Biology

24 pages, 6245 KiB

Open AccessArticle

An In Silico Design of a Vaccine against All Serotypes of the Dengue Virus Based on Virtual Screening of B-Cell and T-Cell Epitopes

by Hikmat Ullah, Shaukat Ullah, Jinze Li, Fan Yang and Lei Tan

Biology 2024, 13(9), 681; https://doi.org/10.3390/biology13090681 - 30 Aug 2024

Abstract

Dengue virus poses a significant global health challenge, particularly in tropical and subtropical regions. Despite the urgent demand for vaccines in the control of the disease, the two approved vaccines, Dengvaxia and TV003/TV005, there are current questions regarding their effectiveness due to an [...] Read more.

Dengue virus poses a significant global health challenge, particularly in tropical and subtropical regions. Despite the urgent demand for vaccines in the control of the disease, the two approved vaccines, Dengvaxia and TV003/TV005, there are current questions regarding their effectiveness due to an increased risk of antibody-dependent enhancement (ADE) and reduced protection. These challenges have underscored the need for further development of improved vaccines for Dengue Virus. This study presents a new design using an in silico approach to generate a more effective dengue vaccine. Initially, our design process began with the collection of Dengue polyprotein sequences from 10 representative countries worldwide. And then conserved fragments of viral proteins were retrieved as the bases for epitope screening. The selection of epitopes was then carried out with criteria such as antigenicity, immunogenicity, and binding affinity with MHC molecules, while the exclusion criteria were according to their allergenicity, toxicity, and potential for antibody-dependent enhancement. We then constructed a core antigen with the selected epitopes and linked the outcomes with distinct adjuvant proteins, resulting in three candidate vaccines: PSDV-1, PSDV-2, and PSDV-3. Among these, PSDV-2 was selected for further validation due to its superior physicochemical and structural properties. Extensive simulations demonstrated that PSDV-2 exhibited strong binding to pattern recognition receptors, high stability, and robust immune induction, confirming its potential as a high-quality vaccine candidate. For its recombinant expression, a plasmid was subsequently designed. Our new vaccine design offers a promising additional option for Dengue virus protection. Further experimental validations will be conducted to confirm its protective efficacy and safety. Full article

(This article belongs to the Special Issue Innovative Biotechnologies for Advancing Protein Function Investigation)

► Show Figures

Graphical abstract

15 pages, 4251 KiB

Open AccessArticle

Proteomic Analysis Identifies Dysregulated Proteins in Albuminuria: A South African Pilot Study

by Siyabonga Khoza, Jaya A. George, Previn Naicker, Stoyan H. Stoychev, June Fabian and Ireshyn S. Govender

Biology 2024, 13(9), 680; https://doi.org/10.3390/biology13090680 - 30 Aug 2024

Abstract

Albuminuria may precede decreases in the glomerular filtration rate (GFR) and both tests are insensitive predictors of early stages of kidney disease. Our aim was to characterise the urinary proteome in black African individuals with albuminuria and well-preserved GFR from South Africa. This [...] Read more.

Albuminuria may precede decreases in the glomerular filtration rate (GFR) and both tests are insensitive predictors of early stages of kidney disease. Our aim was to characterise the urinary proteome in black African individuals with albuminuria and well-preserved GFR from South Africa. This case-controlled study compared the urinary proteomes of 52 normoalbuminuric (urine albumin: creatinine ratio (uACR) < 3 mg/mmol) and 56 albuminuric (uACR ≥ 3 mg/mmol) adults of black African ethnicity. Urine proteins were precipitated, reduced, alkylated, digested, and analysed using an Evosep One LC (Evosep Biosystems, Odense, Denmark) coupled to a Sciex 5600 Triple-TOF (Sciex, Framingham, MA, USA) in data-independent acquisition mode. The data were searched on Spectronaut^TM 15. Differentially abundant proteins (DAPs) were filtered to include those with a ≥2.25-fold change and a false discovery rate ≤ 1%. Receiver–operating characteristic curves were used to assess the discriminating abilities of proteins of interest. Pathway analysis was performed using Enrichr software. As expected, the albuminuric group had higher uACR (7.9 vs. 0.55 mg/mmol, p < 0.001). The median eGFR (mL/min/1.73 m²) showed no difference between the groups (111 vs. 114, p = 0.707). We identified 80 DAPs in the albuminuria group compared to the normoalbuminuria group, of which 59 proteins were increased while 21 proteins were decreased in abundance. We found 12 urinary proteins with an AUC > 0.8 and a p < 0.001 in the multivariate analysis. Furthermore, an 80-protein model was developed that showed a high AUC ˃ 0.907 and a predictive accuracy of 91.3% between the two groups. Pathway analysis found that the DAPs were involved in insulin growth factor (IGF) functions, innate immunity, platelet degranulation, and extracellular matrix organization. In albuminuric individuals with a well-preserved eGFR, pathways involved in preventing the release and uptake of IGF by insulin growth factor binding protein were significantly enriched. These proteins are indicative of a homeostatic imbalance in a variety of cellular processes underlying renal dysfunction and are implicated in chronic kidney disease. Full article

(This article belongs to the Special Issue Applications of Proteomics in Biological Fluids and Biopsies)

► Show Figures

Figure 1

10 pages, 2170 KiB

Open AccessArticle

Imipramine Increases Norepinephrine and Serotonin in the Salivary Glands of Rats

by Kosuke Shirose, Masanobu Yoshikawa, Takugi Kan, Masaaki Miura, Mariko Watanabe, Mitsumasa Matsuda, Hiroyuki Kobayashi, Mitsuru Kawaguchi, Kenji Ito and Takeshi Suzuki

Biology 2024, 13(9), 679; https://doi.org/10.3390/biology13090679 - 30 Aug 2024

Abstract

Xerostomia induced by antidepressants such as imipramine has long been thought to be due to their anticholinergic effects. However, even antidepressants with low anticholinergic effects may have a high incidence of xerostomia. In salivary glands, norepinephrine activates alpha-adrenergic receptors in blood vessels and [...] Read more.

Xerostomia induced by antidepressants such as imipramine has long been thought to be due to their anticholinergic effects. However, even antidepressants with low anticholinergic effects may have a high incidence of xerostomia. In salivary glands, norepinephrine activates alpha-adrenergic receptors in blood vessels and beta-adrenergic receptors in acinar cells, respectively, causing a decrease in the blood flow and an increase in the protein secretion, resulting in the secretion of viscous saliva with low water content and high protein content. A previous study demonstrated that perfusion of the submandibular glands of rats with serotonin significantly decreased saliva secretion. The results of the present study revealed the following: (1) that norepinephrine and serotonin, but not epinephrine nor dopamine, were detected in the interstitial fluids in rat submandibular glands; (2) that norepinephrine and serotonin concentrations in the dialysate was 4.3 ± 2.8 nM and 32.3 ± 19.6 nM at stable level, respectively; (3) that infusion with imipramine, a reuptake inhibitor of norepinephrine and serotonin, significantly and dose-dependently increased both norepinephrine and serotonin concentrations in the dialysate; and (4) that intraperitoneal administration of imipramine significantly increased both norepinephrine and serotonin concentrations in the dialysate. These results suggested that one of the mechanisms of xerostomia induced by reuptake inhibitors of norepinephrine and serotonin involves the activation of adrenergic and serotonin receptors in the salivary glands, respectively. Full article

► Show Figures

Figure 1

30 pages, 3343 KiB

Open AccessReview

Typical Marine Ecological Disasters in China Attributed to Marine Organisms and Their Significant Insights

by Lulu Yao, Peimin He, Zhangyi Xia, Jiye Li and Jinlin Liu

Biology 2024, 13(9), 678; https://doi.org/10.3390/biology13090678 - 30 Aug 2024

Abstract

Owing to global climate change or the ever-more frequent human activities in the offshore areas, it is highly probable that an imbalance in the offshore ecosystem has been induced. However, the importance of maintaining and protecting marine ecosystems’ balance cannot be overstated. In [...] Read more.

Owing to global climate change or the ever-more frequent human activities in the offshore areas, it is highly probable that an imbalance in the offshore ecosystem has been induced. However, the importance of maintaining and protecting marine ecosystems’ balance cannot be overstated. In recent years, various marine disasters have occurred frequently, such as harmful algal blooms (green tides and red tides), storm surge disasters, wave disasters, sea ice disasters, and tsunami disasters. Additionally, overpopulation of certain marine organisms (particularly marine faunas) has led to marine disasters, threatening both marine ecosystems and human safety. The marine ecological disaster monitoring system in China primarily focuses on monitoring and controlling the outbreak of green tides (mainly caused by outbreaks of some Ulva species) and red tides (mainly caused by outbreaks of some diatom and dinoflagellate species). Currently, there are outbreaks of Cnidaria (Hydrozoa and Scyphozoa organisms; outbreak species are frequently referred to as jellyfish), Annelida (Urechis unicinctus Drasche, 1880), Mollusca (Philine kinglipini S. Tchang, 1934), Arthropoda (Acetes chinensis Hansen, 1919), and Echinodermata (Asteroidea organisms, Ophiuroidea organisms, and Acaudina molpadioides Semper, 1867) in China. They not only cause significant damage to marine fisheries, tourism, coastal industries, and ship navigation but also have profound impacts on marine ecosystems, especially near nuclear power plants, sea bathing beaches, and infrastructures, posing threats to human lives. Therefore, this review provides a detailed introduction to the marine organisms (especially marine fauna species) causing marine biological disasters in China, the current outbreak situations, and the biological backgrounds of these outbreaks. This review also provides an analysis of the causes of these outbreaks. Furthermore, it presents future prospects for marine biological disasters, proposing corresponding measures and advocating for enhanced resource utilization and fundamental research. It is recommended that future efforts focus on improving the monitoring of marine biological disasters and integrating them into the marine ecological disaster monitoring system. The aim of this review is to offer reference information and constructive suggestions for enhancing future monitoring, early warning systems, and prevention efforts related to marine ecological disasters in support of the healthy development and stable operation of marine ecosystems. Full article

(This article belongs to the Special Issue Biology, Ecology and Management of Aquatic Macrophytes)

► Show Figures

Figure 1

17 pages, 1242 KiB

Open AccessArticle

Impacts of Whole-Grain Soft Red, Whole-Grain Soft White, and Refined Soft White Wheat Flour Crackers on Gastrointestinal Inflammation and the Gut Microbiota of Adult Humans

by Gigi A. Kinney, Eliot N. Haddad, Neha Gopalakrishnan, Kameron Y. Sugino, Linda S. Garrow, Perry K. W. Ng and Sarah S. Comstock

Biology 2024, 13(9), 677; https://doi.org/10.3390/biology13090677 - 30 Aug 2024

Abstract

Consumption of whole-grain wheat has been associated with positive health outcomes, but it remains unclear whether different types of wheat elicit varying effects on the gut microbiome and intestinal inflammation. The objectives of this research were to investigate the effect of two whole-grain [...] Read more.

Consumption of whole-grain wheat has been associated with positive health outcomes, but it remains unclear whether different types of wheat elicit varying effects on the gut microbiome and intestinal inflammation. The objectives of this research were to investigate the effect of two whole-grain wheat flours versus refined wheat flour on the diversity of the human gut microbiota, as well as on butyrate production capacity and gastrointestinal inflammation, using one-week dietary interventions. For this study, 28 participants were recruited, with ages ranging from 18 to 55 years and a mean BMI of 26.0 kg/m². For four weeks, participants were provided 80 g daily servings of different wheat crackers: Week A was a run-in period of crackers made from soft white wheat flour, Week B crackers were whole-grain soft white wheat flour, Week C crackers were a wash-out period identical to Week A, and Week D crackers were whole-grain soft red wheat flour. At the end of each week, participants provided fecal samples that were analyzed for markers of intestinal inflammation, including lipocalin and calprotectin, using enzyme-linked immunosorbent assays and quantitative real-time PCR. The primary outcome, gut bacterial community alpha and beta diversity, was similar across timepoints. Three taxa significantly differed in abundance following both whole-grain wheat flour interventions: Escherichia/Shigella and Acidaminococcus were significantly depleted, and Lachnospiraceae NK4A136 group was enriched. Secondary outcomes determined that protein markers of intestinal inflammation and genes related to putative butyrate production capacity were similar throughout the study period, with no significant changes. Lipocalin concentrations ranged from 14.8 to 22.6 ng/mL while calprotectin ranged from 33.2 to 62.5 ng/mL across all 4 weeks. The addition of wheat crackers to the adult human subjects’ usual diet had a minimal impact on their gastrointestinal inflammation or the gut microbiota. Full article

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

► Show Figures

Figure 1

13 pages, 1852 KiB

Open AccessArticle

Antibacterial, Antibiofilm, and Wound Healing Activities of Rutin and Quercetin and Their Interaction with Gentamicin on Excision Wounds in Diabetic Mice

by Yasir Almuhanna, Abdulrahman Alshalani, Hamood AlSudais, Fuad Alanazi, Mohammed Alissa, Mohammed Asad and Babu Joseph

Biology 2024, 13(9), 676; https://doi.org/10.3390/biology13090676 - 29 Aug 2024

Viewed by 172

Abstract

Phytochemicals are effective and are gaining attention in fighting against drug-resistant bacterial strains. In the present study, rutin and quercetin were tested for antibacterial, antibiofilm, and wound healing activities on excision wounds infected with MDR-P. aeruginosa in diabetic mice. Antibacterial and antibiofilm [...] Read more.

Phytochemicals are effective and are gaining attention in fighting against drug-resistant bacterial strains. In the present study, rutin and quercetin were tested for antibacterial, antibiofilm, and wound healing activities on excision wounds infected with MDR-P. aeruginosa in diabetic mice. Antibacterial and antibiofilm activities were studied in vitro using broth dilution assay and crystal violet assay, respectively. These phytochemicals were tested alone for wound-healing activities at different concentrations (0.5% and 1% in ointment base) and in combination with gentamicin to evaluate any additive effects. Rutin and quercetin demonstrated effectiveness against MDR-P. aeruginosa at higher concentrations. Both phytochemicals inhibited biofilm formation in vitro and contributed to the healing of diabetic wounds by eradicating biofilm in the wounded tissue. Rutin at a low concentration (0.5%) had a lesser effect on reducing the epithelization period and regeneration of the epithelial layer compared to quercetin. When combined with gentamicin, quercetin (1%) displayed the maximum effect on epithelium regeneration, followed by rutin (1%) in combination with gentamicin. Both phytochemicals were found to be more effective in controlling biofilm and wound-healing activities when used as an additive with gentamicin. The study supports the traditional use of phytochemicals with antibacterial, antibiofilm, and wound-healing activities in managing diabetic infections. Full article

(This article belongs to the Special Issue Physiology and Pathophysiology of Skin)

► Show Figures

Figure 1

18 pages, 6477 KiB

Open AccessArticle

A New Chimeric Antibody against the HIV-1 Fusion Inhibitory Peptide MT-C34 with a High Affinity and Fc-Mediated Cellular Cytotoxicity

by Svetlana V. Kalinichenko, Lama Ramadan, Natalia A. Kruglova, Konstantin I. Balagurov, Marina I. Lukashina, Dmitriy V. Mazurov and Mikhail V. Shepelev

Biology 2024, 13(9), 675; https://doi.org/10.3390/biology13090675 - 29 Aug 2024

Viewed by 198

Abstract

Peptides from heptad repeat (HR1 and HR2) regions of gp41 are effective inhibitors of HIV-1 entry that block the fusion of viral and cellular membranes, but the generation of antibodies highly specific for these peptides is challenging. We have previously described a mouse [...] Read more.

Peptides from heptad repeat (HR1 and HR2) regions of gp41 are effective inhibitors of HIV-1 entry that block the fusion of viral and cellular membranes, but the generation of antibodies highly specific for these peptides is challenging. We have previously described a mouse hybridoma that recognizes MT-C34-related peptides derived from HR2. It was used for the selection of HIV-1-resistant CD4 lymphocytes engineered to express the MT-C34 peptide via a CRISPR/Cas9-mediated knock-in into the CXCR4 locus. In this study, we cloned variable domains of this antibody and generated a recombinant chimeric antibody (chAb) by combining it with the constant regions of the humanized antibody Trastuzumab. The new chAb displayed a high specificity and two-fold higher level of affinity than the parental mouse monoclonal antibody. In addition, chAb mediated up to 27–43% of the antibody-dependent cellular cytotoxicity towards cells expressing MT-C34 on their surface. The anti-MT-C34 chAb can be easily generated using plasmids available for the research community and can serve as a valuable tool for the detection, purification, and even subsequent elimination of HIV-1-resistant CD4 cells or CAR cells engineered to fight HIV-1 infection. Full article

(This article belongs to the Special Issue B and T Cells in HIV and Other Viral Infections)

► Show Figures

Graphical abstract

16 pages, 1556 KiB

Open AccessReview

High-Salt Diet and Intestinal Microbiota: Influence on Cardiovascular Disease and Inflammatory Bowel Disease

by Xueyang Wang, Fuyuan Lang and Dan Liu

Biology 2024, 13(9), 674; https://doi.org/10.3390/biology13090674 - 29 Aug 2024

Viewed by 180

Abstract

Salt, or sodium chloride, is an essential component of the human diet. Recent studies have demonstrated that dietary patterns characterized by a high intake of salt can influence the abundance and diversity of the gut microbiota, and may play a pivotal role in [...] Read more.

Salt, or sodium chloride, is an essential component of the human diet. Recent studies have demonstrated that dietary patterns characterized by a high intake of salt can influence the abundance and diversity of the gut microbiota, and may play a pivotal role in the etiology and exacerbation of certain diseases, including inflammatory bowel disease and cardiovascular disease. The objective of this review is to synthesize the effects of elevated salt consumption on the gut microbiota, including its influence on gut microbial metabolites and the gut immune system. Additionally, this review will investigate the potential implications of these effects for the development of cardiovascular disease and inflammatory bowel disease. The findings of this study offer novel insights and avenues for the management of two common conditions with significant clinical implications. Full article

(This article belongs to the Special Issue Diet-Microbiota Impacts on Intestinal Inflammation)

► Show Figures

Figure 1

27 pages, 1667 KiB

Open AccessReview

Regulatory Dynamics of Plant Hormones and Transcription Factors under Salt Stress

by Muhammad Aizaz, Lubna, Rahmatullah Jan, Sajjad Asaf, Saqib Bilal, Kyung-Min Kim and Ahmed AL-Harrasi

Biology 2024, 13(9), 673; https://doi.org/10.3390/biology13090673 - 29 Aug 2024

Viewed by 354

Abstract

The negative impacts of soil salinization on ion homeostasis provide a significant global barrier to agricultural production and development. Plant physiology and biochemistry are severely affected by primary and secondary NaCl stress impacts, which damage cellular integrity, impair water uptake, and trigger physiological [...] Read more.

The negative impacts of soil salinization on ion homeostasis provide a significant global barrier to agricultural production and development. Plant physiology and biochemistry are severely affected by primary and secondary NaCl stress impacts, which damage cellular integrity, impair water uptake, and trigger physiological drought. Determining how transcriptional factors (TFs) and hormone networks are regulated in plants in response to salt stress is necessary for developing crops that tolerate salt. This study investigates the complex mechanisms of several significant TF families that influence plant responses to salt stress, involving AP2/ERF, bZIP, NAC, MYB, and WRKY. It demonstrates how these transcription factors (TFs) help plants respond to the detrimental effects of salinity by modulating gene expression through mechanisms including hormone signaling, osmotic stress pathway activation, and ion homeostasis. Additionally, it explores the hormonal imbalances triggered by salt stress, which entail complex interactions among phytohormones like jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) within the hormonal regulatory networks. This review highlights the regulatory role of key transcription factors in salt-stress response, and their interaction with plant hormones is crucial for developing genome-edited crops that can enhance agricultural sustainability and address global food security challenges. Full article

(This article belongs to the Special Issue Uncovering the Mechanisms of Plant Salinity Stress Response and Tolerance)

► Show Figures

Figure 1

14 pages, 2223 KiB

Open AccessArticle

Dapagliflozin: A Promising Strategy to Combat Cisplatin-Induced Hepatotoxicity in Wistar Rats

by Shakta Mani Satyam, Laxminarayana Kurady Bairy, Abdul Rehman, Mohamed Farook, Sofiya Khan, Anuradha Asokan Nair, Nirmal Nachiketh Binu, Mohamed Yehya and Mohammed Moin Khan

Biology 2024, 13(9), 672; https://doi.org/10.3390/biology13090672 - 29 Aug 2024

Viewed by 298

Abstract

Recognizing the challenges posed by chemotherapy, specifically the hepatotoxic effects of drugs like cisplatin, this study aimed to examine the hepatoprotective potential of dapagliflozin to mitigate cisplatin-induced hepatotoxicity in a rat model. This study focused on repurposing drugs such as dapagliflozin and natural [...] Read more.

Recognizing the challenges posed by chemotherapy, specifically the hepatotoxic effects of drugs like cisplatin, this study aimed to examine the hepatoprotective potential of dapagliflozin to mitigate cisplatin-induced hepatotoxicity in a rat model. This study focused on repurposing drugs such as dapagliflozin and natural agents like silymarin as potential interventions to address cisplatin-induced hepatotoxicity. Thirty adult female Wistar rats were distributed into five groups and treated with cisplatin alone, silymarin, dapagliflozin, or a combination of dapagliflozin and silymarin accordingly for 45 days. Body weight, fasting blood glucose levels, liver function tests, and histopathological analysis were conducted to evaluate the hepatoprotective effects. Cisplatin-induced hepatotoxicity significantly (p < 0.05) increased the serum levels of ALT, AST, TB, and reduced the TP and albumin levels. Dapagliflozin administration led to significant reductions in ALT, AST, TB, and increased albumin levels. Silymarin demonstrated comparable effects. Combining dapagliflozin and silymarin showed synergistic effects, further reducing the liver enzymes and improving albumin levels. Histopathological examination supported these findings, revealing the restoration of liver structure with dapagliflozin and silymarin treatment. Dapagliflozin and silymarin exhibited substantial hepatoprotective benefits against cisplatin-induced hepatotoxicity in rats. The combination therapy demonstrated synergistic effects, highlighting a potential therapeutic approach for mitigating chemotherapy-induced liver damage. Further research into molecular mechanisms and clinical translation is warranted, offering hope for improved clinical outcomes in cancer patients undergoing cisplatin-based chemotherapy. Full article

(This article belongs to the Special Issue Animal Models in Toxicology)

► Show Figures

Figure 1

18 pages, 2311 KiB

Open AccessArticle

Cell-Free Extracts of the Ginseng Soil Bacterium Pseudomonas plecoglossicida Promote Suppression of Resistance of American Ginseng (Panax quinquefolius) to Root Rot Caused by Ilyonectria mors-panacis

by Paul H. Goodwin and Tom Hsiang

Biology 2024, 13(9), 671; https://doi.org/10.3390/biology13090671 - 29 Aug 2024

Viewed by 171

Abstract

A prior report showed that soil previously planted with American ginseng (Panax quinquefolius) contained compound(s) which could reduce ginseng resistance to root infection by Ilyonectria mors-panacis, and this was not found in extracts from ginseng roots or soils not previously [...] Read more.

A prior report showed that soil previously planted with American ginseng (Panax quinquefolius) contained compound(s) which could reduce ginseng resistance to root infection by Ilyonectria mors-panacis, and this was not found in extracts from ginseng roots or soils not previously planted with ginseng. However, the origin of this ginseng-related factor in ginseng soils is unknown. An isolate of Pseudomonas plecoglossicida obtained from soil where P. quinquefolius had been harvested grew more in culture media when ginseng root extract was included, indicating the use of compounds in the extract as nutrients. Treatment with cell-free extracts from media containing ginseng root extracts where P. plecoglossicida had been cultured resulted in root lesions caused by I. mors-panacis being significantly larger than roots treated with fresh media containing root extract or with cell-free media inoculated with the same bacterial isolate without root extract. Levels of ginsenosides in the media decreased over time with incubation. Genome sequencing revealed that the bacterium had genes homologous to those reported for ginsenoside metabolism, which can release sugars for microbial growth. Thus, a ginseng soil bacterium, P. plecoglossicida, can create compound(s) suppressive to root rot resistance, similar to that found in soils previously planted with ginseng, indicating that the activity suppressing root rot resistance in soil previously planted with ginseng may be of microbial origin, utilizing compounds from ginseng roots. Full article

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

► Show Figures

Figure 1

21 pages, 12420 KiB

Open AccessArticle

Agricultural and Ecological Resources Safeguarded by the Prevention of Wild Pig Population Expansion

by Colin Jareb, Kim M. Pepin, Ryan S. Miller, Sarah Sykora, Stephanie A. Shwiff and Sophie C. McKee

Biology 2024, 13(9), 670; https://doi.org/10.3390/biology13090670 - 29 Aug 2024

Viewed by 198

Abstract

Wild pigs (Sus scrofa) are one of the most destructive invasive species in the US, known for causing extensive damage to agricultural commodities, natural resources, and property, and for transmitting diseases to livestock. Following the establishment of the National Feral Swine [...] Read more.

Wild pigs (Sus scrofa) are one of the most destructive invasive species in the US, known for causing extensive damage to agricultural commodities, natural resources, and property, and for transmitting diseases to livestock. Following the establishment of the National Feral Swine Damage Management Program (NFSDMP) in 2014, the expansion of wild pig populations has been successfully slowed. This paper combines two modeling approaches across eight separate models to characterize the expansion of wild pig populations in the absence of intervention by the NFSDMP and forecasts the value of a subset of resources safeguarded from the threat of wild pigs. The results indicate that if wild pigs had continued spreading at pre-program levels, they would have spread extensively across the US, with significant geographic variation across modeling scenarios. Further, by averting the threat of wild pigs, a substantial amount of crops, land, property, and livestock was safeguarded by the NFSDMP. Cumulatively, between 2014 and 2021, wild pig populations were prevented from spreading to an average of 724 counties and an average of USD 40.2 billion in field crops, pasture, grasses, and hay was safeguarded. The results demonstrate that intervention by the NFSDMP has delivered significant ecological and economic benefits that were not previously known. Full article

(This article belongs to the Special Issue Risk Assessment for Biological Invasions)

► Show Figures

Figure 1

16 pages, 3434 KiB

Open AccessReview

Cellular Stress in Dry Eye Disease—Key Hub of the Vicious Circle

by Gysbert-Botho van Setten

Biology 2024, 13(9), 669; https://doi.org/10.3390/biology13090669 - 28 Aug 2024

Viewed by 300

Abstract

Disturbance or insufficiency of the tear film challenges the regulatory systems of the ocular surfaces. The reaction of the surfaces includes temporary mechanisms engaged in the preservation of homeostasis. However, strong or persisting challenges can lead to the potential exhaustion of the coping [...] Read more.

Disturbance or insufficiency of the tear film challenges the regulatory systems of the ocular surfaces. The reaction of the surfaces includes temporary mechanisms engaged in the preservation of homeostasis. However, strong or persisting challenges can lead to the potential exhaustion of the coping capacity. This again activates the vicious circle with chronic inflammation and autocatalytic deterioration. Hence, the factors challenging the homeostasis should be addressed in time. Amongst them are a varying osmolarity, constant presence of small lesions at the epithelium, acidification, attrition with mechanical irritation, and onset of pain and discomfort. Each of them and, especially when occurring simultaneously, impose stress on the coping mechanisms and lead to a stress response. Many stressors can culminate, leading to an exhaustion of the coping capacity, outrunning normal resilience. Reaching the limits of stress tolerance leads to the manifestation of a lubrication deficiency as the disease we refer to as dry eye disease (DED). To postpone its manifestation, the avoidance or amelioration of stress factors is one key option. In DED, this is the target of lubrication therapy, substituting the missing tear film or its components. The latter options include the management of secondary sequelae such as the inflammation and activation of reparative cascades. Preventive measures include the enhancement in resilience, recovery velocity, and recovery potential. The capacity to handle the external load factors is the key issue. The aim is to guard homeostasis and to prevent intercellular stress responses from being launched, triggering and invigorating the vicious circle. Considering the dilemma of the surface to have to cope with increased time of exposure to stress, with simultaneously decreasing time for cellular recovery, it illustrates the importance of the vicious circle as a hub for ocular surface stress. The resulting imbalance triggers a continuous deterioration of the ocular surface condition. After an initial phase of the reaction and adaption of the ocular surface to the surrounding challenges, the normal coping capacity will be exhausted. This is the time when the integrated stress response (ISR), a protector for cellular survival, will inevitably be activated, and cellular changes such as altered translation and ribosome pausing are initiated. Once activated, this will slow down any recovery, in a phase where apoptosis is imminent. Premature senescence of cells may also occur. The process of prematurization due to permanent stress exposures contributes to the risk for constant deterioration. The illustrated flow of events in the development of DED outlines that the ability to cope, and to recover, has limited resources in the cells at the ocular surface. The reduction in and amelioration of stress hence should be one of the key targets of therapy and begin early. Here, lubrication optimization as well as causal treatment such as the correction of anatomical anomalies (leading to anatomical dry eye) should be a prime intent of any therapy. The features of cellular stress as a key hub for the vicious circle will be outlined and discussed. Full article

(This article belongs to the Special Issue New Horizons in Ocular Surface Biology)

► Show Figures

Figure 1

27 pages, 10083 KiB

Open AccessArticle

Comparative Study of Bacillus-Based Plant Biofertilizers: A Proposed Index

by Adoración Barros-Rodríguez, Pamela Pacheco, María Peñas-Corte, Antonio J. Fernández-González, José F. Cobo-Díaz, Yasmira Enrique-Cruz and Maximino Manzanera

Biology 2024, 13(9), 668; https://doi.org/10.3390/biology13090668 - 28 Aug 2024

Viewed by 248

Abstract

The market for bacteria as agricultural biofertilizers is growing rapidly, offering plant-growth stimulants; biofungicides; and, more recently, protectors against extreme environmental factors, such as drought. This abundance makes it challenging for the end user to decide on the product to use. In this [...] Read more.

The market for bacteria as agricultural biofertilizers is growing rapidly, offering plant-growth stimulants; biofungicides; and, more recently, protectors against extreme environmental factors, such as drought. This abundance makes it challenging for the end user to decide on the product to use. In this work, we describe the isolation of a strain of Bacillus velezensis (belonging to the operational group Bacillus amyloliquefaciens) for use as a plant-growth-promoting rhizobacterium, a biofungicide, and a protector against drought. To compare its effectiveness with other commercial strains of the same operational group, Bacillus amyloliquefaciens, we analyzed its ability to promote the growth of pepper plants and protect them against drought, as well as its fungicidal activity through antibiosis and antagonism tests, its ability to solubilize potassium and phosphates, and its ability to produce siderophores. Finally, we used a probit function, a type of regression analysis used to model the outcomes of analyses, to quantify the biostimulatory effectiveness of the different plant-growth-promoting rhizobacteria, developing what we have called the Agricultural Protection Against Stress Index, which allowed us to numerically compare the four commercial strains of the operational group Bacillus amyloliquefaciens, based on a Delphi method—a type of regression analysis that can be used to model a cumulative normal distribution—and integrate the results from our panel of tests into a single value. Full article

(This article belongs to the Collection Plant Growth-Promoting Bacteria: Mechanisms and Applications)

► Show Figures

Figure 1

20 pages, 8904 KiB

Open AccessArticle

Habitat Loss in the IUCN Extent: Climate Change-Induced Threat on the Red Goral (Naemorhedus baileyi) in the Temperate Mountains of South Asia

by Imon Abedin, Tanoy Mukherjee, Joynal Abedin, Hyun-Woo Kim and Shantanu Kundu

Biology 2024, 13(9), 667; https://doi.org/10.3390/biology13090667 - 27 Aug 2024

Viewed by 480

Abstract

Climate change has severely impacted many species, causing rapid declines or extinctions within their essential ecological niches. This deterioration is expected to worsen, particularly in remote high-altitude regions like the Himalayas, which are home to diverse flora and fauna, including many mountainous ungulates. [...] Read more.

Climate change has severely impacted many species, causing rapid declines or extinctions within their essential ecological niches. This deterioration is expected to worsen, particularly in remote high-altitude regions like the Himalayas, which are home to diverse flora and fauna, including many mountainous ungulates. Unfortunately, many of these species lack adaptive strategies to cope with novel climatic conditions. The Red Goral (Naemorhedus baileyi) is a cliff-dwelling species classified as “Vulnerable” by the IUCN due to its small population and restricted range extent. This species has the most restricted range of all goral species, residing in the temperate mountains of northeastern India, northern Myanmar, and China. Given its restricted range and small population, this species is highly threatened by climate change and habitat disruptions, making habitat mapping and modeling crucial for effective conservation. This study employs an ensemble approach (BRT, GLM, MARS, and MaxEnt) in species distribution modeling to assess the distribution, habitat suitability, and connectivity of this species, addressing critical gaps in its understanding. The findings reveal deeply concerning trends, as the model identified only 21,363 km² (13.01%) of the total IUCN extent as suitable habitat under current conditions. This limited extent is alarming, as it leaves the species with very little refuge to thrive. Furthermore, this situation is compounded by the fact that only around 22.29% of this identified suitable habitat falls within protected areas (PAs), further constraining the species’ ability to survive in a protected landscape. The future projections paint even degraded scenarios, with a predicted decline of over 34% and excessive fragmentation in suitable habitat extent. In addition, the present study identifies precipitation seasonality and elevation as the primary contributing predictors to the distribution of this species. Furthermore, the study identifies nine designated transboundary PAs within the IUCN extent of the Red Goral and the connectivity among them to highlight the crucial role in supporting the species’ survival over time. Moreover, the Dibang Wildlife Sanctuary (DWLS) and Hkakaborazi National Park are revealed as the PAs with the largest extent of suitable habitat in the present scenario. Furthermore, the highest mean connectivity was found between DWLS and Mehao Wildlife Sanctuary (0.0583), while the lowest connectivity was observed between Kamlang Wildlife Sanctuary and Namdapha National Park (0.0172). The study also suggests strategic management planning that is a vital foundation for future research and conservation initiatives, aiming to ensure the long-term survival of the species in its natural habitat. Full article

(This article belongs to the Special Issue Editorial Board Members' Collection Series: “Biodiversity and Ecosystem Function under Global Change”)

► Show Figures

Figure 1

1 pages, 135 KiB

Open AccessCorrection

Correction: Esmaeilzadeh et al. RETRACTED: Identify Biomarkers and Design Effective Multi-Target Drugs in Ovarian Cancer: Hit Network-Target Sets Model Optimizing. Biology 2022, 11, 1851

by Biology Editorial Office

Biology 2024, 13(9), 666; https://doi.org/10.3390/biology13090666 - 27 Aug 2024

Viewed by 179

Abstract

A correction has been made to the authorship list of this article [...] Full article

(This article belongs to the Special Issue Bioinformatics and Machine Learning for Cancer Biology (Volume II))

11 pages, 4354 KiB

Open AccessBrief Report

Factors Affecting Cell Viability during the Enzymatic Dissociation of Human Endocrine Tumor Tissues

by Anastasia Shcherbakova, Marina Utkina, Anna Valyaeva, Nano Pachuashvili, Ekaterina Bondarenko, Liliya Urusova, Sergey Popov and Natalya Mokrysheva

Biology 2024, 13(9), 665; https://doi.org/10.3390/biology13090665 - 27 Aug 2024

Viewed by 298

Abstract

The enzymatic dissociation of human solid tissues is a critical process for disaggregating extracellular matrix and the isolation of individual cells for various applications, including the immortalizing primary cells, creating novel cell lines, and performing flow cytometry and its specialized type, FACS, as [...] Read more.

The enzymatic dissociation of human solid tissues is a critical process for disaggregating extracellular matrix and the isolation of individual cells for various applications, including the immortalizing primary cells, creating novel cell lines, and performing flow cytometry and its specialized type, FACS, as well as conducting scRNA-seq studies. Tissue dissociation procedures should yield intact, highly viable single cells that preserve morphology and cell surface markers. However, endocrine tissues, such as adrenal gland tumors, thyroid carcinomas, and pituitary neuroendocrine tumors, present unique challenges due to their complex tissue organization and morphological features. Our study conducted a morphological examination of these tissues, highlighting the intricate structures and secondary degenerative changes that complicate the dissociation process. We investigated the effects of various dissociation parameters, including the types of enzymes, incubation duration, and post-dissociation purification procedures, such as debris removal and nontarget blood cell lysis, on the viability of cells derived from different tumor types. The findings emphasize the importance of optimizing tissue digestion protocols to preserve cell viability and integrity, ensuring reliable outcomes for downstream analyses. Full article

(This article belongs to the Section Cell Biology)

► Show Figures

Figure 1

15 pages, 3928 KiB

Open AccessArticle

Reproductive Strategies and Embryonic Development of Autumn-Spawning Bitterling (Acheilognathus rhombeus) within the Mussel Host

by Hyeongsu Kim, Jongryeol Choe and Myeonghun Ko

Biology 2024, 13(9), 664; https://doi.org/10.3390/biology13090664 - 26 Aug 2024

Viewed by 311

Abstract

We investigated the reproductive strategies and embryonic development of Acheilognathus rhombeus (a bitterling species that spawns in autumn) within its freshwater mussel host in the Bongseo Stream, South Korea. By focusing on survival mechanisms during critical stages of embryonic development, the selective use [...] Read more.

We investigated the reproductive strategies and embryonic development of Acheilognathus rhombeus (a bitterling species that spawns in autumn) within its freshwater mussel host in the Bongseo Stream, South Korea. By focusing on survival mechanisms during critical stages of embryonic development, the selective use of mussel gill demibranchs by the bitterlings and associated adaptive traits were observed over 1 year. A significant diapause phase occurs at developmental stage D, which lasts for approximately 7 months, allowing embryos to survive winter. Development resumes when the temperature exceeds 10 °C. Minute tubercles on the embryos (crucial for anchoring within the host gill demibranchs and preventing premature ejection) exhibit the largest height during diapause, and the height decreases when developmental stage E is reached, when growth resumes. Acheilognathus rhombeus embryos were observed in 30.5% of the mussels, mostly within the inner gills, thereby maximizing spatial use and oxygen access to enhance survival. These results highlight the intricate relationship between A. rhombeus and its mussel hosts, demonstrating the evolutionary adaptations that enhance reproductive success and survival. This study provides valuable insights into the ecological dynamics and conservation requirements of such symbiotic relationships. Full article

(This article belongs to the Section Ecology)

► Show Figures

Figure 1

14 pages, 1157 KiB

Open AccessReview

The Role of Milk Oligosaccharides in Enhancing Intestinal Microbiota, Intestinal Integrity, and Immune Function in Pigs: A Comparative Review

by Alexa Gormley, Yesid Garavito-Duarte and Sung Woo Kim

Biology 2024, 13(9), 663; https://doi.org/10.3390/biology13090663 - 26 Aug 2024

Viewed by 377

Abstract

The objective of this review was to identify the characteristics and functional roles of milk coproducts from human, bovine, and porcine sources and their impacts on the intestinal microbiota and intestinal immunity of suckling and nursery pigs. Modern pig production weans piglets at [...] Read more.

The objective of this review was to identify the characteristics and functional roles of milk coproducts from human, bovine, and porcine sources and their impacts on the intestinal microbiota and intestinal immunity of suckling and nursery pigs. Modern pig production weans piglets at 3 to 4 weeks of age, which is earlier than pigs would naturally be weaned outside of artificial rearing. As a result, the immature intestines of suckling and nursery pigs face many challenges associated with intestinal dysbiosis, which can be caused by weaning stress or the colonization of the intestines by enteric pathogens. Milk oligosaccharides are found in sow milk and function as a prebiotic in the intestines of pigs as they cannot be degraded by mammalian enzymes and are thus utilized by intestinal microbial populations. The consumption of milk oligosaccharides during suckling and through the nursery phase can provide benefits to young pigs by encouraging the proliferation of beneficial microbial populations, preventing pathogen adhesion to enterocytes, and through directly modulating immune responses. Therefore, this review aims to summarize the specific functional components of milk oligosaccharides from human, bovine, and porcine sources, and identify potential strategies to utilize milk oligosaccharides to benefit young pigs through the suckling and nursery periods. Full article

(This article belongs to the Special Issue Milk Oligosaccharides: Biological Functions and Application Prospects)

► Show Figures

Figure 1

23 pages, 1005 KiB

Open AccessReview

The Constellation of Risk Factors and Paraneoplastic Syndromes in Cholangiocarcinoma: Integrating the Endocrine Panel Amid Tumour-Related Biology (A Narrative Review)

by Mihai-Lucian Ciobica, Bianca-Andreea Sandulescu, Liana-Maria Chicea, Mihaela Iordache, Maria-Laura Groseanu, Mara Carsote, Claudiu Nistor and Ana-Maria Radu

Biology 2024, 13(9), 662; https://doi.org/10.3390/biology13090662 - 26 Aug 2024

Viewed by 457

Abstract

Cholangiocarcinomas (CCAs), a heterogeneous group of challenging malignant tumours which originate from the biliary epithelium, are associated with an alarming increasing incidence during recent decades that varies between different regions of the globe. Thus, awareness represents the key operating factor. Our purpose was [...] Read more.

Cholangiocarcinomas (CCAs), a heterogeneous group of challenging malignant tumours which originate from the biliary epithelium, are associated with an alarming increasing incidence during recent decades that varies between different regions of the globe. Thus, awareness represents the key operating factor. Our purpose was to overview the field of CCAs following a double perspective: the constellation of the risk factors, and the presence of the paraneoplastic syndromes, emphasizing the endocrine features amid the entire multidisciplinary panel. This is a narrative review. A PubMed-based search of English-language original articles offered the basis of this comprehensive approach. Multiple risk factors underlying different levels of statistical evidence have been listed such as chronic biliary diseases and liver conditions, inflammatory bowel disease, parasitic infections (e.g., Opisthorchis viverrini, Clonorchis sinensis), lifestyle influence (e.g., alcohol, smoking), environmental exposure (e.g., thorotrast, asbestos), and certain genetic and epigenetic interplays. With regard to the endocrine panel, a heterogeneous spectrum should be taken into consideration: non-alcoholic fatty liver disease, obesity, type 2 diabetes mellitus, and potential connections with vitamin D status, glucagon-like peptide 1 receptor, or the galanin system, respectively, with exposure to sex hormone therapy. Amid the numerous dermatologic, hematologic, renal, and neurologic paraneoplastic manifestations in CCAs, the endocrine panel is less described. Humoral hypercalcaemia of malignancy stands as the most frequent humoral paraneoplastic syndrome in CCAs, despite being exceptional when compared to other paraneoplastic (non-endocrine) manifestations and to its reported frequency in other (non-CCAs) cancers (it accompanies 20–30% of all cancers). It represents a poor prognosis marker in CCA; it may be episodic once the tumour relapses. In addition to the therapy that targets the originating malignancy, hypercalcaemia requires the administration of bisphosphonates (e.g., intravenous zoledronic acid) or denosumab. Early detection firstly helps the general wellbeing of a patient due to a prompt medical control of high serum calcium and it also provides a fine biomarker of disease status in selected cases that harbour the capacity of PTHrP secretion. The exact molecular biology and genetic configuration of CCAs that display such endocrine traits is still an open matter, but humoral hypercalcaemia adds to the overall disease burden. Full article

(This article belongs to the Special Issue Biology of Liver Diseases)

► Show Figures

Figure 1

12 pages, 3472 KiB

Open AccessArticle

Observations on an Aggregation of Grey Reef Sharks (Carcharhinus amblyrhynchos) in the Mozambique Channel Off the Coast of Nosy Be (Madagascar) and Tools for Photo-Identification—A New Aggregation Nursery Site?

by Primo Micarelli, Marco Pireddu, Damiano Persia, Marco Sanna, Consuelo Vicariotto, Antonio Pacifico, Pietro Storelli, Makenna Mahrer, Emanuele Venanzi and Francesca Romana Reinero

Biology 2024, 13(9), 661; https://doi.org/10.3390/biology13090661 - 26 Aug 2024

Viewed by 560

Abstract

Following preliminary underwater observations of about 1000 h carried out monthly between 2012 and 2023 (except the years 2021 and 2022), 23 specimens of grey reef sharks were spotted and photo-identified off the coast of Nosy Be in Madagascar, on an emerging reef [...] Read more.

Following preliminary underwater observations of about 1000 h carried out monthly between 2012 and 2023 (except the years 2021 and 2022), 23 specimens of grey reef sharks were spotted and photo-identified off the coast of Nosy Be in Madagascar, on an emerging reef called “Mokarran” at a depth between 15 and 30 m. Over 10 years of observations, eight specimens were re-sighted, identified with a non-invasive photo-identification technique of part of the first dorsal and the caudal fin, and one specimen was re-identified after 1982 days from the first sighting, i.e., after more than 5 years. In addition, six specimens of probably pregnant females were also identified in the same area. The population was entirely made up of females. The aggregation area could represent a new nursery site which, if confirmed after further investigations, will require greater protection. Full article

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

► Show Figures

Figure 1

14 pages, 10500 KiB

Open AccessArticle

Morphological Analysis of a New Species of Micropterus (Teleostei: Centrarchidae) from Lake Erie, PA, USA

by Andrew T. Ross and Jay R. Stauffer, Jr.

Biology 2024, 13(9), 660; https://doi.org/10.3390/biology13090660 - 26 Aug 2024

Viewed by 1122

Abstract

This previously undescribed species of Micropterus is described from collections in Lake Erie. The species was first recognized by the tri-colored tail of juveniles. This tri-colored tail, the presence of bold parallel lines ventral to the lateral band, and scales in the inter-radial [...] Read more.

This previously undescribed species of Micropterus is described from collections in Lake Erie. The species was first recognized by the tri-colored tail of juveniles. This tri-colored tail, the presence of bold parallel lines ventral to the lateral band, and scales in the inter-radial membranes of the dorsal fin distinguish it from Micropterus nigricans. The large mouth that extends past the eye distinguishes it from Micropterus punctulatus. Full article

(This article belongs to the Special Issue Internal Defense System and Evolution of Aquatic Animals)

► Show Figures

Figure 1

16 pages, 679 KiB

Open AccessReview

Integrated Review of Transcriptomic and Proteomic Studies to Understand Molecular Mechanisms of Rice’s Response to Environmental Stresses

by Naveed Aslam, Qinying Li, Sehrish Bashir, Liuzhen Yuan, Lei Qiao and Wenqiang Li

Biology 2024, 13(9), 659; https://doi.org/10.3390/biology13090659 - 25 Aug 2024

Viewed by 476

Abstract

Rice (Oryza sativa L.) is grown nearly worldwide and is a staple food for more than half of the world’s population. With the rise in extreme weather and climate events, there is an urgent need to decode the complex mechanisms of rice’s [...] Read more.

Rice (Oryza sativa L.) is grown nearly worldwide and is a staple food for more than half of the world’s population. With the rise in extreme weather and climate events, there is an urgent need to decode the complex mechanisms of rice’s response to environmental stress and to breed high-yield, high-quality and stress-resistant varieties. Over the past few decades, significant advancements in molecular biology have led to the widespread use of several omics methodologies to study all aspects of plant growth, development and environmental adaptation. Transcriptomics and proteomics have become the most popular techniques used to investigate plants’ stress-responsive mechanisms despite the complexity of the underlying molecular landscapes. This review offers a comprehensive and current summary of how transcriptomics and proteomics together reveal the molecular details of rice’s response to environmental stresses. It also provides a catalog of the current applications of omics in comprehending this imperative crop in relation to stress tolerance improvement and breeding. The evaluation of recent advances in CRISPR/Cas-based genome editing and the application of synthetic biology technologies highlights the possibility of expediting the development of rice cultivars that are resistant to stress and suited to various agroecological environments. Full article

(This article belongs to the Special Issue Molecular Mechanisms of Plant Stress Adaptation)

► Show Figures

Figure 1

15 pages, 6169 KiB

Open AccessArticle

Tumor Microenvironment-Responsive Magnetotactic Bacteria-Based Multi-Drug Delivery Platform for MRI-Visualized Tumor Photothermal Chemodynamic Therapy

by Feng Feng, Qilong Li, Xuefei Sun, Li Yao and Xiuyu Wang

Biology 2024, 13(9), 658; https://doi.org/10.3390/biology13090658 - 25 Aug 2024

Viewed by 300

Abstract

Cancer cells display elevated reactive oxygen species (ROS) and altered redox status. Herein, based on these characteristics, we present a multi-drug delivery platform, AMB@PDAP-Fe (APPF), from the magnetotactic bacterium AMB-1 and realize MRI-visualized tumor-microenvironment-responsive photothermal–chemodynamic therapy. The Fe³⁺ in PDAP-Fe is reduced [...] Read more.

Cancer cells display elevated reactive oxygen species (ROS) and altered redox status. Herein, based on these characteristics, we present a multi-drug delivery platform, AMB@PDAP-Fe (APPF), from the magnetotactic bacterium AMB-1 and realize MRI-visualized tumor-microenvironment-responsive photothermal–chemodynamic therapy. The Fe³⁺ in PDAP-Fe is reduced by the GSH at the tumor site and is released in the form of highly active Fe²⁺, which catalyzes the generation of ROS through the Fenton reaction and inhibits tumor growth. At the same time, the significant absorption of the mineralized magnetosomes in AMB-1 cells in the NIR region enables them to efficiently convert near-infrared light into heat energy for photothermal therapy (PTT), to which PDAP also contributes. The heat generated in the PTT process accelerates the process of Fe²⁺ release, thereby achieving an enhanced Fenton reaction in the tumor microenvironment. In addition, the magnetosomes in AMB-1 are used as an MRI contrast agent, and the curing process is visualized. This tumor microenvironment-responsive MTB-based multi-drug delivery platform displays the potency to combat tumors and demonstrates the utility and practicality of understanding the cooperative molecular mechanism when designing multi-drug combination therapies. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Molecular Imaging of Cancer)

► Show Figures

Figure 1

10 pages, 1613 KiB

Open AccessArticle

iPhyDSDB: Phytoplasma Disease and Symptom Database

by Wei Wei, Jonathan Shao, Yan Zhao, Junichi Inaba, Algirdas Ivanauskas, Kristi D. Bottner-Parker, Stefano Costanzo, Bo Min Kim, Kailin Flowers and Jazmin Escobar

Biology 2024, 13(9), 657; https://doi.org/10.3390/biology13090657 - 24 Aug 2024

Viewed by 338

Abstract

Phytoplasmas are small, intracellular bacteria that infect a vast range of plant species, causing significant economic losses and impacting agriculture and farmers’ livelihoods. Early and rapid diagnosis of phytoplasma infections is crucial for preventing the spread of these diseases, particularly through early symptom [...] Read more.

Phytoplasmas are small, intracellular bacteria that infect a vast range of plant species, causing significant economic losses and impacting agriculture and farmers’ livelihoods. Early and rapid diagnosis of phytoplasma infections is crucial for preventing the spread of these diseases, particularly through early symptom recognition in the field by farmers and growers. A symptom database for phytoplasma infections can assist in recognizing the symptoms and enhance early detection and management. In this study, nearly 35,000 phytoplasma sequence entries were retrieved from the NCBI nucleotide database using the keyword “phytoplasma” and information on phytoplasma disease-associated plant hosts and symptoms was gathered. A total of 945 plant species were identified to be associated with phytoplasma infections. Subsequently, links to symptomatic images of these known susceptible plant species were manually curated, and the Phytoplasma Disease Symptom Database (iPhyDSDB) was established and implemented on a web-based interface using the MySQL Server and PHP programming language. One of the key features of iPhyDSDB is the curated collection of links to symptomatic images representing various phytoplasma-infected plant species, allowing users to easily access the original source of the collected images and detailed disease information. Furthermore, images and descriptive definitions of typical symptoms induced by phytoplasmas were included in iPhyDSDB. The newly developed database and web interface, equipped with advanced search functionality, will help farmers, growers, researchers, and educators to efficiently query the database based on specific categories such as plant host and symptom type. This resource will aid the users in comparing, identifying, and diagnosing phytoplasma-related diseases, enhancing the understanding and management of these infections. Full article

(This article belongs to the Special Issue Phytoplasmas: Molecular Characterization and Host–Pathogen Interactions (2nd Edition))

► Show Figures

Figure 1

17 pages, 657 KiB

Open AccessArticle

Circular Economy, Dairy Cow Feed Leftovers, and Withania somnifera Supplementation: Effects on Black Belly Ram’s Libido, Sperm Quality, Sexual Behavior, and Hemogram Values

by Andrés J. Rodriguez-Sánchez, Cesar A. Meza-Herrera, Angeles De Santiago-Miramontes, Cayetano Navarrete-Molina, Francisco G. Veliz-Deras, Julieta Z. Ordoñez-Morales, Jessica M. Flores-Salas and Ruben I. Marin-Tinoco

Biology 2024, 13(9), 656; https://doi.org/10.3390/biology13090656 - 24 Aug 2024

Viewed by 305

Abstract

Considering a circular economy perspective, this study evaluates the possible effect of targeted short-term supplementation with Withania somnifera L. (WS; Ashwagandha) on ram’s seminal quality, socio-sexual behaviors, and blood constituents. Black Belly rams (n = 20) received a basal diet comprising feed-leftovers from [...] Read more.

Considering a circular economy perspective, this study evaluates the possible effect of targeted short-term supplementation with Withania somnifera L. (WS; Ashwagandha) on ram’s seminal quality, socio-sexual behaviors, and blood constituents. Black Belly rams (n = 20) received a basal diet comprising feed-leftovers from dairy cows in the north-arid Mexico (i.e., Comarca Lagunera CL). The experimental units, with proven libido and fertility, were homogeneous in terms of age (3.41 ± 0.21 yr.), live weight (LW; 53.8 ± 3.3 kg), body condition (BC; 2.96 ± 0.01 units), initial sperm concentration (2387 ± 804 × 10⁶), and viability (23.9 ± 15.6%). Rams were randomly assigned during the transition reproductive period (i.e., May to Jun; 25° NL) to three treatment groups: non-supplemented control group (CONT; n = 6), low WS-supplemented (LWS; i.e., 100 mg kg LW⁻¹ d⁻¹ × 40 d; n = 7), and high-WS-supplemented (HWS; i.e., 200 mg kg LW⁻¹ d⁻¹ × 40 d; n = 7). The basal leftover diet was offered twice daily (0700 and 1600 h); the experimental period (EP) lasted 47 d. No differences (p > 0.05) among treatments occurred regarding LW and BCS at the onset of the EP. Whereas the greater scrotal circumference (SCRC, cm) arose in the LWS and CONT rams, an increased ejaculated volume (VOLEJA, mL) occurred in the WS-rams. A total of 5/9 (i.e., 55%) appetitive and 3/3 (i.e., 100%) consummatory sexual behaviors favored (p < 0.05) the WS-rams, particularly the HWS rams, towards the final EP. The same was true (p < 0.05) regarding the hemogram variables white blood cell count (×10⁹ cells L⁻¹), hemoglobin concentration (g dL⁻¹), and medium corpuscular volume (fL). This study, based on a rethink–reuse–reduce enquiry approach, enabled connectedness between two noteworthy animal systems in the CL: dairy cows and meat sheep schemes. Certainly, the use of dairy cow feed-leftovers aligned with the short-term supplementation with WS promoted enhanced testicular function, augmented seminal volume, and an increased sexual behavior in Black Belly rams in northern Mexico. Finally, while our research outcomes should enhance not only the resilience and sustainability of sheep production and the well-being of sheep-producers and their families, it may also embrace clinical translational applications. Full article

(This article belongs to the Special Issue Reproductive Management of Goats and Sheep)

► Show Figures

Figure 1

15 pages, 3076 KiB

Open AccessArticle

Transcriptome Analysis of the Effect of Nickel on Lipid Metabolism in Mouse Kidney

by Jing Zhang, Yahong Gao, Yuewen Li, Dongdong Liu, Wenpeng Sun, Chuncheng Liu and Xiujuan Zhao

Biology 2024, 13(9), 655; https://doi.org/10.3390/biology13090655 - 24 Aug 2024

Viewed by 331

Abstract

Although the human body needs nickel as a trace element, too much nickel exposure can be hazardous. The effects of nickel on cells include inducing oxidative stress, interfering with DNA damage repair, and altering epigenetic modifications. Glucose metabolism and lipid metabolism are closely [...] Read more.

Although the human body needs nickel as a trace element, too much nickel exposure can be hazardous. The effects of nickel on cells include inducing oxidative stress, interfering with DNA damage repair, and altering epigenetic modifications. Glucose metabolism and lipid metabolism are closely related to oxidative stress; however, their role in nickel-induced damage needs further study. In Institute of Cancer Research (ICR) mice, our findings indicated that nickel stress increased the levels of blood lipid indicators (triglycerides, high-density lipoprotein, and cholesterol) by about 50%, blood glucose by more than two-fold, and glycated serum protein by nearly 20%. At the same time, nickel stress increased oxidative stress (malondialdehyde) and inflammation (Interleukin 6) by about 30% in the kidney. Based on next-generation sequencing technology, we detected and analyzed differentially expressed genes in the kidney caused by nickel stress. Bioinformatics analysis and experimental verification showed that nickel inhibited the expression of genes related to lipid metabolism and the AMPK and PPAR signaling pathways. The finding that nickel induces kidney injury and inhibits key genes involved in lipid metabolism and the AMPK and PPAR signaling pathways provides a theoretical basis for a deeper understanding of the mechanism of nickel-induced kidney injury. Full article

(This article belongs to the Section Genetics and Genomics)

► Show Figures

Figure 1

17 pages, 2132 KiB

Open AccessArticle

Inflammation and Tumor Progression: The Differential Impact of SAA in Breast Cancer Models

by Daniel Wilhelm Olivier, Carla Eksteen, Manisha du Plessis, Louis de Jager, Lize Engelbrecht, Nathaniel Wade McGregor, Preetha Shridas, Frederick C. de Beer, Willem J. S. de Villiers, Etheresia Pretorius and Anna-Mart Engelbrecht

Biology 2024, 13(9), 654; https://doi.org/10.3390/biology13090654 - 23 Aug 2024

Viewed by 311

Abstract

Background: Previous research has shown that the Serum Amyloid A (SAA) protein family is intricately involved in inflammatory signaling and various disease pathologies. We have previously demonstrated that SAA is associated with increased colitis disease severity and the promotion of tumorigenesis. However, the [...] Read more.

Background: Previous research has shown that the Serum Amyloid A (SAA) protein family is intricately involved in inflammatory signaling and various disease pathologies. We have previously demonstrated that SAA is associated with increased colitis disease severity and the promotion of tumorigenesis. However, the specific role of SAA proteins in breast cancer pathology remains unclear. Therefore, we investigated the role of systemic SAA1 and SAA2 (SAA1/2) in a triple-negative breast cancer mouse model. Methods: Syngeneic breast tumors were established in wild-type mice, and mice lacking the SAA1/2 (SAADKO). Subsequently, tumor volume was monitored, species survival determined, the inflammatory profiles of mice assessed with a multiplex assay, and tumor molecular biology and histology characterized with Western blotting and H&E histological staining. Results: WT tumor-bearing mice had increased levels of plasma SAA compared to wild-type control mice, while SAADKO control and tumor-bearing mice presented with lower levels of SAA in their plasma. SAADKO tumor-bearing mice also displayed significantly lower concentrations of systemic inflammatory markers. Tumors from SAADKO mice overall had lower levels of SAA compared to tumors from wild-type mice, decreased apoptosis and inflammasome signaling, and little to no tumor necrosis. Conclusions: We demonstrated that systemic SAA1/2 stimulates the activation of the NLRP3 inflammasome in breast tumors, leading to the production of pro-inflammatory cytokines. This, in turn, promoted apoptosis and tumor necrosis but did not significantly impact tumor growth or histological grading. Full article

(This article belongs to the Special Issue Advances in Biological Breast Cancer Research)

► Show Figures

Figure 1

10 pages, 1985 KiB

Open AccessArticle

Addition of Mitoquinone (MitoQ) to Fresh Human Sperm Enhances Sperm Motility without Attenuating Viability

by Nehad Al-Tarayra, Zina M. Al-Alami, Abdelkader Battah and Nadia Muhaidat

Biology 2024, 13(9), 653; https://doi.org/10.3390/biology13090653 - 23 Aug 2024

Viewed by 288

Abstract

The preparation of human sperm in an andrology laboratory subjects it to oxidative stress. Reactive oxygen species are produced by mitochondria, making it susceptible to oxidative damage; hence, mitochondria-targeted antioxidants like Mitoquinone (MitoQ) might have therapeutic potential for oxidative-damage-associated disorders. The current research [...] Read more.

The preparation of human sperm in an andrology laboratory subjects it to oxidative stress. Reactive oxygen species are produced by mitochondria, making it susceptible to oxidative damage; hence, mitochondria-targeted antioxidants like Mitoquinone (MitoQ) might have therapeutic potential for oxidative-damage-associated disorders. The current research aims to establish whether MitoQ has any positive effects during in vitro preparation of fresh human sperm. Viability and motility are evaluated to determine the effective MitoQ concentration and to assess whether MitoQ supplementation is affected by sperm concentration by incubating normospermia semen samples at 37 °C for 2 h and 4 h, respectively. The effect of semen centrifugation following supplementation of 20 × 10⁶ sperm/mL with 200 nM MitoQ is also assessed by measuring viability, motility and sperm DNA fragmentation. The best sperm motility is achieved after 2 h of incubation with 200 nM MitoQ at 37 °C. Sperm concentration of 20 × 10⁶ sperm/mL is the best concentration where 200 nM MitoQ works efficiently. For semen centrifugation at 300× g for 20 min, supplementation with 200 nM MitoQ shows higher sperm motility. The current results demonstrate that MitoQ supplementation during in vitro human semen preparation procedures positively affects fresh sperm motility without affecting viability or increasing DNA fragmentation. Full article

(This article belongs to the Section Reproductive Biology)

► Show Figures

Figure 1

17 pages, 8040 KiB

Open AccessArticle

The Putative Virulence Plasmid pYR4 of the Fish Pathogen Yersinia ruckeri Is Conjugative and Stabilized by a HigBA Toxin–Antitoxin System

by Fisentzos Floras, Chantell Mawere, Manvir Singh, Victoria Wootton, Luke Hamstead, Gareth McVicker and Jack C. Leo

Biology 2024, 13(9), 652; https://doi.org/10.3390/biology13090652 - 23 Aug 2024

Viewed by 288

Abstract

The bacterium Yersinia ruckeri causes enteric redmouth disease in salmonids and hence has substantial economic implications for the farmed fish industry. The Norwegian Y. ruckeri outbreak isolate NVH_3758 carries a relatively uncharacterized plasmid, pYR4, which encodes both type 4 pili and a type [...] Read more.

The bacterium Yersinia ruckeri causes enteric redmouth disease in salmonids and hence has substantial economic implications for the farmed fish industry. The Norwegian Y. ruckeri outbreak isolate NVH_3758 carries a relatively uncharacterized plasmid, pYR4, which encodes both type 4 pili and a type 4 secretion system. In this study, we demonstrate that pYR4 does not impose a growth burden on the Y. ruckeri host bacterium, nor does the plasmid contribute to twitching motility (an indicator of type 4 pilus function) or virulence in a Galleria mellonella larval model of infection. However, we show that pYR4 is conjugative. We also reveal, through mutagenesis, that pYR4 encodes a functional post-segregational killing system, HigBA, that is responsible for plasmid maintenance within Y. ruckeri. This is the first toxin–antitoxin system to be characterized for this organism. Whilst further work is needed to elucidate the virulence role of pYR4 and whether it contributes to bacterial disease under non-laboratory conditions, our results suggest that the plasmid possesses substantial stability and transfer mechanisms that imply importance within the organism. These results add to our understanding of the mobile genetic elements and evolutionary trajectory of Y. ruckeri as an important commercial pathogen, with consequences for human food production. Full article

(This article belongs to the Collection Feature Papers in Microbial Biology)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Biology, Volume 13, Issue 9 (September 2024) – 36 articles

Further Information

Guidelines

MDPI Initiatives

Follow MDPI