, Ali Akhtar, Perwez Alam and Swati Madan

Biology 2024, 13(9), 732; https://doi.org/10.3390/biology13090732 - 18 Sep 2024

Cited by 1 | Viewed by 726

Abstract

(1) Background: Diabetic retinopathy (DR) is a major complication of diabetes, marked by abnormal angiogenesis, microaneurysms, and retinal hemorrhages. Traditional Ayurvedic medicine advocates multi-target strategies for DR management. However, the mechanisms by which Solanum xanthocarpum (SX) and Plumbago zeylanica (PZ) exert therapeutic effects [...] Read more.

(1) Background: Diabetic retinopathy (DR) is a major complication of diabetes, marked by abnormal angiogenesis, microaneurysms, and retinal hemorrhages. Traditional Ayurvedic medicine advocates multi-target strategies for DR management. However, the mechanisms by which Solanum xanthocarpum (SX) and Plumbago zeylanica (PZ) exert therapeutic effects are not well understood; (2) Methods: To investigate these mechanisms, we employed network pharmacology and molecular docking techniques. Phytochemicals from SX and PZ were identified using the IMPPAT database and Swiss Target Prediction tool. DR-related protein targets were sourced from the GeneCards database, and common targets were identified through Venn diagram analysis. STRING and Cytoscape were used to construct and analyze protein–protein interaction networks. Pathway enrichment was performed with Gene Ontology and KEGG databases; (3) Results: We identified 28 active phytoconstituents, targeting proteins such as EGFR, SRC, STAT3, AKT1, and HSP90AA1. Molecular docking and dynamics simulations confirmed the strong binding affinities of these compounds to their targets; (4) Conclusions: The study highlights the multi-target activity of SX and PZ, particularly in pathways related to EGFR tyrosine kinase inhibitor resistance and PI3K–AKT signaling. These findings provide valuable insights into their therapeutic potential for DR, suggesting the effective modulation of key molecular pathways involved in the disease. Full article

(This article belongs to the Section Bioinformatics)

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12 pages, 2678 KiB

Open AccessArticle

Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in Litopenaeus vannamei through a Genome-Wide Association Study

by Sukhuman Whankaew, Phassorn Suksri, Ammara Sinprasertporn, Jumroensri Thawonsuwan and Ponsit Sathapondecha

Biology 2024, 13(9), 731; https://doi.org/10.3390/biology13090731 - 18 Sep 2024

Viewed by 928

Abstract

Shrimp aquaculture is facing a serious disease, acute hepatopancreatic necrosis disease (AHPND), caused by Vibrio paraheamolyticus (Vp_APHND). For sustainable shrimp aquaculture, massive losses of shrimp infected with Vp_APHND must be prevented. Research and selection of shrimp tolerant to Vp_APHND [...] Read more.

Shrimp aquaculture is facing a serious disease, acute hepatopancreatic necrosis disease (AHPND), caused by Vibrio paraheamolyticus (Vp_APHND). For sustainable shrimp aquaculture, massive losses of shrimp infected with Vp_APHND must be prevented. Research and selection of shrimp tolerant to Vp_APHND infection is a sustainable approach to reducing the risk of AHPND. This study focused on the identification and development of potential DNA markers associated with AHPND using DArT sequencing (DArTSeq) and a genome-wide association study. Three populations of post-larval Litopenaeus vannamei were immersed in Vp_APHND to collect susceptible (D) and tolerant (S) samples. The 45 D and 48 S shrimp had their genotypes analyzed using DArTSeq. A total of 108,983 SNPs and 17,212 InDels were obtained from the DArTseq data, while the biallelic 516 SNPs and 2293 InDels were finally filtered with PIC < 0.1, MAF < 0.05, and a call rate ≥ 80%. The filtered variants were analyzed for their association with AHPND tolerance. Although there were no significantly associated SNPs and InDels above the Bonferroni correction threshold, candidate variants, four SNPs and 17 InDels corresponding to p < 0.01, were provided for further validation of the AHPND tolerance trait. The candidate SNPs are located on an exon of the zinc finger protein 239-like gene, an intron of an uncharacterized gene, and in intergenic regions. Most of the candidate InDels are in the intergenic regions, with fewer in the intronic and exonic regions. This study provides information on SNPs and InDels for white shrimp. These markers will support the variant database of shrimp and be useful in shrimp aquaculture for breeding selection. Full article

(This article belongs to the Special Issue Advances in Biological Research into Shrimps, Crabs and Lobsters)

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14 pages, 2529 KiB

Open AccessBrief Report

Clonostachys rosea, a Pathogen of Brown Rot in Gastrodia elata in China

by Huan Yao, Kang Liu, Lei Peng, Touli Huang, Jinzhen Shi, Beilin Sun and Juan Zou

Biology 2024, 13(9), 730; https://doi.org/10.3390/biology13090730 - 17 Sep 2024

Viewed by 887

Abstract

Gastrodia elata, commonly known as Tian Ma, is a perennial mycoheterotrophic orchid. Qianyang Tian Ma (QTM), a geographical indication agricultural product from Hongjiang City, Hunan Province, China, is primarily characterized by the red variety, G. elata f. elata. A severe outbreak [...] Read more.

Gastrodia elata, commonly known as Tian Ma, is a perennial mycoheterotrophic orchid. Qianyang Tian Ma (QTM), a geographical indication agricultural product from Hongjiang City, Hunan Province, China, is primarily characterized by the red variety, G. elata f. elata. A severe outbreak of tuber brown rot disease was documented in QTM during the harvesting season in Hunan. The fungal pathogen associated with the disease was isolated on potato saccharose agar (PSA) and identified through morphological and phylogenetic analyses. Pathogenicity tests were performed on healthy tubers of G. elata f. elata. The results showed that the representative isolate, named TMB, produced white hyphal colonies with a ring structure, broom-like phialides, partially curved ellipsoidal conidia, and orange–yellow spherical ascocarps on PSA. Phylogenetic analysis of the ITS, LSU, rpb2 and tub2 sequences using Bayesian and maximum-likelihood methods identified the isolate TMB as Clonostachys rosea, based on morphological and phylogenetic data. Pathogenicity tests revealed typical disease symptoms on healthy G. elata tubers 15 days post-inoculation with the isolate TMB. C. rosea is known to cause diseases in economically important crops, but there are no reports of its occurrence on G. elata f. elata in China. This study provides valuable insights into the occurrence, prevention, and control of brown rot disease in G. elata f. elata. Full article

(This article belongs to the Special Issue Advances in Research on Diseases of Plants)

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31 pages, 7275 KiB

Open AccessArticle

Euterpe oleracea Mart. Bioactive Molecules: Promising Agents to Modulate the NLRP3 Inflammasome

by Carolina Bordin Davidson, Dana El Soufi El Sabbagh, Amanda Kolinski Machado, Lauren Pappis, Michele Rorato Sagrillo, Sabrina Somacal, Tatiana Emanuelli, Júlia Vaz Schultz, João Augusto Pereira da Rocha, André Flores dos Santos, Solange Binotto Fagan, Ivana Zanella da Silva, Ana Cristina Andreazza and Alencar Kolinski Machado

Biology 2024, 13(9), 729; https://doi.org/10.3390/biology13090729 - 17 Sep 2024

Viewed by 995

Abstract

Inflammation is a vital mechanism that defends the organism against infections and restores homeostasis. However, when inflammation becomes uncontrolled, it leads to chronic inflammation. The NLRP3 inflammasome is crucial in chronic inflammatory responses and has become a focal point in research for new [...] Read more.

Inflammation is a vital mechanism that defends the organism against infections and restores homeostasis. However, when inflammation becomes uncontrolled, it leads to chronic inflammation. The NLRP3 inflammasome is crucial in chronic inflammatory responses and has become a focal point in research for new anti-inflammatory therapies. Flavonoids like catechin, apigenin, and epicatechin are known for their bioactive properties (antioxidant, anti-inflammatory, etc.), but the mechanisms behind their anti-inflammatory actions remain unclear. This study aimed to explore the ability of various flavonoids (isolated and combined) to modulate the NLRP3 inflammasome using in silico and in vitro models. Computer simulations, such as molecular docking, molecular dynamics, and MM/GBSA calculations examined the interactions between bioactive molecules and NLRP3 PYD. THP1 cells were treated with LPS + nigericin to activate NLRP3, followed by flavonoid treatment at different concentrations. THP1-derived macrophages were also treated following NLRP3 activation protocols. The assays included colorimetric, fluorometric, microscopic, and molecular techniques. The results showed that catechin, apigenin, and epicatechin had high binding affinity to NLRP3 PYD, similar to the known NLRP3 inhibitor MCC950. These flavonoids, particularly at 1 µg/mL, 0.1 µg/mL, and 0.01 µg/mL, respectively, significantly reduced LPS + nigericin effects in both cell types and decreased pro-inflammatory cytokine, caspase-1, and NLRP3 gene expression, suggesting their potential as anti-inflammatory agents through NLRP3 modulation. Full article

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

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11 pages, 266 KiB

Open AccessArticle

Intact FGF23 and Markers of Iron Homeostasis, Inflammation, and Bone Mineral Metabolism in Acute Pediatric Infections

by Eleni Papastergiou, Dimitrios Rallis, Afroditi Papagianni, Vasileios Cholevas, Nikolaos Katzilakis, Ekaterini Siomou, Eftichia Stiakaki and Alexandros Makis

Biology 2024, 13(9), 728; https://doi.org/10.3390/biology13090728 - 17 Sep 2024

Viewed by 773

Abstract

We intend to evaluate the association of intact Fibroblast Growth Factor 23 (i-FGF23), a phosphaturic hormone that contributes to anemia of inflammation, with markers of iron homeostasis, inflammation, and bone mineral metabolism in acute pediatric infections. Seventy-nine children, aged 1 month–13 years, out [...] Read more.

We intend to evaluate the association of intact Fibroblast Growth Factor 23 (i-FGF23), a phosphaturic hormone that contributes to anemia of inflammation, with markers of iron homeostasis, inflammation, and bone mineral metabolism in acute pediatric infections. Seventy-nine children, aged 1 month–13 years, out of which forty-two were males and thirty-seven females, participated in this study. Children with diseases and nutrient deficiencies causing anemia were excluded. Twenty-six patients had bacterial infections, twenty-six had viral infections, and twenty-seven children served as healthy controls. Complete blood count, markers of inflammation, iron and mineral metabolism, serum hepcidin, and i-FGF23 were compared between the groups. Thirty-nine percent of patients with bacterial infection and twelve percent of patients with viral infection presented characteristics of anemia of inflammation (p < 0.001). Ninety-two percent of patients with bacterial infection and eighty-one percent of patients with viral infection had functional iron deficiency (p < 0.001). Hepcidin was significantly positively correlated with the duration of fever, markers of inflammation, and negatively with iron, mineral metabolism parameters, and i-FGF23. i-FGF23 was positively correlated with iron metabolism parameters and negatively with the duration of fever, markers of inflammation, and hepcidin. Hepcidin levels increase, whereas i-FGF23 levels decrease in acute pediatric infections. Further research is required to understand the role of FGF23 in the hepcidin–ferroportin axis and for hepcidin in the diagnosis of bacterial infections and mineral metabolism. Full article

(This article belongs to the Section Infection Biology)

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12 pages, 1023 KiB

Open AccessArticle

Insights into Population Status and Habitat Patches of Conservation Concern for the Endangered Indian Pangolin (Manis crassicaudata) in Nowshera District, Northwestern Pakistan

by Romaan Hayat Khattak, Shakeel Ahmad, Tahir Mehmood, Hongliang Dou, Haiyang Gao, Song Sun and Yan Hua

Biology 2024, 13(9), 727; https://doi.org/10.3390/biology13090727 - 16 Sep 2024

Viewed by 1226

Abstract

The Indian pangolin (Manis crassicaudata) stands out among the four surviving species of Asian pangolins, being the sole species present in Pakistan and listed as endangered owing to trafficking and illicit commerce. In the present study, we explored the population status [...] Read more.

The Indian pangolin (Manis crassicaudata) stands out among the four surviving species of Asian pangolins, being the sole species present in Pakistan and listed as endangered owing to trafficking and illicit commerce. In the present study, we explored the population status of the Indian pangolin and the existing suitable habitats in Nowshera district, Pakistan. We employed the line transect method to confirm the species presence and subsequent population estimation. In a survey effort of 156 km², a total of 56 signs of Indian pangolin were recorded within the research area. Amongst the 56 signs, 46 were burrows (living burrows (53.57%) and feeding burrows (28.57%)). Digging was observed nine (16.07%) times, along with one direct sighting (1.7%). Our results revealed a population estimate of only 29 pangolins in the Nowshera district, with a population density of 0.013 individuals/km². Later, MaxEnt was applied to the species’ presence points, along with climatic and topographical variables. The MaxEnt model accuracy was good (AUC = 0.811). Of the total area studied, 210 km² (12.01%) were highly suitable and 238 km² (13.61%) were moderately suitable habitat for the Indian pangolin. To safeguard the fragile population and habitat of the Indian pangolin, we highly suggest strengthening watch and ward and law enforcement in the study area. By adopting a comprehensive approach that addresses both the direct threats to Indian pangolins and the underlying factors driving their decline, we can effectively protect this endangered species and ensure the preservation of its essential habitats for robust conservation. Full article

(This article belongs to the Special Issue Advances in Wildlife Conservation and Habitat Management in the Anthropocene)

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19 pages, 2944 KiB

Open AccessArticle

Dynamic Membrane Lipid Changes in Physcomitrium patens Reveal Developmental and Environmental Adaptations

by Deepshila Gautam, Jyoti R. Behera, Suhas Shinde, Shivakumar D. Pattada, Mary Roth, Libin Yao, Ruth Welti and Aruna Kilaru

Biology 2024, 13(9), 726; https://doi.org/10.3390/biology13090726 - 16 Sep 2024

Viewed by 1180

Abstract

Membrane lipid composition is critical for an organism’s growth, adaptation, and functionality. Mosses, as early non-vascular land colonizers, show significant adaptations and changes, but their dynamic membrane lipid alterations remain unexplored. Here, we investigated the temporal changes in membrane lipid composition of the [...] Read more.

Membrane lipid composition is critical for an organism’s growth, adaptation, and functionality. Mosses, as early non-vascular land colonizers, show significant adaptations and changes, but their dynamic membrane lipid alterations remain unexplored. Here, we investigated the temporal changes in membrane lipid composition of the moss Physcomitrium patens during five developmental stages and analyzed the acyl content and composition of the lipids. We observed a gradual decrease in total lipid content from the filamentous protonema stage to the reproductive sporophytes. Notably, we found significant levels of very long-chain polyunsaturated fatty acids, particularly arachidonic acid (C20:4), which are not reported in vascular plants and may aid mosses in cold and abiotic stress adaptation. During vegetative stages, we noted high levels of galactolipids, especially monogalactosyldiacylglycerol, associated with chloroplast biogenesis. In contrast, sporophytes displayed reduced galactolipids and elevated phosphatidylcholine and phosphatidic acid, which are linked to membrane integrity and environmental stress protection. Additionally, we observed a gradual decline in the average double bond index across all lipid classes from the protonema stage to the gametophyte stage. Overall, our findings highlight the dynamic nature of membrane lipid composition during moss development, which might contribute to its adaptation to diverse growth conditions, reproductive processes, and environmental challenges. Full article

(This article belongs to the Special Issue Lipid Metabolism in Plant Growth and Development)

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20 pages, 4407 KiB

Open AccessArticle

Transcriptomic Analysis Provides New Insights into the Tolerance Mechanisms of Green Macroalgae Ulva prolifera to High Temperature and Light Stress

by Kifat Jahan, Mst Shamim Ara Supty, Jun-Seok Lee and Keun-Hyung Choi

Biology 2024, 13(9), 725; https://doi.org/10.3390/biology13090725 - 16 Sep 2024

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Abstract

Our research focused on understanding the genetic mechanisms that contribute to the tolerance of Ulva prolifera (Chlorophyta), a marine macroalgae, to the combined stress of high temperature and high light intensity. At the mRNA level, the up-regulated DEGs showed enrichment in pathways related [...] Read more.

Our research focused on understanding the genetic mechanisms that contribute to the tolerance of Ulva prolifera (Chlorophyta), a marine macroalgae, to the combined stress of high temperature and high light intensity. At the mRNA level, the up-regulated DEGs showed enrichment in pathways related to ribosomes, proteasomes, and peroxisomes. The spliceosome pathway genes were found to be vital for U. prolifera’s ability to adapt to various challenging situations in all the comparison groups. In response to elevated temperature and light intensity stress, there was a significant increase in genes and pathways related to ribosomes, proteasomes, and peroxisomes, whereas autophagy showed an increase in response to stress after 24 h, but not after 48 h. These findings provide novel insights into how U. prolifera adapts to elevated temperature and light stress. Full article

(This article belongs to the Section Marine Biology)

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13 pages, 2051 KiB

Open AccessArticle

Tumorspheres as In Vitro Model for Identifying Predictive Chemoresistance and Tumor Aggressiveness Biomarkers in Breast and Colorectal Cancer

by Toni Martinez-Bernabe, Pere Miquel Morla-Barcelo, Lucas Melguizo-Salom, Margalida Munar-Gelabert, Alba Maroto-Blasco, Margalida Torrens-Mas, Jordi Oliver, Pilar Roca, Mercedes Nadal-Serrano, Daniel Gabriel Pons and Jorge Sastre-Serra

Biology 2024, 13(9), 724; https://doi.org/10.3390/biology13090724 - 15 Sep 2024

Viewed by 976

Abstract

Chemoresistance remains a major challenge in the treatment of breast and colorectal cancer. For this reason, finding reliable predictive biomarkers of response to chemotherapy has become a significant research focus in recent years. However, validating in vitro results may be problematic due to [...] Read more.

Chemoresistance remains a major challenge in the treatment of breast and colorectal cancer. For this reason, finding reliable predictive biomarkers of response to chemotherapy has become a significant research focus in recent years. However, validating in vitro results may be problematic due to the outcome heterogeneity. In this study, we evaluate the use of tumorspheres as an in vitro model for validating biomarkers of chemoresistance in breast and colorectal cancer. Our investigation highlights the crucial role of inflammation-related pathways in modulating the response to chemotherapy. Using in silico approaches, we identified specific markers elevated in responders versus non-responders patients. These markers were consistently higher in three-dimensional (3D) tumorsphere models compared to traditional adherent cell culture models. Furthermore, the number of tumorspheres from breast and colorectal cancer cells increased in response to cisplatin and oxaliplatin treatment, respectively, whereas cell viability decreased in adherent cell culture. This differential response underscores the importance of the 3D tumorsphere model in mimicking the tumor microenvironment more accurately than adherent cell culture. The enhanced chemoresistance observed in the 3D tumorspheres model and their correlation of data with the in silico study suggest that 3D culture models are a better option to approach the in vivo model and also to validate in silico data. Our findings indicate that tumorspheres are an ideal model for validating chemoresistance biomarkers and exploring the interplay between inflammation and chemoresistance in breast and colon cancer. Full article

(This article belongs to the Special Issue Cancer and Signalling: Targeting Cellular Pathways)

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14 pages, 9059 KiB

Open AccessArticle

Dynamic Metabolic Responses of Resistant and Susceptible Poplar Clones Induced by Hyphantria cunea Feeding

by Zheshu Wang, Liangjian Qu, Zhibin Fan, Luxuan Hou, Jianjun Hu and Lijuan Wang

Biology 2024, 13(9), 723; https://doi.org/10.3390/biology13090723 - 14 Sep 2024

Viewed by 687

Abstract

Poplar trees are significant for both economic and ecological purposes, and the fall webworm (Hyphantria cunea Drury) poses a major threat to their plantation in China. The preliminary resistance assessment in the previous research indicated that there were differences in resistance to [...] Read more.

Poplar trees are significant for both economic and ecological purposes, and the fall webworm (Hyphantria cunea Drury) poses a major threat to their plantation in China. The preliminary resistance assessment in the previous research indicated that there were differences in resistance to the insect among these varieties, with ‘2KEN8’ being more resistant and ‘Nankang’ being more susceptible. The present study analyzed the dynamic changes in the defensive enzymes and metabolic profiles of ‘2KEN8’ and ‘Nankang’ at 24 hours post-infestation (hpi), 48 hpi, and 96 hpi. The results demonstrated that at the same time points, compared to susceptible ‘Nankang’, the leaf consumption by H. cunea in ‘2KEN8’ was smaller, and the larval weight gain was slower, exhibiting clear resistance to the insect. Biochemical analysis revealed that the increased activity of the defensive enzymes in ‘2KEN8’ triggered by the feeding of H. cunea was significantly higher than that of ‘Nankang’. Metabolomics analysis indicated that ‘2KEN8’ initiated an earlier and more intense reprogramming of the metabolic profile post-infestation. In the early stages of infestation, the differential metabolites induced in ‘2KEN8’ primarily included phenolic compounds, flavonoids, and unsaturated fatty acids, which are related to the biosynthesis pathways of phenylpropanoids, flavonoids, unsaturated fatty acids, and jasmonates. The present study is helpful for identifying the metabolic biomarkers for inductive resistance to H. cunea and lays a foundation for the further elucidation of the chemical resistance mechanism of poplar trees against this insect. Full article

(This article belongs to the Special Issue Ecological Regulation of Forest and Grassland Pests)

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17 pages, 1880 KiB

Open AccessArticle

Comparative Study of Nutritional Composition, Physiological Indicators, and Genetic Diversity in Litopenaeus vannamei from Different Aquaculture Populations

by Yundong Li, Siyao Cao, Shigui Jiang, Jianhua Huang, Qibin Yang, Song Jiang, Lishi Yang and Falin Zhou

Biology 2024, 13(9), 722; https://doi.org/10.3390/biology13090722 - 14 Sep 2024

Viewed by 841

Abstract

This study aimed to evaluate the quality and genetic diversity of farmed Litopenaeus vannamei across three distinct populations from Maoming City (MM), Zhanjiang City (ZJ), and Yangjiang City (YJ) in Guangdong Province. Muscle tissues from L. vannamei were analyzed for phenotypic traits, conventional [...] Read more.

This study aimed to evaluate the quality and genetic diversity of farmed Litopenaeus vannamei across three distinct populations from Maoming City (MM), Zhanjiang City (ZJ), and Yangjiang City (YJ) in Guangdong Province. Muscle tissues from L. vannamei were analyzed for phenotypic traits, conventional nutrients, amino acids, and fatty acids, while genetic diversity was assessed using whole genome sequencing techniques. The analysis revealed that the crude protein content in shrimp across the three populations ranged from 20.87 to 21.95 g/100 g, crude fat content ranged from 0.90 to 1.50 g/100 g, essential amino acid content ranged from 5.55 to 5.86 g/100 g, total amino acid content ranged from 14.73 to 15.27 g/100 g, total fatty acid content ranged from 682.73 to 793.97 mg/100 g, total antioxidant capacity (T-AOC) ranged from 2.68 to 2.72 μmol/g, superoxide dismutase (SOD) activity ranged from 1021.97 to 1057.21 U/g, and catalase (CAT) activity ranged from 78.65 to 81.33 μmoL/min. No significant differences were observed in ash and crude fat levels among conventional nutrients, nor in the biochemical indexes T-AOC, CAT, and SOD. Genetic analysis showed that the single nucleotide polymorphism density (SNP/Kb) ranged from 15.323 to 17.461, nucleotide diversity (π) ranged from 2.98 × 10⁻⁵ to 15.84 × 10⁻⁵, polymorphism information content (PIC) ranged from 0.300 to 0.317, heterozygosity (Ho) ranged from 0.033 to 0.048, and inbreeding coefficients (FIS) ranged from 0.834 to 0.887. The genetic differentiation index (FST) values among the three populations ranged from 0.056 to 0.106. This study provides an evaluation of the germplasm resources and genetic diversity of farmed L. vannamei, offering insights for the efficient management and sustainable utilization of this species’ germplasm resources. Full article

(This article belongs to the Special Issue Advances in Biological Research into Shrimps, Crabs and Lobsters)

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