Biology

14 pages, 2768 KiB

Open AccessArticle

Landmark-Based Wing Morphometrics for Three Holotrichia Beetle Species (Coleoptera, Scarabaeoidea)

by Pengliang Pan, Shibao Guo, Fangmei Zhang and Zhou Zhou

Biology 2025, 14(3), 317; https://doi.org/10.3390/biology14030317 - 20 Mar 2025

Viewed by 342

The scarab beetle is an herbivorous pest that causes considerable damage to various agricultural crops. The characteristics of the hind wings have rarely been utilized as indicators for species identification, particularly within the genus Holotrichia. To evaluate the potential of hind wing [...] Read more.

The scarab beetle is an herbivorous pest that causes considerable damage to various agricultural crops. The characteristics of the hind wings have rarely been utilized as indicators for species identification, particularly within the genus Holotrichia. To evaluate the potential of hind wing traits in species identification and gender differentiation, we extracted 25 landmarks from 125 samples of three beetle species (Holotrichia diomphalia, H. titanis, and H. oblita) using TPSDig2 v2.31, with each hind wing image analyzed three times. These landmarks were employed to analyze variations in wing size and shape among species and sexes, and a cross-validation test was conducted in MorphoJ v1.06 to assess classification accuracy. The results demonstrate that both female and male samples exhibit significant differences in wing size and shape variations across species, but not between sexes. Allometry accounts for 16.92% and 25.35% of total shape variation in females and males, separately. After correcting for allometric effects, classification accuracy improves for these beetles. From further analysis, it can be observed that female wings exhibit a wider and shorter morphology in comparison to the more slender and elongated wings of males. In terms of interspecific differences, H. oblita females displayed narrow and elongated wings, whereas H. diomphalia females had a more rectangular wing shape. Among males, the degree of wing narrowness decreased in the order of H. oblita, H. titanis, and H. diomphalia. Full article

(This article belongs to the Section Zoology)

► Show Figures

Figure 1

19 pages, 2528 KiB

Open AccessArticle

Bacterial Diversity at Himalayan Pink Salt Extraction Site

by Yasmeen Malik, Imran Ali, Ashif Sajjad, Luhuai Jing, Irfana Iqbal, Atiq ur Rehman, Toquier Azam and Xiaoming Chen

Biology 2025, 14(3), 316; https://doi.org/10.3390/biology14030316 - 20 Mar 2025

Viewed by 758

Abstract

Table salt, or sodium chloride, is extensively utilized in the culinary business as a flavoring agent, texture garnishing [...] Full article

► Show Figures

Figure 1

17 pages, 8501 KiB

Open AccessArticle

Unraveling the Prognostic Significance of BRCA1-Associated Protein 1 (BAP1) Expression in Advanced and Castrate-Resistant Prostate Cancer

by Norel Salut, Yaser Gamallat, Sima Seyedi, Joema Felipe Lima, Sunita Ghosh and Tarek A. Bismar

Biology 2025, 14(3), 315; https://doi.org/10.3390/biology14030315 - 20 Mar 2025

Viewed by 339

Abstract

Prostate cancer (PCa) is ranked as one of the top cancers affecting men in Western societies. BRCA1-associated protein 1 (BAP1) expression significance has been observed in various cancers, including prostate cancer. The search for prognostic models allowing better risk stratification and prediction of [...] Read more.

Prostate cancer (PCa) is ranked as one of the top cancers affecting men in Western societies. BRCA1-associated protein 1 (BAP1) expression significance has been observed in various cancers, including prostate cancer. The search for prognostic models allowing better risk stratification and prediction of disease progression in prostate cancer patients is still of major clinical need. Our data showed that nuclear BAP1 expression is the most associated with cancer clinical outcomes and other biomarkers. The data confirmed that decreased BAP1 nuclear expression is linked to aggressive tumors and poorer prognosis. We assessed BAP1 expression in 202 cases, including advanced and castrate-resistant PCa (CRPCa). Our data indicated low BAP1 nuclear expression in advanced and castrate-resistant disease (CRPCa). Furthermore, there was a significant difference between high and low BAP1 nuclear expression relative to the patient’s clinical outcome. In the present cohort, decreased BAP1 intensity exhibited a significant association with unfavorable overall survival (OS) (HR 2.31, CI: 1.38–3.86, p = 0.001) and cause-specific survival (CSS) (HR 2.44, CI: 1.24–4.78, p = 0.01). Additionally, this association was more pronounced when low BAP1 expression (high risk) was combined with other common PCa genomic alterations such as phosphatase and tensin homolog (PTEN) loss or ETS-related gene (ERG)-positive cases, resulting in higher unfavorable OS and CSS. Conversely, high BAP1 nuclear expression (moderate and high intensity) combined with no ERG expression or PTEN (moderate or high expression), p53 (wild type), and androgen receptor (AR) (low/moderate intensity) showed better association with higher survival rates. All these data support the notion that BAP1 functions as a tumor suppressor. Integrating BAP1 status with other genomic alterations offers a more comprehensive understanding of disease aggressiveness. Full article

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

► Show Figures

Figure 1

21 pages, 1812 KiB

Open AccessReview

Stem Cell-Based Approaches for Spinal Cord Injury: The Promise of iPSCs

by Chih-Wei Zeng

Biology 2025, 14(3), 314; https://doi.org/10.3390/biology14030314 - 20 Mar 2025

Viewed by 632

Abstract

Spinal cord injury (SCI) is a life-altering condition that leads to severe neurological deficits and significantly impacts patients’ quality of life. Despite advancements in medical care, current treatment options remain largely palliative, with limited ability to promote meaningful functional recovery. Induced pluripotent stem [...] Read more.

Spinal cord injury (SCI) is a life-altering condition that leads to severe neurological deficits and significantly impacts patients’ quality of life. Despite advancements in medical care, current treatment options remain largely palliative, with limited ability to promote meaningful functional recovery. Induced pluripotent stem cells (iPSCs) have emerged as a promising avenue for regenerative medicine, offering patient-specific, cell-based therapeutic potential for SCI repair. This review provides a comprehensive overview of recent advancements in iPSC-based approaches for SCI, detailing the strategies used to generate neural cell types, including neural progenitor cells, oligodendrocytes, astrocytes, and microglia, and their roles in promoting neuroprotection and regeneration. Additionally, we examine key preclinical and clinical studies, highlighting functional recovery assessments and discussing both standardized and debated evaluation metrics. Furthermore, we address critical challenges related to safety, tumorigenicity, immune response, survival, integration, and overcoming the inhibitory microenvironment of the injured spinal cord. We also explore emerging approaches in biomaterial scaffolds, gene editing, and rehabilitation strategies that may enhance the clinical applicability of iPSC-based therapies. By addressing these challenges and refining translational strategies, iPSC-based interventions hold significant potential to revolutionize SCI treatment and improve outcomes for affected individuals. Full article

(This article belongs to the Special Issue Stem Cells in Neurological Disorders: Challenges and Opportunities)

► Show Figures

Figure 1

10 pages, 1395 KiB

Open AccessCommentary

Generation of Current Good Manufacturing Practices-Grade Mesenchymal Stromal Cell-Derived Extracellular Vesicles Using Automated Bioreactors

by Elani F. Wiest and Abba C. Zubair

Biology 2025, 14(3), 313; https://doi.org/10.3390/biology14030313 - 20 Mar 2025

Viewed by 340

Abstract

Interest in Current Good Manufacturing Practices (cGMP)-grade extracellular vesicles (EVs) is expanding. Some obstacles in this new but rapidly growing field include a lack of standardization and scalability. This review focuses on automated biomanufacturing of EVs in conditioned media collected from cultured mesenchymal [...] Read more.

Interest in Current Good Manufacturing Practices (cGMP)-grade extracellular vesicles (EVs) is expanding. Some obstacles in this new but rapidly growing field include a lack of standardization and scalability. This review focuses on automated biomanufacturing of EVs in conditioned media collected from cultured mesenchymal stromal cells (MSCs). Different automated cell culture systems are discussed, including factors affecting EV quantity and quality, isolating EVs manufactured in an automated system, and validations needed. The ultimate goal when manufacturing cGMP-grade EVs is to identify a specific application and characterize the EV population in detail. This is achieved by validating every step of the process, choosing appropriate release criteria, and assuring batch-to-batch consistency. Due to the lack of standards in the field, it is critical to ensure that the cGMP-grade EVs meet FDA standards pertaining to identity, reproducibility, sterility, safety, purity, and potency. A closed-system automated bioreactor can be a valuable tool to generate cGMP-EVs in a scalable, economical, and reproducible manner. Full article

(This article belongs to the Special Issue Extracellular Vesicles and Pathophysiology)

► Show Figures

Figure 1

23 pages, 5220 KiB

Open AccessArticle

Probiotic Fermentation of Astragalus membranaceus and Raphani Semen Ameliorates Cyclophosphamide-Induced Immunosuppression Through Intestinal Short-Chain Fatty Acid-Dependent or -Independent Regulation of B Cell Function

by Yang Chen, Xiaoqing Wei, Binqi Rui, Yutong Du, Zengjie Lei, Xiujie Guo, Chaoran Wang, Donglin Yuan, Xiuli Wang, Ming Li, Binbin Hou and Yinhui Liu

Biology 2025, 14(3), 312; https://doi.org/10.3390/biology14030312 - 19 Mar 2025

Viewed by 346

Abstract

Probiotic fermentation can promote the release of more effective components from traditional Chinese medicines (TCMs). Astragalus membranaceus (Fisch.) Bunge (A. membranaceus) and Raphani Semen are TCMs that have gained attention for their immunoenhancing activities. This study aimed to investigate the effects [...] Read more.

Probiotic fermentation can promote the release of more effective components from traditional Chinese medicines (TCMs). Astragalus membranaceus (Fisch.) Bunge (A. membranaceus) and Raphani Semen are TCMs that have gained attention for their immunoenhancing activities. This study aimed to investigate the effects and underlying mechanisms of probiotic-fermented A. membranaceus and Raphani Semen (PROAS) in cyclophosphamide (CTX)-induced immunocompromised mice. Changes in the composition of A. membranaceus and Raphani Semen after fermentation by probiotic strains, including Bifidobacterium longum SD5219, Lactobacillus fermentum NCIMB5221, and Lactobacillus paracasei SD5219, were identified using high-performance liquid chromatography. The immunostimulatory effects and mechanisms of PROAS were evaluated in immunosuppressed mice 3 and 7 days after CTX treatment. Probiotic fermentation of TCMs resulted in changes in major bioactive components. PROAS supplementation effectively restored intestinal integrity in CTX-treated mice by upregulating the mRNA expression of the tight junction proteins. PROAS significantly ameliorated the reduction in the spleen index and number of B lymphocytes caused by CTX treatment and regulated the secretion of cytokines in serum and colon tissues. PROAS administration modulated gut microbial dysbiosis and short-chain fatty acid (SCFA) content in CTX-treated mice. These results suggest that PROAS enhances B lymphocyte function by increasing the regulation of intestinal microbiota to produce high levels of SCFA, repairs the intestinal barrier damage induced by CTX, and promotes intestinal mucosal immunity. Full article

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

► Show Figures

Graphical abstract

13 pages, 884 KiB

Open AccessArticle

Thermal Tolerance of Crassostrea (Magallana) ariakensis to Nuclear Plant Warm Water Discharges

by Lei Li, Longyu Liu, Cong Yan, Liang Wang, Yuanlv Ye, Lu Chen, Xiong Zou, Haijing Zhang, Mengni Zeng and Mei Jiang

Biology 2025, 14(3), 311; https://doi.org/10.3390/biology14030311 - 19 Mar 2025

Viewed by 198

Abstract

Nuclear power plants utilize great quantities of seawater to cool down, resulting in substantial warm water discharges that may affect nearby fisheries and marine ecosystems. This study focused on Crassostrea (Magallana) ariakensis, a commercially farmed oyster species along the southern [...] Read more.

Nuclear power plants utilize great quantities of seawater to cool down, resulting in substantial warm water discharges that may affect nearby fisheries and marine ecosystems. This study focused on Crassostrea (Magallana) ariakensis, a commercially farmed oyster species along the southern coast of China. To evaluate the thermal impacts of warm water discharges from nuclear power plants, indoor simulations replicated seasonal water temperature conditions near coastal facilities (26 °C in spring and autumn, 16 °C in winter, and 30 °C in summer). We conducted thermal tolerance static and dynamic experiments, along with a 51-day long-term experiment on suitable growth under different acclimation temperatures. The thermal effects of warm water discharges on C. ariakensis were systematically assessed through survival, growth, digestibility, and nutritional quality. The results showed that the discomfort temperature range of C. ariakensis was (48.6 ± 1.2)~(58.9 ± 3.0) °C, the critical thermal maxima (CTM) value range of C. ariakensis was (51.6 ± 1.4)~(61.2 ± 2.2) °C, and the incipient lethal temperature (ILT₅₀) of C. ariakensis was 45.61 °C, 53.71 °C, and 55.90 °C, respectively; all these values increased gradually with the rise of acclimation temperature. After the 51-day long-term experiment on suitable growth, the temperature increase of 1 °C, 2 °C and 4 °C did not affect the soft tissue wet weight, condition index, moisture content, and fat content of C. ariakensis, but the amylase activity in digestive gland tissue decreased in different temperature experimental groups. The experimental results show that the influence of temperature rise on the growth and physiological metabolism of C. ariakensis is limited. However, based on the normal habitat temperature in summer, the long-term effects of temperature rise caused by warm water discharges need to be paid attention to. Full article

(This article belongs to the Special Issue Global Fisheries Resources, Fisheries, and Carbon-Sink Fisheries)

► Show Figures

Figure 1

11 pages, 870 KiB

Open AccessCommunication

The Abundance of Harmful Rare Homozygous Variants in Children of Consanguineous Parents

by Sankar Subramanian

Biology 2025, 14(3), 310; https://doi.org/10.3390/biology14030310 - 19 Mar 2025

Viewed by 220

Abstract

The children born of consanguineous union were found to have a higher incidence of recessive genetic diseases than the offspring of unrelated parents. The reason for this was predicted to be the presence of more deleterious rare homozygous genetic variants in the former [...] Read more.

The children born of consanguineous union were found to have a higher incidence of recessive genetic diseases than the offspring of unrelated parents. The reason for this was predicted to be the presence of more deleterious rare homozygous genetic variants in the former compared to the latter. However, the magnitude of this difference is unknown. Using more than 2500 whole genomes, we show here that the individuals born of the union between double (paternal and maternal) first cousins had 20 times more deleterious rare homozygous single nucleotide variants (SNVs) than those who had unrelated parents. Furthermore, the children of first cousins had 10 times, and the children of second cousins had two times more of these SNVs compared to those present in the offspring of unrelated parents. Similar magnitudes of differences were found for the nonsynonymous deleterious rare homozygous SNVs (19, 10, and 2 times, respectively). In contrast, the differences in the number of deleterious low-frequency and common homozygous variants between the children of cousins and those of unrelated parents were 1–3 times and 1–7%, respectively. These results suggest that the offspring of consanguineous union could have a 20 times higher risk of recessive autosomal diseases caused by rare variants. Conversely, consanguinity appears to have little effect on the risk of common diseases. These findings have implications for future clinical research in identifying genetic variants associated with inherited diseases. Furthermore, the magnitude of the elevated risk revealed in this study could be useful in genetic counseling and for public health in creating awareness. Full article

(This article belongs to the Section Genetics and Genomics)

► Show Figures

Figure 1

24 pages, 3839 KiB

Open AccessArticle

Effects of Liposomal Vitamin C, Coenzyme Q10, and Bee Venom Supplementation on Bacterial Communities and Performance in Nile Tilapia (Oreochromis niloticus)

by Islam I. Teiba, Yasser S. A. Mazrou, Abeer H. Makhlouf, Nabil I. Elsheery, Sahar Hussein Abdalla Hekal, Nermeen M. Abu-Elala, Mahmoud Kamel Bakry, Emad H. El-Bilawy and Akram Ismael Shehata

Biology 2025, 14(3), 309; https://doi.org/10.3390/biology14030309 - 19 Mar 2025

Viewed by 412

Abstract

This experimental study evaluated the impacts of three nutraceuticals [liposomal vitamin C, coenzyme Q10 (CoQ10), and bee venom (BV)] on the physiological parameters of Nile tilapia (Oreochromis niloticus). A total of 360 fish (initial weight: 35.17 ± 0.22 g) were randomly [...] Read more.

This experimental study evaluated the impacts of three nutraceuticals [liposomal vitamin C, coenzyme Q10 (CoQ10), and bee venom (BV)] on the physiological parameters of Nile tilapia (Oreochromis niloticus). A total of 360 fish (initial weight: 35.17 ± 0.22 g) were randomly allocated to four isonitrogenous and isolipidic dietary treatments: a control group and three supplementation groups (liposomal vitamin C at 200 mg/kg, CoQ10 at 60 mg/kg, and BV at 4 mg/kg), with three replicates per treatment, and fish were fed to apparent satiation. After a 60-day feeding trial, comprehensive analyses revealed significant improvements in growth performance, digestive enzyme activities, immune responses, and antioxidant status across supplemented groups, with bee venom exhibiting the most pronounced effects. Nutraceutical supplementation enhanced gastrointestinal enzyme activities, modulated gut microbiota composition, and improved liver and intestinal histological characteristics. Immunological assessments demonstrated elevated lysozyme levels, bactericidal activity, and respiratory burst activity, while antioxidant markers showed increased superoxide dismutase, catalase, and glutathione peroxidase activities, accompanied by reduced malondialdehyde levels. These findings suggest that strategic nutraceutical supplementation can substantially optimize physiological functions and health parameters in Nile tilapia aquaculture. Full article

(This article belongs to the Special Issue Structure, Function and Diversity of Gut Microbes in Animals)

► Show Figures

Figure 1

12 pages, 2060 KiB

Open AccessArticle

Influence of Naturally Occurring Bacteria on Embryonic and Larval Development of Common Toad Tadpoles

by Olga Jovanović Glavaš, Ines Sviličić Petrić and Goran Palijan

Biology 2025, 14(3), 308; https://doi.org/10.3390/biology14030308 - 19 Mar 2025

Viewed by 198

Abstract

Amphibians, as the most threatened group of vertebrates, are the focus of investigation of various agents that could affect their fitness and survival. In this context, we examined the effects of naturally occurring bacteria and their combinations on the embryonic and larval development [...] Read more.

Amphibians, as the most threatened group of vertebrates, are the focus of investigation of various agents that could affect their fitness and survival. In this context, we examined the effects of naturally occurring bacteria and their combinations on the embryonic and larval development of common toad tadpoles (Bufo bufo). One egg string that was collected from the wild was disinfected in the lab and divided into short strings, each containing 20 eggs. These strings were exposed to three different control treatments, i.e., a sterile FETAX solution, water collected from the tadpoles’ native habitat, and sterilized habitat water, as well as to three different bacterial cultures isolated from habitat water (Bacillus sp., Mesobacillus sp.). We analyzed several morphometric variables (snout–vent length, total length, and weight), the energy budget by measuring body composition (proteins, carbohydrates, and lipids), and biomarker activity (acetylcholinesterase and lactate dehydrogenase). Our results indicate that the native microbial community had a negative effect on egg and tadpole development, as sterilized habitat water supported their highest development. Additionally, when grown in FETAX, pure bacterial cultures and their combinations decreased acetylcholinesterase activity but positively affected both tadpole size and energy budget. These findings suggest that bacteria can influence the larval development of common toads by modifying physiological traits. Future research should identify which microbes have beneficial or detrimental effects on amphibian development. Full article

► Show Figures

Graphical abstract

16 pages, 2610 KiB

Open AccessArticle

Hepatoprotective Effects of Glycyrrhiza glabra in Diabetic Male Rats: Addressing Liver Function, Oxidative Stress, and Histopathological Changes

by Abdulmajeed F. Alrefaei and Mohamed E. Elbeeh

Biology 2025, 14(3), 307; https://doi.org/10.3390/biology14030307 - 18 Mar 2025

Viewed by 329

Abstract

Diabetes mellitus is a chronic metabolic disorder that often leads to hepatic complications, including oxidative stress, inflammation, and structural damage, highlighting the need for effective hepatoprotective agents. Glycyrrhiza glabra (licorice), known for its bioactive compounds with medicinal properties, has gained attention as a [...] Read more.

Diabetes mellitus is a chronic metabolic disorder that often leads to hepatic complications, including oxidative stress, inflammation, and structural damage, highlighting the need for effective hepatoprotective agents. Glycyrrhiza glabra (licorice), known for its bioactive compounds with medicinal properties, has gained attention as a potential therapeutic option. This study investigated its hepatoprotective effects in a diabetic rat model. Diabetes was induced using streptozotocin, and animals were divided into four groups: a healthy control, a non-diabetic group treated with Glycyrrhiza glabra extract, an untreated diabetic group, and a diabetic group receiving daily doses of the extract. Liver function was assessed through serum enzyme levels (ALT, AST, and ALP), while oxidative stress markers, including malondialdehyde (MDA) and glutathione (GSH), were analyzed. Histological examination was conducted to evaluate inflammation, fibrosis, and fatty degeneration. Treatment with Glycyrrhiza glabra significantly improved liver function in diabetic rats, as evidenced by lower ALT, AST, and ALP levels compared to untreated diabetic rats (p < 0.05), suggesting hepatocyte protection through its antioxidant and anti-inflammatory properties. Favorable changes in oxidative stress markers were observed, with lower MDA levels indicating reduced lipid peroxidation and higher GSH activity reflecting enhanced antioxidant defense. Histological analysis confirmed these protective effects, showing reduced inflammation, diminished fatty degeneration, and overall structural improvements. These findings highlight the hepatoprotective potential of Glycyrrhiza glabra, suggesting it may be a promising therapeutic agent for managing hepatic complications associated with diabetes mellitus, though further research with larger sample sizes and mechanistic studies is needed for confirmation. Full article

(This article belongs to the Section Medical Biology)

► Show Figures

Figure 1

19 pages, 41489 KiB

Open AccessReview

Storytelling of Myocardial Biopsy

by Gaetano Thiene

Biology 2025, 14(3), 306; https://doi.org/10.3390/biology14030306 - 18 Mar 2025

Viewed by 279

Abstract

A biopsy involves the removal of a piece or an entire organ from a living patient. The former began with open heart surgery (surgical pathology) and the latter with the recipient heart in cardiac transplantation. Transvenous or transarterial catheterization is the current procedure [...] Read more.

A biopsy involves the removal of a piece or an entire organ from a living patient. The former began with open heart surgery (surgical pathology) and the latter with the recipient heart in cardiac transplantation. Transvenous or transarterial catheterization is the current procedure to performed endomyocardial biopsy with bioptome from the ventricles. This manoeuvre was first carried out by Werner Forssmann through a urological catheter in 1929, which he introduced into his radial left vein until it reached the RV. Then, in London in 1974, Richardson invented a new technique with a catheter via the right femoral vein, which he applied with success in patients with multiple myocardial diseases, both inflammatory and non-inflammatory. Subsequently, a transjugular endomyocardial biopsy was accomplished by Margaret Billingham to monitor heart rejection during cardiac transplantation. In the beginning, only histology for a light microscope, and rarely during electron microscopy, was employed. With the advent of molecular techniques and the discovery of polymerase chain reaction (PCR), molecular investigation became part of the gold standard for diagnosis involving EMB: histology, immunohistochemistry and molecular investigation, the latter in search of a viral cause. Nowadays, EMB is frequently employed in infiltrative (amyloidosis) and storage diseases (e.g., hemochromatosis and Fabry diseases). Diagnosis of myocarditis is now possible through Magnetic Cardiac Resonance (MCR), in place of BEM histology, thanks to oedema. With the help of ECMO, it is possible to allow the heart to rest, supporting its recovery from ejection fraction even in fulminant myocarditis. Cardiac transplantation with the pathological study of the recipient heart offers the opportunity to discover and study new diseases, like restrictive cardiomyopathy and a non-compacted left ventricle. Full article

(This article belongs to the Special Issue Experimental Biology 100 Years after the Foundation of the Italian Society: A Celebratory Special Issue)

► Show Figures

Figure 1

19 pages, 49846 KiB

Open AccessCase Report

Population Status of Sympatrically Breeding Skuas (Catharacta spp.) at Admiralty Bay, King George Island, Antarctica: A Case Report for 2020–2024

by Katarzyna Komarowska, Katarzyna Fudala, Michał Dziembowski, Alexander Hagge and Robert Józef Bialik

Biology 2025, 14(3), 305; https://doi.org/10.3390/biology14030305 - 17 Mar 2025

Viewed by 269

Abstract

The present study sets out to examine the status of sympatric populations of south polar (Catharacta maccormicki) (SPSs) and brown skuas (Catharacta antarctica) (BSs) at two sites on King George Island, Antarctica. The study sites were designated as Important [...] Read more.

The present study sets out to examine the status of sympatric populations of south polar (Catharacta maccormicki) (SPSs) and brown skuas (Catharacta antarctica) (BSs) at two sites on King George Island, Antarctica. The study sites were designated as Important Bird and Biodiversity Areas (IBAs) and were monitored for three (for Point Hennequin (PH)) and four (for West Admiralty Bay (WAB)) consecutive breeding seasons, concluding with the 2023/24 season. The most recently reported data from these areas are from the 2004/05 season, and the data presented herein allow both areas to be assessed in the context of their IBA and Antarctic Specially Protected Area values. The mean number of total pairs for the investigated seasons for WAB was 67 ± 7, while for PH, it was 157 ± 18. The number of pairs of SPSs at PH and WAB justifies the positive evaluation of the areas as IBAs based on global designation criterion A4 proposed jointly by BirdLife International and the Scientific Committee on Antarctic Research (SCAR). PH is of particular interest, as it has been determined that at least 2.3% of the global population of SPSs, estimated by BirdLife International to be between 6000 and 15,000 adult individuals, breeds at this site. The expansion of both IBA boundaries is also recommended based on this study. Full article

(This article belongs to the Special Issue Bird Biology and Conservation)

► Show Figures

Figure 1

19 pages, 4936 KiB

Open AccessArticle

Evaluating Habitat Suitability for the Endangered Sinojackia xylocarpa (Styracaceae) in China Under Climate Change Based on Ensemble Modeling and Gap Analysis

by Chenye Hu, Hang Wu and Guangfu Zhang

Biology 2025, 14(3), 304; https://doi.org/10.3390/biology14030304 - 17 Mar 2025

Viewed by 241

Abstract

Climate change has a profound effect on plant growth and distribution on a global scale [...] Full article

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

► Show Figures

Figure 1

21 pages, 980 KiB

Open AccessReview

Diffusible Signal Factors and Xylella fastidiosa: A Crucial Mechanism Yet to Be Revealed

by Letizia Portaccio, Marzia Vergine, Mariarosaria De Pascali, Luigi De Bellis and Andrea Luvisi

Biology 2025, 14(3), 303; https://doi.org/10.3390/biology14030303 - 17 Mar 2025

Viewed by 677

Abstract

Xylella fastidiosa (Xf) is a xylem-limited Gram-negative phytopathogen responsible for severe plant diseases globally. Colonization and dissemination on host plants are regulated primarily by diffusible signal factors (DSFs) and quorum sensing (QS) molecules regulating biofilm formation, motility, and virulence factor synthesis. [...] Read more.

Xylella fastidiosa (Xf) is a xylem-limited Gram-negative phytopathogen responsible for severe plant diseases globally. Colonization and dissemination on host plants are regulated primarily by diffusible signal factors (DSFs) and quorum sensing (QS) molecules regulating biofilm formation, motility, and virulence factor synthesis. DSFs play a critical role in the transition of bacteria from adhesion to dispersal phases, influencing plant infection and transmission by vector. Because of Xf’s host range (over 550 plant species), effective containment strategies are highly demanded. In this review, we discuss the molecular mechanism of DSF-mediated signalling in Xf, especially concerning its role in pathogenicity and adaptation. Moreover, we shed light on innovative approaches to manage Xf, including quorum-quenching (QQ) strategies and transgenic plants targeted to disrupt QS pathways. Improved knowledge of DSF interactions with host plants and bacterial communities could provide an entry point for novel, sustainable disease control strategies to decrease Xf’s agricultural and ecological impact. Full article

(This article belongs to the Special Issue Biological Control and Molecular Biology of Bacterial Plant Diseases)

► Show Figures

Figure 1

18 pages, 5087 KiB

Open AccessArticle

Effects of Difenoconazole on Tubifex tubifex: Antioxidant Activity, Insights from GUTS Predictions, and Multi-Biomarker Analysis

by Subhajit Saha, Shubhajit Saha, Paolo Pastorino and Nimai Chandra Saha

Biology 2025, 14(3), 302; https://doi.org/10.3390/biology14030302 - 17 Mar 2025

Cited by 1 | Viewed by 343

Abstract

The increasing demand for agricultural products has led to a rise in pesticide use, resulting in the pollution of aquatic habitats and raising significant health concerns for both aquatic life and humans. Difenoconazole, a triazole fungicide, is becoming increasingly popular in agriculture, yet [...] Read more.

The increasing demand for agricultural products has led to a rise in pesticide use, resulting in the pollution of aquatic habitats and raising significant health concerns for both aquatic life and humans. Difenoconazole, a triazole fungicide, is becoming increasingly popular in agriculture, yet its effects on non-target organisms, such as annelids, are not well understood. This study aimed to investigate the toxicological effects of difenoconazole and assess its potential impact on toxicity biomarkers, using Tubifex tubifex as a model organism, to better understand the ecotoxicity of difenoconazole on freshwater annelids. The 96-h LC₅₀ value of difenoconazole was determined to be 2.68 mg/L. Sublethal concentrations (10% and 20% of the 96-h LC₅₀ value; 0.268 and 0.536 mg/L, respectively) caused significant changes in the activities of oxidative stress enzymes. A concentration- and time-dependent decrease in the activities of superoxide dismutase (SOD), catalase (CAT), and glutathione transferase (GST) was observed compared to control organisms. Additionally, malondialdehyde (MDA) concentrations increased throughout the exposure period. An Integrated Biomarker Response (IBR) assessment was used to characterize and illustrate the impact of difenoconazole on T. tubifex. In conclusion, exposure to this fungicide appears to reduce the survival rate of T. tubifex at acute levels and disrupt its normal behavioral patterns. Moreover, it alters oxidative stress enzyme levels during sublethal exposure. Long-term exposure to the fungicide could potentially have population-level consequences, including a reduction in the number of individuals within a population. Full article

(This article belongs to the Section Toxicology)

► Show Figures

Figure 1

10 pages, 202 KiB

Open AccessArticle

Detection of Genetic Variants in Thai Population by Trio-Based Whole-Genome Sequencing Study

by Patcharin Boonin, Sommon Klumsathian, Nareenart Iemwimangsa, Insee Sensorn, Angkana Charoenyingwatana, Wasun Chantratita and Takol Chareonsirisuthigul

Biology 2025, 14(3), 301; https://doi.org/10.3390/biology14030301 - 17 Mar 2025

Viewed by 475

Abstract

This trio-based whole-genome sequencing (WGS) study enhances the accuracy of variant detection by leveraging parental genotypes, which facilitates the identification of de novo mutations and population-specific variants. Nonetheless, the comprehensive genetic variation data of the Thai population remain limited, posing challenges to advancing [...] Read more.

This trio-based whole-genome sequencing (WGS) study enhances the accuracy of variant detection by leveraging parental genotypes, which facilitates the identification of de novo mutations and population-specific variants. Nonetheless, the comprehensive genetic variation data of the Thai population remain limited, posing challenges to advancing personalized medicine and population-based screening strategies. We establish the genetic variation information of a healthy Thai population by analyzing the sequences of 40 trios, yielding 120 whole genomes (excluding offspring). The resulting dataset encompasses 20.2 million variants, including 1.1 million novel and 19.1 million known variants. Within this dataset, we identify 169 pathogenic variants, of which 56 are classified as rare and 87 are absent from the ClinVar database as of version 2023. These pathogenic variants, particularly the rare and de novo mutations, will likely be of significant interest for genetic association studies. Notably, one pathogenic variant linked to a de novo mutation is found in the SF3B2 gene, which is associated with craniofacial microsomia. With its innovative methodology and comprehensive dataset, our trio-based whole-genome sequencing study provides an invaluable representation of the genetic variations in the Thai population. These data provide a critical foundation for further analyses of the pathogenic variants related to human disease phenotypes in genetic association studies. Full article

(This article belongs to the Section Bioinformatics)

22 pages, 14960 KiB

Open AccessArticle

Utilization of Algal Biochar for Biopassivation of Copper Sulfide Tailings to Reduce Acid Mine Drainage

by Zhiyuan Peng, Can Liu, Yuhang Fu, Hongwei Liu, Hongchang Liu and Hongpeng Cao

Biology 2025, 14(3), 300; https://doi.org/10.3390/biology14030300 - 16 Mar 2025

Viewed by 286

Abstract

Acid mine drainage (AMD) has serious impacts on the environment. To inhibit the generation of AMD from copper sulfide tailings at the source, in this paper, a strategy is developed for promoting the biopassivation of copper sulfide tailings using algal biochar, and the [...] Read more.

Acid mine drainage (AMD) has serious impacts on the environment. To inhibit the generation of AMD from copper sulfide tailings at the source, in this paper, a strategy is developed for promoting the biopassivation of copper sulfide tailings using algal biochar, and the effects of the pyrolysis temperature and concentration of algal biochar on the passivation efficiency and stability are investigated. The results reveal that the introduction of algal biochar during the biopassivation of copper sulfide tailings significantly enhances the tailings passivation effect of the tested Acidithiobacillus ferrooxidans strain and greatly stabilizes the formed passivation layer. Algal biochar prepared with a pyrolysis temperature of 300 °C and applied at a concentration of 6 g/L not only optimizes biopassivation but also significantly improves the stability of the passivation layer. The complex mechanisms of algal biochar in this system include regulating the pH and oxidation‒reduction potential of the reaction system, effectively adsorbing microbial cells, efficiently aggregating metal cations in solution, stimulating the synthesis of extracellular polymeric substances, and accelerating electron transfer. This research offers a novel method for the benign treatment of copper sulfide tailings and resource utilization of algae. Full article

► Show Figures

Figure 1

34 pages, 4139 KiB

Open AccessReview

Mutual Interactions Between Microbiota and the Human Immune System During the First 1000 Days of Life

by Muy Heang Tang, Ishbel Ligthart, Samuel Varga, Sarah Lebeer, Frans J. van Overveld and Ger T. Rijkers

Biology 2025, 14(3), 299; https://doi.org/10.3390/biology14030299 - 16 Mar 2025

Viewed by 1499

Abstract

The development of the human immune system starts during the fetal period in a largely, but probably not completely, sterile environment. During and after birth, the immune system is exposed to an increasingly complex microbiota. The first microbiota encountered during passage through the [...] Read more.

The development of the human immune system starts during the fetal period in a largely, but probably not completely, sterile environment. During and after birth, the immune system is exposed to an increasingly complex microbiota. The first microbiota encountered during passage through the birth canal colonize the infant gut and induce the tolerance of the immune system. Transplacentally derived maternal IgG as well as IgA from breast milk protect the infant from infections during the first 100 days, during which the immune system further develops and immunological memory is formed. The Weaning and introduction of solid food expose the immune system to novel (food) antigens and allow for other microbiota to colonize. The cells and molecules involved in the mutual and intricate interactions between microbiota and the developing immune system are now beginning to be recognized. These include bacterial components such as polysaccharide A from Bacteroides fragilis, as well as bacterial metabolites such as the short-chain fatty acid butyrate, indole-3-aldehyde, and indole-3-propionic acid. All these, and probably more, bacterial metabolites have specific immunoregulatory functions which shape the development of the human immune system during the first 1000 days of life. Full article

(This article belongs to the Section Immunology)

► Show Figures

Graphical abstract

16 pages, 2968 KiB

Open AccessArticle

Achromatic Markings as Male Quality Indicators in a Crepuscular Bird

by Richard Schnürmacher, Rhune Vanden Eynde, Jitse Creemers, Eddy Ulenaers, Marcel Eens, Ruben Evens and Michiel Lathouwers

Biology 2025, 14(3), 298; https://doi.org/10.3390/biology14030298 - 16 Mar 2025

Viewed by 761

Abstract

Secondary sexual traits, such as specific body parts or colouration, play an important role in mating interactions. It has been proposed that they function as quality indicators driven by sexual selection. In birds, much attention has been paid to the study of feather [...] Read more.

Secondary sexual traits, such as specific body parts or colouration, play an important role in mating interactions. It has been proposed that they function as quality indicators driven by sexual selection. In birds, much attention has been paid to the study of feather pigmentation, especially in diurnal passerines. However, recent research demonstrates that structural achromatic colours are likely to be of similar importance for communication, especially for species inhabiting poorly lit environments and that are active at night. Using 15 years of capture–recapture data from a long-term study on adult European Nightjars (Caprimulgus europaeus), we investigated the role of males’ white tail and wing markings as secondary sexual traits. We show that the inter-individual variation in marking size exceeds that of the other morphometric variables, suggesting that wing and tail markings could be subject to sexual selection. Older males, individuals with a higher body condition index, and long-term territory holders had larger markings, while these effects were particularly pronounced in terminal tail feather markings. The importance of markings for signalling is likely related to their observed use in social displays. Pronounced site differences in tail marking sizes and annual variation suggest environmental factors acting on the ornaments that remain to be further examined. Full article

(This article belongs to the Section Evolutionary Biology)

► Show Figures

Figure 1

13 pages, 1099 KiB

Open AccessCommunication

Feathers of Grace: The “After You” Gesture in Japanese Tits

by Sergio Da Silva and Raul Matsushita

Biology 2025, 14(3), 297; https://doi.org/10.3390/biology14030297 - 16 Mar 2025

Viewed by 499

Abstract

A recent study found evidence of symbolic gesture use in Japanese tits (Parus minor). The study reveals how these birds use wing-fluttering movements to transmit an “after you” directive to their partners, implying a degree of cognitive skill previously thought to [...] Read more.

A recent study found evidence of symbolic gesture use in Japanese tits (Parus minor). The study reveals how these birds use wing-fluttering movements to transmit an “after you” directive to their partners, implying a degree of cognitive skill previously thought to be unique to humans and great apes. If confirmed, this research contradicts long-held notions about animal communication by proving that Japanese tits not only participate in intricate vocal communications, which can comprise phrases with specific grammatical rules, but also use body language as a form of engagement. Here, we evaluate this claim by inspecting the data and utilizing bootstrapping to expand the sample size. We find a large variation in how frequently the “after you” gesture is employed in different bootstrap samples, suggesting that while the gesture is a consistent behavior, its frequency can vary significantly. Moreover, the timing of the male’s response to the female’s gesture can fluctuate, though the response itself appears to be a stable phenomenon. Beyond evaluating the bootstrapping technique, we employ causal inference to examine whether wing fluttering by female Japanese tits leads to a quicker response by males, entering the nest more swiftly. The analysis supports this hypothesis, suggesting that wing fluttering functions as an effective communicative gesture in this species, influencing male nesting behavior. However, because the frequency of the “after you” gesture varied greatly, especially in light of potential cognitive and other biases influencing the study, this bold claim should be taken with caution. Full article

(This article belongs to the Special Issue Bird Biology and Conservation)

► Show Figures

Figure 1

13 pages, 1978 KiB

Open AccessArticle

How to Define Spacing Among Forest Trees to Mitigate Competition: A Technical Note

by Khodabakhsh Zabihi, Vivek Vikram Singh, Aleksei Trubin, Nataliya Korolyova and Rastislav Jakuš

Biology 2025, 14(3), 296; https://doi.org/10.3390/biology14030296 - 15 Mar 2025

Viewed by 476

Abstract

Establishing an optimum range of inter-species spacing that reduces competition among trees and mitigates the effects of drought is a critical yet complex challenge in forest management. Stand density plays a crucial role in forest functioning by regulating resource allocation within individual trees. [...] Read more.

Establishing an optimum range of inter-species spacing that reduces competition among trees and mitigates the effects of drought is a critical yet complex challenge in forest management. Stand density plays a crucial role in forest functioning by regulating resource allocation within individual trees. Higher stand densities have been shown to reduce sap velocities, indicating intensified competition for water and other resources. However, determining the precise spacing that minimizes competition while maintaining ecosystem balance remains unclear. In this study, conducted in temperate Norway spruce forests at an altitude range of 400–500 m in the Czech Republic, we propose a novel technique to define tree spacing that reduces competitive interactions. We used xylem sap flow residuals of an ordinary least square (OLS) regression model to filter out the effects of elevation and diameter at breast height (DBH) on field-measured sap flow for 101 planted Norway spruce trees with a DBH range of 40 ± 5 cm (≈90–100 years old). The model residuals allowed us to account for the most important driver of sap flow variability: tree density and its underlying effects on individual tree traits. To minimize the confounding effects of temporal and spatial variability, we used twelve consecutive daily measurements of sap flow (6 a.m. to 6 p.m.) taken at the start of the growing season. By constructing an experimental variogram, we quantified sap flow variability as a function of tree spacing. The results showed a steady sap flow pattern at tree densities of 12, 11, and 10 trees per 314 m² (equivalent to 350 ± 32 trees per hectare), corresponding to inter-tree spacing measurements of 5.12 m, 5.34 m, and 5.60 m, respectively. These findings suggest that when the N number of trees (median) per unit area (A) is in equilibrium with resource availability, increasing or decreasing the n number of trees may not significantly change competition levels (A; f(A) = N ± n). The size or deviation of n depends on the area to define the minimum and maximum thresholds or tolerance capacity for the number of trees allowed to be in the area. This technique—using a variogram of sap flow residuals to determine tree spacing—can be periodically applied, such as every 10–15 years, and adapted for different elevation gradients (e.g., within 100 m intervals). It offers a practical tool for forest managers and policymakers, guiding thinning and planting strategies to enhance forest resilience in the face of water-stress conditions. Full article

(This article belongs to the Special Issue Young Researchers in Plant Sciences)

► Show Figures

Figure 1

29 pages, 3987 KiB

Open AccessReview

Tryptophan-2,3-Dioxygenase as a Therapeutic Target in Digestive System Diseases

by Zhengsen Wang, Xianxian Xie, Yu Xue and Yixuan Chen

Biology 2025, 14(3), 295; https://doi.org/10.3390/biology14030295 - 15 Mar 2025

Viewed by 547

Abstract

Tryptophan (Trp) is an essential amino acid that must be acquired exclusively through dietary intake. The metabolism of tryptophan plays a critical role in maintaining immune homeostasis and tolerance, as well as in preventing excessive inflammatory responses. Tryptophan-2,3-dioxygenase (TDO2) is a tetrameric heme [...] Read more.

Tryptophan (Trp) is an essential amino acid that must be acquired exclusively through dietary intake. The metabolism of tryptophan plays a critical role in maintaining immune homeostasis and tolerance, as well as in preventing excessive inflammatory responses. Tryptophan-2,3-dioxygenase (TDO2) is a tetrameric heme protein and serves as one of the pivotal rate-limiting enzymes in the first step of tryptophan metabolism. Dysregulation of TDO2 expression has been observed in various digestive system diseases, encompassing those related to the oral cavity, esophagus, liver, stomach, pancreas, and colon and rectum. Digestive system diseases are the most common clinical diseases, with complex clinical manifestations and interrelated symptoms, and have become a research hotspot in the field of medicine. Studies have demonstrated that aberrant TDO2 expression is closely associated with various clinical manifestations and disease outcomes in patients with digestive system disorders. Consequently, TDO2 has garnered increasing recognition as a promising therapeutic target for digestive system diseases in recent years, attracting growing attention. This article provides a brief overview of the role of TDO2 in the tryptophan pathway, emphasizing its significant involvement in diseases of the digestive system. Strategies targeting TDO2 through specific inhibitors suggest considerable promise in enhancing therapeutic outcomes for digestive diseases. Thus, this review concludes by discussing recent advancements in the development of TDO2 inhibitors. We believe that targeted inhibition of TDO2 combined with immunotherapy, the screening of a large number of natural products, and the assistance of artificial intelligence in drug design will be important directions for developing more effective TDO2 inhibitors and improving treatment outcomes in the future. Full article

(This article belongs to the Special Issue Pathophysiology of Chronic Inflammatory Diseases)

► Show Figures

Figure 1

13 pages, 3042 KiB

Open AccessArticle

Mucus Trail Proteins May Infer Reproductive Readiness for Land Snails

by Kate R. Ballard, Tomer Ventura, Tianfang Wang, Abigail Elizur and Scott F. Cummins

Biology 2025, 14(3), 294; https://doi.org/10.3390/biology14030294 - 14 Mar 2025

Viewed by 455

Abstract

Mucus trails are defining features of the class Gastropoda, which includes snails and slugs. While several studies have shown that mucus trails are followed by conspecifics, the detectable elements in the mucus have not been clearly identified. This is particularly relevant during periods [...] Read more.

Mucus trails are defining features of the class Gastropoda, which includes snails and slugs. While several studies have shown that mucus trails are followed by conspecifics, the detectable elements in the mucus have not been clearly identified. This is particularly relevant during periods of reproduction, whereby conspecific cues are critical for mate finding. A better understanding of the mucus’ molecular components, including proteins differentially represented between the reproductive and non-reproductive stages, could aid the development of novel eco-friendly biocontrol approaches. In this study, we investigated the mucus trails of the globally invasive land snail Cernuella virgata, which has become a significant pest to the grain industry. We conducted a comparative proteomic analysis of the non-reproductive- and reproductive-stage trail mucus, whereby 533 proteins were identified, including 191 and 226 stage-exclusive proteins, respectively. Subsequent comparative tissue transcriptomic analysis found that the albumen gland, which is the key gland for the preparation of fertilized eggs prior to egg laying, was the primary source of secreted proteins present in the reproductive stage trail mucus. This included leukocyte elastase inhibitors, achacin, perlucin, and other proteins without any known function (uncharacterized). In summary, our results strongly implicate the albumen gland as a source for snail trail mucus proteins deposited during the reproductive stage, suggesting a mechanism that could convey their reproductive status to conspecifics. Further research testing their bioactivity related to chemical communication is paramount and may assist in the development of a novel biocontrol strategy. Full article

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

► Show Figures

Figure 1

28 pages, 5433 KiB

Open AccessArticle

Endophytic Diversity in Vitis vinifera with Different Vineyard Managements and Vitis sylvestris Populations from Northern Italy: A Comparative Study of Culture-Dependent and Amplicon Sequencing Methods

by Simona Pizzi, Angela Conti, Alessandra Di Canito, Debora Casagrande Pierantoni, Roberto Foschino, Mathabatha Evodia Setati and Ileana Vigentini

Biology 2025, 14(3), 293; https://doi.org/10.3390/biology14030293 - 14 Mar 2025

Viewed by 470

Abstract

This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, [...] Read more.

This study aimed to investigate the endophytic microbial populations associated with wild and domesticated grapevines using both culture-based and culture-independent methods. Through culture-based methods, 148 endophytes were identified. The dominant fungal species included Aureobasidium pullulans, Alternaria alternata, and Cladosporium allicinum, while predominant bacterial species were Ralstonia pikettii, Nocardia niigatensis, and Sphingomonas echinoides. Culture-independent methods employed metagenomic techniques to explore microbial biodiversity, focusing on targeted amplification of bacterial 16S rRNA as well as fungal ITS and 26S rRNA gene regions. The main bacterial species identified included Halomonas sp., Sphingomonas sp. and Massilia sp., whereas the fungal population was dominated by Cladosporium sp., Malassezia sp. and Mucor sp. The findings revealed that vineyard management practices did not lead to statistically significant variations in microbial communities. The consistent presence of these genera across all samples suggests that they are stable components of the grapevine endophytic microbiota, remaining relatively unaffected by external environmental factors. Full article

► Show Figures

Figure 1

16 pages, 5274 KiB

Open AccessArticle

Modulatory Effects of the Recombinant Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Spike S1 Subunit Protein on the Phenotype of Camel Monocyte-Derived Macrophages

by Jamal Hussen, Abdullah I. A. Al-Mubarak, Turke Shawaf, Khulud Bukhari and Khaled R. Alkharsah

Biology 2025, 14(3), 292; https://doi.org/10.3390/biology14030292 - 13 Mar 2025

Viewed by 620

Abstract

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging zoonotic pathogen with different pathogenesis in humans and camels. The mechanisms behind the higher tolerance of camels to MERS-CoV infection are still unknown. Monocytes are innate myeloid cells that are able, depending on the [...] Read more.

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging zoonotic pathogen with different pathogenesis in humans and camels. The mechanisms behind the higher tolerance of camels to MERS-CoV infection are still unknown. Monocytes are innate myeloid cells that are able, depending on the local stimulation in their microenvironment, to differentiate into different functional subtypes of macrophages with an impact on the adaptive immune response. Several in vitro protocols have been used to induce the differentiation of monocyte-derived macrophages (MDMs) in human and several veterinary species. Such protocols are not available for camel species. In the present study, monocytes were separated from camel blood and differentiated in vitro in the presence of different stimuli into MDM. Camel MDMs generated in the presence of a combined stimulation of monocytes with LPS and GM-CSF resulted in the development of an M1 macrophages phenotype with increased abundance of the antigen-presentation receptor MHCII molecules and a decreased expression of the scavenger receptor CD163. The expression pattern of the cell markers CD163, CD14, CD172a, CD44, and CD9 on MDM generated in the presence of the MERS-CoV S1 protein revealed similarity with M-CSF-induced MDM, suggesting the potential of the MERS-CoV S1 protein to induce an M2 macrophages phenotype. Similarly to the effect of M-CSF, MERS-CoV-S protein-induced MDMs showed enhanced phagocytosis activity compared to non-polarized or LPS/GM-CSF-polarized MDMs. Collectively, our study represents the first report on the in vitro generation of monocyte-derived macrophages (MDMs) in camels and the characterization of some phenotypic and functional properties of camel MDM under the effect of M1 and M2 polarizing stimuli. In addition, the results suggest a polarizing effect of the MERS-CoV S1 protein on camel MDMs, developing an M2-like phenotype with enhanced phagocytosis activity. To understand the clinical relevance of these in vitro findings on disease pathogenesis and camel immune response toward MERS-CoV infection, further studies are required. Full article

(This article belongs to the Special Issue Zoonotic Diseases)

► Show Figures

Figure 1

16 pages, 5926 KiB

Open AccessArticle

Imbalance of Bile Acids Metabolism Mediated by Gut Microbiota Contributed to Metabolic Disorders in Diabetic Model Mice

by Hongwang Dong, Xinguo Liu, Ge Song, Wenting Peng, Xihan Sun, Wei Fang and Wentao Qi

Biology 2025, 14(3), 291; https://doi.org/10.3390/biology14030291 - 13 Mar 2025

Viewed by 569

Abstract

Type 2 diabetes (T2D) is a chronic disease prevalent in the world, accompanied by a variety of diseases, endangering human health and safety. Bile acids (BAs) play an important role in the regulation of host glucose and lipid metabolism homeostasis, and are strictly [...] Read more.

Type 2 diabetes (T2D) is a chronic disease prevalent in the world, accompanied by a variety of diseases, endangering human health and safety. Bile acids (BAs) play an important role in the regulation of host glucose and lipid metabolism homeostasis, and are strictly regulated by gut microbiota. However, the relationship between key BAs, BAs transporters and signaling, as well as gut microbiota, and host metabolism in T2D remains elusive. In this study, 9-week-old db/db mice were used as diabetes model (db/db group, n = 10), and their wild-type (wt) littermates of same age were used as the healthy control (CON group, n = 10). After 8 weeks of feeding, the BA profiles and microbial composition in the colon, and gene expression level of BA regulatory factors were analyzed in the db/db and CON groups to explore the underlying mechanisms of T2D. Compared with healthy mice, the body weight, blood glucose and lipid levels of db/db mice were significantly increased. The concentrations of total BAs, primary BAs, conjugated BAs and non-12α–hydroxylated BAs (non-12–OH BAs) were significantly decreased, while Deoxycholic acid (DCA) in secondary BAs was increased in db/db group. Compared with wt mice, the synthesis of BAs in the liver was transformed from the alternative pathway to the classical pathway, and hepatic BAs transporters (NTCP, BSEP, MRP2, OATP–1 and OSTβ) and receptors (FXR and TGR5) were significantly down-regulated in the db/db mice. In the colon, the mRNA level of FXR was up-regulated, while TGR5 was down-regulated. The diabetic (db/db) mice presented a changed gut microbiota composition, including an increased abundance of secondary BAs-producing bacteria, Escherichia–Shigella, and a decreased the abundance of Akkermansia, which are involved in the synthesis of non-12–OH BAs. We further found that the reduced BA types in db/db mice were negatively correlated with metabolic-disorder-related indicators, while an increased DCA level had the opposite correlation. Our results shed light into how the imbalance of BAs’ metabolism mediated by intestinal flora may be potential mechanisms of T2D. Full article

(This article belongs to the Special Issue Metabolic Interactions between the Gut Microbiome and Host)

► Show Figures

Graphical abstract

3 pages, 140 KiB

Open AccessEditorial

Editorial for the Special Issue “Neurobiology of Invertebrates Inaccessible from Mammalian Studies”

by Etsuro Ito and Kengo Namiki

Biology 2025, 14(3), 290; https://doi.org/10.3390/biology14030290 - 13 Mar 2025

Viewed by 314

Abstract

This Special Issue features five excellent papers on invertebrate neurobiology [...] Full article

(This article belongs to the Special Issue Neurobiology of Invertebrates Inaccessible from Mammalian Studies)

16 pages, 3212 KiB

Open AccessArticle

Unraveling the Evolutionary Patterns of Genus Frontonia: An Integrative Approach with Morphological and Molecular Data

by Ratih Kusuma Wardani, Ragib Ahsan and Mann Kyoon Shin

Biology 2025, 14(3), 289; https://doi.org/10.3390/biology14030289 - 13 Mar 2025

Viewed by 456

Abstract

Ciliates of the genus Frontonia have been extensively studied to resolve their phylogenetic and evolutionary history, but challenges remain. This study used molecular analyses of SSU rRNA genes, phylogenetic tree reconstruction, molecular dating, and diversification analysis, together with ancestral state reconstruction of morphological [...] Read more.

Ciliates of the genus Frontonia have been extensively studied to resolve their phylogenetic and evolutionary history, but challenges remain. This study used molecular analyses of SSU rRNA genes, phylogenetic tree reconstruction, molecular dating, and diversification analysis, together with ancestral state reconstruction of morphological traits and habitat preferences. Data included newly sequenced Korean species, GenBank records and published morphological information. Phylogenetic trees revealed paraphyly within Frontonia, identifying four groups that emerged in the Mesozoic era: Group I (~172 mya), Group II (~83 mya), Group III (~115 mya), and Group IV (~190 mya), with a common ancestor dating to ~420 mya in the Palaeozoic era. Diversification analysis revealed higher extinction rates (0.826 and 0.613 species/year) than speciation rates (0.011 and 0.016 species/year). Morphological evolution showed habitat adaptation and plasticity, with habitat transitions unrelated to contractile vacuolar traits. The SSU rRNA gene polymorphism likely contributed to the paraphyletic state of Frontonia. These results highlight the complex evolutionary patterns of the genus, shaped by genetic diversity, morphology, and environmental constraints. Full article

(This article belongs to the Section Evolutionary Biology)

► Show Figures

Figure 1

18 pages, 3483 KiB

Open AccessArticle

Enhancing Single-Cell and Bulk Hi-C Data Using a Generative Transformer Model

by Ruoying Gao, Thomas N. Ferraro, Liang Chen, Shaoqiang Zhang and Yong Chen

Biology 2025, 14(3), 288; https://doi.org/10.3390/biology14030288 - 12 Mar 2025

Viewed by 708

Abstract

The 3D organization of chromatin in the nucleus plays a critical role in regulating gene expression and maintaining cellular functions in eukaryotic cells. High-throughput chromosome conformation capture (Hi-C) and its derivative technologies have been developed to map genome-wide chromatin interactions at the population [...] Read more.

The 3D organization of chromatin in the nucleus plays a critical role in regulating gene expression and maintaining cellular functions in eukaryotic cells. High-throughput chromosome conformation capture (Hi-C) and its derivative technologies have been developed to map genome-wide chromatin interactions at the population and single-cell levels. However, insufficient sequencing depth and high noise levels in bulk Hi-C data, particularly in single-cell Hi-C (scHi-C) data, result in low-resolution contact matrices, thereby limiting diverse downstream computational analyses in identifying complex chromosomal organizations. To address these challenges, we developed a transformer-based deep learning model, HiCENT, to impute and enhance both scHi-C and Hi-C contact matrices. Validation experiments on large-scale bulk Hi-C and scHi-C datasets demonstrated that HiCENT achieves superior enhancement effects compared to five popular methods. When applied to real Hi-C data from the GM12878 cell line, HiCENT effectively enhanced 3D structural features at the scales of topologically associated domains and chromosomal loops. Furthermore, when applied to scHi-C data from five human cell lines, it significantly improved clustering performance, outperforming five widely used methods. The adaptability of HiCENT across different datasets and its capacity to improve the quality of chromatin interaction data will facilitate diverse downstream computational analyses in 3D genome research, single-cell studies and other large-scale omics investigations. Full article

(This article belongs to the Special Issue Artificial Intelligence Research for Complex Biological Systems)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Biology, Volume 14, Issue 3 (March 2025) – 99 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI