Editor’s Choice Articles

Editor’s Choice articles are based on recommendations by the scientific editors of MDPI journals from around the world. Editors select a small number of articles recently published in the journal that they believe will be particularly interesting to readers, or important in the respective research area. The aim is to provide a snapshot of some of the most exciting work published in the various research areas of the journal.

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13 pages, 2860 KiB  
Review
Vesicular Trafficking, a Mechanism Controlled by Cascade Activation of Rab Proteins: Focus on Rab27
by Camille Menaceur, Océane Dusailly, Fabien Gosselet, Laurence Fenart and Julien Saint-Pol
Biology 2023, 12(12), 1530; https://doi.org/10.3390/biology12121530 - 15 Dec 2023
Viewed by 1457
Abstract
Vesicular trafficking is essential for the cell to internalize useful proteins and soluble substances, for cell signaling or for the degradation of pathogenic elements such as bacteria or viruses. This vesicular trafficking also enables the cell to engage in secretory processes for the [...] Read more.
Vesicular trafficking is essential for the cell to internalize useful proteins and soluble substances, for cell signaling or for the degradation of pathogenic elements such as bacteria or viruses. This vesicular trafficking also enables the cell to engage in secretory processes for the elimination of waste products or for the emission of intercellular communication vectors such as cytokines, chemokines and extracellular vesicles. Ras-related proteins (Rab) and their effector(s) are of crucial importance in all of these processes, and mutations/alterations to them have serious pathophysiological consequences. This review presents a non-exhaustive overview of the role of the major Rab involved in vesicular trafficking, with particular emphasis on their involvement in the biogenesis and secretion of extracellular vesicles, and on the role of Rab27 in various pathophysiological processes. Therefore, Rab and their effector(s) are central therapeutic targets, given their involvement in vesicular trafficking and their importance for cell physiology. Full article
(This article belongs to the Special Issue Cell Transport in Health and Disease)
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15 pages, 871 KiB  
Review
Immune Escape in Glioblastoma: Mechanisms of Action and Implications for Immune Checkpoint Inhibitors and CAR T-Cell Therapy
by Catherine Yu, Kristin Hsieh, Daniel R. Cherry, Anthony D. Nehlsen, Lucas Resende Salgado, Stanislav Lazarev and Kunal K. Sindhu
Biology 2023, 12(12), 1528; https://doi.org/10.3390/biology12121528 - 15 Dec 2023
Viewed by 1597
Abstract
Glioblastoma, the most common primary brain cancer in adults, is characterized by a poor prognosis and resistance to standard treatments. The advent of immunotherapy has revolutionized the treatment of several cancers in recent years but has failed to demonstrate benefit in patients with [...] Read more.
Glioblastoma, the most common primary brain cancer in adults, is characterized by a poor prognosis and resistance to standard treatments. The advent of immunotherapy has revolutionized the treatment of several cancers in recent years but has failed to demonstrate benefit in patients with glioblastoma. Understanding the mechanisms by which glioblastoma exerts tumor-mediated immune suppression in both the tumor microenvironment and the systemic immune landscape is a critical step towards developing effective immunotherapeutic strategies. In this review, we discuss the current understanding of immune escape mechanisms in glioblastoma that compromise the efficacy of immunotherapies, with an emphasis on immune checkpoint inhibitors and chimeric antigen receptor T-cell therapy. In parallel, we review data from preclinical studies that have identified additional therapeutic targets that may enhance overall treatment efficacy in glioblastoma when administered alongside existing immunotherapies. Full article
(This article belongs to the Special Issue Progression of the Immune Escape Mechanism in Tumors)
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16 pages, 1539 KiB  
Article
Octopus vulgaris Exhibits Interindividual Differences in Behavioural and Problem-Solving Performance
by Andrea Dissegna, Luciana Borrelli, Giovanna Ponte, Cinzia Chiandetti and Graziano Fiorito
Biology 2023, 12(12), 1487; https://doi.org/10.3390/biology12121487 - 04 Dec 2023
Viewed by 1735
Abstract
By presenting individual Octopus vulgaris with an extractive foraging problem with a puzzle box, we examined the possible correlation between behavioural performances (e.g., ease of adaptation to captive conditions, prevalence of neophobic and neophilic behaviours, and propensity to learn individually or by observing [...] Read more.
By presenting individual Octopus vulgaris with an extractive foraging problem with a puzzle box, we examined the possible correlation between behavioural performances (e.g., ease of adaptation to captive conditions, prevalence of neophobic and neophilic behaviours, and propensity to learn individually or by observing conspecifics), biotic (body and brain size, age, sex) and abiotic (seasonality and place of origin) factors. We found more neophilic animals showing shorter latencies to approach the puzzle box and higher probability of solving the task; also, shorter times to solve the task were correlated with better performance on the individual learning task. However, the most neophilic octopuses that approached the puzzle box more quickly did not reach the solution earlier than other individuals, suggesting that strong neophilic tendency may lead to suboptimal performance at some stages of the problem-solving process. In addition, seasonal and environmental characteristics of location of origin appear to influence the rate of expression of individual traits central to problem solving. Overall, our analysis provides new insights into the traits associated with problem solving in invertebrates and highlights the presence of adaptive mechanisms that promote population-level changes in octopuses’ behavioural traits. Full article
(This article belongs to the Section Behavioural Biology)
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12 pages, 1824 KiB  
Article
SLC16a6, mTORC1, and Autophagy Regulate Ketone Body Excretion in the Intestinal Cells
by Takashi Uebanso, Moeka Fukui, Chisato Naito, Takaaki Shimohata, Kazuaki Mawatari and Akira Takahashi
Biology 2023, 12(12), 1467; https://doi.org/10.3390/biology12121467 - 26 Nov 2023
Viewed by 1457
Abstract
Ketone bodies serve several functions in the intestinal epithelium, such as stem cell maintenance, cell proliferation and differentiation, and cancer growth. Nevertheless, there is limited understanding of the mechanisms governing the regulation of intestinal ketone body concentration. In this study, we elucidated the [...] Read more.
Ketone bodies serve several functions in the intestinal epithelium, such as stem cell maintenance, cell proliferation and differentiation, and cancer growth. Nevertheless, there is limited understanding of the mechanisms governing the regulation of intestinal ketone body concentration. In this study, we elucidated the factors responsible for ketone body production and excretion using shRNA-mediated or pharmacological inhibition of specific genes or functions in the intestinal cells. We revealed that a fasting-mimicked culture medium, which excluded glucose, pyruvate, and glutamine, augmented ketone body production and excretion in the Caco2 and HT29 colorectal cells. This effect was attenuated by glucose or glutamine supplementation. On the other hand, the inhibition of the mammalian target of rapamycin complex1 (mTORC1) recovered a fraction of the excreted ketone bodies. In addition, the pharmacological or shbeclin1-mediated inhibition of autophagy suppressed ketone body excretion. The knockdown of basigin, a transmembrane protein responsible for targeting monocarboxylate transporters (MCTs), such as MCT1 and MCT4, suppressed lactic acid and pyruvic acid excretion but increased ketone body excretion. Finally, we found that MCT7 (SLC16a6) knockdown suppressed ketone body excretion. Our findings indicate that the mTORC1–autophagy axis and MCT7 are potential targets to regulate ketone body excretion from the intestinal epithelium. Full article
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34 pages, 4361 KiB  
Article
Anatomy of the Female Koala Reproductive Tract
by Sara Pagliarani, Chiara Palmieri, Michael McGowan, Frank Carrick, Jackson Boyd and Stephen D. Johnston
Biology 2023, 12(11), 1445; https://doi.org/10.3390/biology12111445 - 17 Nov 2023
Viewed by 2046
Abstract
The koala (Phascolarctos cinereus), while being an iconic Australian marsupial, has recently been listed as endangered. To establish an improved understanding of normal reproductive anatomy, this paper brings together unpublished research which has approached the topic from two perspectives: (1) the [...] Read more.
The koala (Phascolarctos cinereus), while being an iconic Australian marsupial, has recently been listed as endangered. To establish an improved understanding of normal reproductive anatomy, this paper brings together unpublished research which has approached the topic from two perspectives: (1) the establishment of an artificial insemination program, and (2) the definition of Chlamydia spp.-derived histopathological changes of the female koala urogenital system. Based on the presentation and histological processing of over 70 opportunistic specimens, recovered from wildlife hospitals in Southeast Queensland (Australia), we describe the gross and microanatomy of the koala ovary, oviduct, uteri, vaginal complex, and urogenital sinus during the interestrous, proliferative, and luteal phases of the reproductive cycle. Full article
(This article belongs to the Section Reproductive Biology)
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15 pages, 3055 KiB  
Review
Iron Homeostasis in Azotobacter vinelandii
by Elena Rosa-Núñez, Carlos Echavarri-Erasun, Alejandro M. Armas, Viviana Escudero, César Poza-Carrión, Luis M. Rubio and Manuel González-Guerrero
Biology 2023, 12(11), 1423; https://doi.org/10.3390/biology12111423 - 12 Nov 2023
Viewed by 1297
Abstract
Iron is an essential nutrient for all life forms. Specialized mechanisms exist in bacteria to ensure iron uptake and its delivery to key enzymes within the cell, while preventing toxicity. Iron uptake and exchange networks must adapt to the different environmental conditions, particularly [...] Read more.
Iron is an essential nutrient for all life forms. Specialized mechanisms exist in bacteria to ensure iron uptake and its delivery to key enzymes within the cell, while preventing toxicity. Iron uptake and exchange networks must adapt to the different environmental conditions, particularly those that require the biosynthesis of multiple iron proteins, such as nitrogen fixation. In this review, we outline the mechanisms that the model diazotrophic bacterium Azotobacter vinelandii uses to ensure iron nutrition and how it adapts Fe metabolism to diazotrophic growth. Full article
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20 pages, 3870 KiB  
Review
The Skin and Inflamm-Aging
by Rashi Agrawal, Anne Hu and Wendy B. Bollag
Biology 2023, 12(11), 1396; https://doi.org/10.3390/biology12111396 - 02 Nov 2023
Cited by 3 | Viewed by 2706
Abstract
With its unique anatomical location facing both the external and internal environment, the skin has crucial functions, including shielding the body from damage caused by ultraviolet radiation and chemicals, preventing water loss, acting as a primary barrier against pathogens, participating in metabolic processes [...] Read more.
With its unique anatomical location facing both the external and internal environment, the skin has crucial functions, including shielding the body from damage caused by ultraviolet radiation and chemicals, preventing water loss, acting as a primary barrier against pathogens, participating in metabolic processes like vitamin D production and temperature control and relaying information to the body through sensory and proprioceptor nerves. Like all organ systems, skin is known to undergo multiple changes with aging. A better understanding of the mechanisms that mediate aging-related skin dysfunction may allow the creation of targeted therapeutics that have beneficial effects not only on aged skin but also on other organs and tissues that experience a loss of or decline in function with aging. The skin is the largest organ of the body and can contribute to serum inflammatory mediator levels. One alteration known to occur with age is an impairment of skin barrier function; since disruption of the barrier is known to induce inflammation, skin may be a major contributor to the sustained, sub-clinical systemic inflammation associated with aging. Such “inflamm-aging” may underlie many of the deleterious changes observed in aged individuals. This review explores the role of age-related skin changes, skin inflammation and inflamm-aging. Full article
(This article belongs to the Collection Molecular Mechanisms of Aging)
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18 pages, 385 KiB  
Review
Telomere Dynamics in Livestock
by Nan Zhang, Emilie C. Baker, Thomas H. Welsh, Jr. and David G. Riley
Biology 2023, 12(11), 1389; https://doi.org/10.3390/biology12111389 - 31 Oct 2023
Viewed by 1689
Abstract
Telomeres are repeated sequences of nucleotides at the end of chromosomes. They deteriorate across mitotic divisions of a cell. In Homo sapiens this process of lifetime reduction has been shown to correspond with aspects of organismal aging and exposure to stress or other [...] Read more.
Telomeres are repeated sequences of nucleotides at the end of chromosomes. They deteriorate across mitotic divisions of a cell. In Homo sapiens this process of lifetime reduction has been shown to correspond with aspects of organismal aging and exposure to stress or other insults. The early impetus to characterize telomere dynamics in livestock related to the concern that aged donor DNA would result in earlier cell senescence and overall aging in cloned animals. Telomere length investigations in dairy cows included breed effects, estimates of additive genetic control (heritability 0.12 to 0.46), and effects of external stressors on telomere degradation across animal life. Evaluation of telomeres with respect to aging has also been conducted in pigs and horses, and there are fewer reports of telomere biology in beef cattle, sheep, and goats. There were minimal associations of telomere length with animal productivity measures. Most, but not all, work in livestock has documented an inverse relationship between peripheral blood cell telomere length and age; that is, a longer telomere length was associated with younger age. Because livestock longevity affects productivity and profitability, the role of tissue-specific telomere attrition in aging may present alternative improvement strategies for genetic improvement while also providing translational biomedical knowledge. Full article
(This article belongs to the Section Biotechnology)
21 pages, 957 KiB  
Review
Prevalence of Cobalt in the Environment and Its Role in Biological Processes
by Giuseppe Genchi, Graziantonio Lauria, Alessia Catalano, Alessia Carocci and Maria Stefania Sinicropi
Biology 2023, 12(10), 1335; https://doi.org/10.3390/biology12101335 - 16 Oct 2023
Cited by 2 | Viewed by 2789
Abstract
Cobalt (Co) is an essential trace element for humans and other animals, but high doses can be harmful to human health. It is present in some foods such as green vegetables, various spices, meat, milk products, seafood, and eggs, and in drinking water. [...] Read more.
Cobalt (Co) is an essential trace element for humans and other animals, but high doses can be harmful to human health. It is present in some foods such as green vegetables, various spices, meat, milk products, seafood, and eggs, and in drinking water. Co is necessary for the metabolism of human beings and animals due to its key role in the formation of vitamin B12, also known as cobalamin, the biological reservoir of Co. In high concentrations, Co may cause some health issues such as vomiting, nausea, diarrhea, bleeding, low blood pressure, heart diseases, thyroid damage, hair loss, bone defects, and the inhibition of some enzyme activities. Conversely, Co deficiency can lead to anorexia, chronic swelling, and detrimental anemia. Co nanoparticles have different and various biomedical applications thanks to their antioxidant, antimicrobial, anticancer, and antidiabetic properties. In addition, Co and cobalt oxide nanoparticles can be used in lithium-ion batteries, as a catalyst, a carrier for targeted drug delivery, a gas sensor, an electronic thin film, and in energy storage. Accumulation of Co in agriculture and humans, due to natural and anthropogenic factors, represents a global problem affecting water quality and human and animal health. Besides the common chelating agents used for Co intoxication, phytoremediation is an interesting environmental technology for cleaning up soil contaminated with Co. The occurrence of Co in the environment is discussed and its involvement in biological processes is underlined. Toxicological aspects related to Co are also examined in this review. Full article
(This article belongs to the Special Issue Essential Trace Elements in the Human Metabolism)
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23 pages, 2259 KiB  
Review
Bioactive Components in Fruit Interact with Gut Microbes
by Yuanyuan Jin, Ling Chen, Yufen Yu, Muhammad Hussain and Hao Zhong
Biology 2023, 12(10), 1333; https://doi.org/10.3390/biology12101333 - 13 Oct 2023
Cited by 1 | Viewed by 1754
Abstract
Fruits contain many bioactive compounds, including polysaccharides, oligosaccharides, polyphenols, anthocyanins, and flavonoids. All of these bioactives in fruit have potentially beneficial effects on gut microbiota and host health. On the one hand, fruit rich in active ingredients can act as substrates to interact [...] Read more.
Fruits contain many bioactive compounds, including polysaccharides, oligosaccharides, polyphenols, anthocyanins, and flavonoids. All of these bioactives in fruit have potentially beneficial effects on gut microbiota and host health. On the one hand, fruit rich in active ingredients can act as substrates to interact with microorganisms and produce metabolites to regulate the gut microbiota. On the other hand, gut microbes could promote health effects in the host by balancing dysbiosis of gut microbiota. We have extensively analyzed significant information on bioactive components in fruits based on Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). Although the deep mechanism of action of bioactive components in fruits on gut microbiota needs further study, these results also provide supportive information on fruits as a source of dietary active ingredients to provide support for the adjunctive role of fruits in disease prevention and treatment. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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23 pages, 2416 KiB  
Review
An Overview of D7 Protein Structure and Physiological Roles in Blood-Feeding Nematocera
by Patricia H. Alvarenga and John F. Andersen
Biology 2023, 12(1), 39; https://doi.org/10.3390/biology12010039 - 26 Dec 2022
Cited by 1 | Viewed by 1991
Abstract
Each time an insect bites a vertebrate host, skin and vascular injury caused by piercing triggers a series of responses including hemostasis, inflammation and immunity. In place, this set of redundant and interconnected responses would ultimately cause blood coagulation, itching and pain leading [...] Read more.
Each time an insect bites a vertebrate host, skin and vascular injury caused by piercing triggers a series of responses including hemostasis, inflammation and immunity. In place, this set of redundant and interconnected responses would ultimately cause blood coagulation, itching and pain leading to host awareness, resulting in feeding interruption in the best-case scenario. Nevertheless, hematophagous arthropod saliva contains a complex cocktail of molecules that are crucial to the success of blood-feeding. Among important protein families described so far in the saliva of blood sucking arthropods, is the D7, abundantly expressed in blood feeding Nematocera. D7 proteins are distantly related to insect Odorant-Binding Proteins (OBP), and despite low sequence identity, observation of structural similarity led to the suggestion that like OBPs, they should bind/sequester small hydrophobic compounds. Members belonging to this family are divided in short forms and long forms, containing one or two OBP-like domains, respectively. Here, we provide a review of D7 proteins structure and function, discussing how gene duplication and some modifications in their OBP-like domains during the course of evolution lead to gain and loss of function among different hematophagous Diptera species. Full article
(This article belongs to the Special Issue New Sights in Odorant-Binding Proteins)
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14 pages, 2621 KiB  
Article
Linoleate-Enrichment of Mitochondrial Cardiolipin Molecular Species Is Developmentally Regulated and a Determinant of Metabolic Phenotype
by Genevieve C. Sparagna, Raleigh L. Jonscher, Sydney R. Shuff, Elisabeth K. Phillips, Cortney E. Wilson, Kathleen C. Woulfe, Anastacia M. Garcia, Brian L. Stauffer and Kathryn C. Chatfield
Biology 2023, 12(1), 32; https://doi.org/10.3390/biology12010032 - 24 Dec 2022
Cited by 2 | Viewed by 1772
Abstract
Cardiolipin (CL), the major mitochondrial phospholipid, regulates the activity of many mitochondrial membrane proteins. CL composition is shifted in heart failure with decreases in linoleate and increases in oleate side chains, but whether cardiolipin composition directly regulates metabolism is unknown. This study defines [...] Read more.
Cardiolipin (CL), the major mitochondrial phospholipid, regulates the activity of many mitochondrial membrane proteins. CL composition is shifted in heart failure with decreases in linoleate and increases in oleate side chains, but whether cardiolipin composition directly regulates metabolism is unknown. This study defines cardiolipin composition in rat heart and liver at three distinct ages to determine the influence of CL composition on beta-oxidation (ß-OX). CL species, expression of ß-OX and glycolytic genes, and carnitine palmitoyltransferase (CPT) activity were characterized in heart and liver from neonatal, juvenile, and adult rats. Ventricular myocytes were cultured from neonatal, juvenile, and adult rats and cardiolipin composition and CPT activity were measured. Cardiolipin composition in neonatal rat ventricular cardiomyocytes (NRVMs) was experimentally altered and mitochondrial respiration was assessed. Linoleate-enrichment of CL was observed in rat heart, but not liver, with increasing age. ß-OX genes and CPT activity were generally higher in adult heart and glycolytic genes lower, as a function of age, in contrast to liver. Palmitate oxidation increased in NRVMs when CL was enriched with linoleate. Our results indicate (1) CL is developmentally regulated, (2) linoleate-enrichment is associated with increased ß-OX and a more oxidative mitochondrial phenotype, and (3) experimentally induced linoleate-enriched CL in ventricular myocytes promotes a shift from pyruvate metabolism to fatty acid ß-OX. Full article
(This article belongs to the Special Issue The Role of Cardiolipin in Mitochondrial Health and Disease)
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17 pages, 2534 KiB  
Article
Rapid Response to Experimental Warming of a Microbial Community Inhabiting High Arctic Patterned Ground Soil
by Kevin K. Newsham, Birgitte Kortegaard Danielsen, Elisabeth Machteld Biersma, Bo Elberling, Guy Hillyard, Priyanka Kumari, Anders Priemé, Cheolwoon Woo and Naomichi Yamamoto
Biology 2022, 11(12), 1819; https://doi.org/10.3390/biology11121819 - 14 Dec 2022
Cited by 2 | Viewed by 2110
Abstract
The influence of climate change on microbial communities inhabiting the sparsely vegetated patterned ground soils that are widespread across the High Arctic is poorly understood. Here, in a four-year experiment on Svalbard, we warmed patterned ground soil with open top chambers and biannually [...] Read more.
The influence of climate change on microbial communities inhabiting the sparsely vegetated patterned ground soils that are widespread across the High Arctic is poorly understood. Here, in a four-year experiment on Svalbard, we warmed patterned ground soil with open top chambers and biannually irrigated the soil to predict the responses of its microbial community to rising temperatures and precipitation. A 1 °C rise in summertime soil temperature caused 44% and 78% increases in CO2 efflux and CH4 consumption, respectively, and a 32% increase in the frequency of bacterial 16S ribosomal RNA genes. Bacterial alpha diversity was unaffected by the treatments, but, of the 40 most frequent bacterial taxa, warming caused 44–45% reductions in the relative abundances of a Sphingomonas sp. and Ferruginibacter sp. and 33–91% increases in those of a Phenylobacterium sp. and a member of the Acetobacteraceae. Warming did not influence the frequency of fungal internal transcribed spacer 2 copies, and irrigation had no effects on the measured variables. Our study suggests rapid changes to the activities and abundances of microbes, and particularly bacteria, in High Arctic patterned ground soils as they warm. At current rates of soil warming on Svalbard (0.8 °C per decade), we anticipate that similar effects to those reported here will manifest themselves in the natural environment by approximately the mid 2030s. Full article
(This article belongs to the Special Issue Polar Ecosystem: Response of Organisms to Changing Climate)
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15 pages, 2965 KiB  
Article
Methionine Metabolism Is Down-Regulated in Heart of Long-Lived Mammals
by Natalia Mota-Martorell, Mariona Jové, Rebeca Berdún, Èlia Òbis, Gustavo Barja and Reinald Pamplona
Biology 2022, 11(12), 1821; https://doi.org/10.3390/biology11121821 - 14 Dec 2022
Cited by 3 | Viewed by 2115
Abstract
Methionine constitutes a central hub of intracellular metabolic adaptations leading to an extended longevity (maximum lifespan). The present study follows a comparative approach analyzing methionine and related metabolite and amino acid profiles using an LC-MS/MS platform in the hearts of seven mammalian species [...] Read more.
Methionine constitutes a central hub of intracellular metabolic adaptations leading to an extended longevity (maximum lifespan). The present study follows a comparative approach analyzing methionine and related metabolite and amino acid profiles using an LC-MS/MS platform in the hearts of seven mammalian species with a longevity ranging from 3.8 to 57 years. Our findings demonstrate the existence of species-specific heart phenotypes associated with high longevity characterized by: (i) low concentration of methionine and its related sulphur-containing metabolites; (ii) low amino acid pool; and (iii) low choline concentration. Our results support the existence of heart metabotypes characterized by a down-regulation in long-lived species, supporting the idea that in longevity, less is more. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Mechanisms of Longevity and Aging)
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27 pages, 7319 KiB  
Article
Endophytic Pseudomonas sp. from Agave palmeri Participate in the Rhizophagy Cycle and Act as Biostimulants in Crop Plants
by Qiuwei Zhang, Kathryn L. Kingsley and James F. White
Biology 2022, 11(12), 1790; https://doi.org/10.3390/biology11121790 - 09 Dec 2022
Cited by 1 | Viewed by 2233
Abstract
Plant growth-promoting bacteria are generating increasing interest in the agricultural industry as a promising alternative to traditional chemical fertilizers; however, much of the focus has been on rhizosphere bacteria. Bacterial endophytes are another promising source of plant growth-promoting bacteria, and though many plants [...] Read more.
Plant growth-promoting bacteria are generating increasing interest in the agricultural industry as a promising alternative to traditional chemical fertilizers; however, much of the focus has been on rhizosphere bacteria. Bacterial endophytes are another promising source of plant growth-promoting bacteria, and though many plants have already been prospected for beneficial microbes, desert plants have been underrepresented in such studies. In this study, we show the growth-promoting potential of five strains of endophytic Pseudomonas sp. isolated from Agave palmeri, an agave from the Sonoran Desert. When inoculated onto Kentucky bluegrass, clover, carrot, coriander, and wheat, endophytic Pseudomonas sp. increased seedling root lengths in all hosts and seedling shoot lengths in Kentucky bluegrass, carrot, and wheat. Transformation of the Pseudomonas sp. strain P3AW to express the fluorescent protein mCherry revealed that Pseudomonas sp. becomes endophytic in non-native hosts and participates in parts of the rhizophagy cycle, a process by which endophytic bacteria cycle between the soil and roots, bringing in nutrients from the soil which are then extracted through reactive oxygen-mediated bacterial degradation in the roots. Tracking of the Pseudomonas sp. strain P3AW also provided evidence for a system of endophyte, or endophyte cell content, transport via the vascular bundle. These results provide further evidence of the rhizophagy cycle in plants and how it relates to growth promotion in plants by biostimulant bacteria. Full article
(This article belongs to the Section Plant Science)
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13 pages, 1798 KiB  
Article
Visual Monitoring Strategies of Sentinels in a Cooperative Breeder
by Guy Beauchamp and Reed Bowman
Biology 2022, 11(12), 1769; https://doi.org/10.3390/biology11121769 - 06 Dec 2022
Cited by 2 | Viewed by 1361
Abstract
Vigilance is important for early detection of threats. Previous studies have focused on the allocation of time to vigilance but neglected how animals monitor their surroundings during vigilance. Where animals look and how long each look lasts can affect the quality of visual [...] Read more.
Vigilance is important for early detection of threats. Previous studies have focused on the allocation of time to vigilance but neglected how animals monitor their surroundings during vigilance. Where animals look and how long each look lasts can affect the quality of visual monitoring and thus the ability to detect threats during vigilance. We examined visual monitoring strategies in the Florida scrub-jay (Aphelocoma coerulescens), a cooperative breeder with sentinel behaviour. Sentinels in this species make head turns from vantage points to detect the arrival of predators and intruding neighbours. We found that sentinels initiated head turns at regular intervals and also returned their gaze to areas previously monitored at regular intervals, which is predicted when predators and intruders rely on surprise rather than stealth to approach. Sentinels made head turns in several directions, but often more frequently on one side of the body than the other, which was not predicted for regular vigilance. Average look duration during sentinel bouts was shorter in smaller groups and in juveniles. We argue that shorter looks are beneficial to increase visual coverage in more threatening situations. Our study highlights how visual monitoring strategies during vigilance reflect the risk posed by predators and intruders. Full article
(This article belongs to the Section Behavioural Biology)
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10 pages, 1023 KiB  
Review
Brain-Derived Estrogen and Neurological Disorders
by Darrell W. Brann, Yujiao Lu, Jing Wang, Gangadhara R. Sareddy, Uday P. Pratap, Quanguang Zhang, Rajeshwar R. Tekmal and Ratna K. Vadlamudi
Biology 2022, 11(12), 1698; https://doi.org/10.3390/biology11121698 - 24 Nov 2022
Cited by 4 | Viewed by 3296
Abstract
Astrocytes and neurons in the male and female brains produce the neurosteroid brain-derived 17β-estradiol (BDE2) from androgen precursors. In this review, we discuss evidence that suggest BDE2 has a role in a number of neurological conditions, such as focal and [...] Read more.
Astrocytes and neurons in the male and female brains produce the neurosteroid brain-derived 17β-estradiol (BDE2) from androgen precursors. In this review, we discuss evidence that suggest BDE2 has a role in a number of neurological conditions, such as focal and global cerebral ischemia, traumatic brain injury, excitotoxicity, epilepsy, Alzheimer’s disease, and Parkinson’s disease. Much of what we have learned about BDE2 in neurological disorders has come from use of aromatase inhibitors and global aromatase knockout mice. Recently, our group developed astrocyte- and neuron-specific aromatase knockout mice, which have helped to clarify the precise functions of astrocyte-derived 17β-estradiol (ADE2) and neuron-derived 17β-estradiol (NDE2) in the brain. The available evidence to date suggests a primarily beneficial role of BDE2 in facilitating neuroprotection, synaptic and cognitive preservation, regulation of reactive astrocyte and microglia activation, and anti-inflammatory effects. Most of these beneficial effects appear to be due to ADE2, which is induced in most neurological disorders, but there is also recent evidence that NDE2 exerts similar beneficial effects. Furthermore, in certain situations, BDE2 may also have deleterious effects, as recent evidence suggests its overproduction in epilepsy contributes to seizure induction. In this review, we examine the current state of this quickly developing topic, as well as possible future studies that may be required to provide continuing growth in the field. Full article
(This article belongs to the Special Issue Roles and Functions of Brain-Derived Estrogen)
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13 pages, 1163 KiB  
Article
A Biomarker Approach as Responses of Bioindicator Commercial Fish Species to Microplastic Ingestion: Assessing Tissue and Biochemical Relationships
by Xavier Capó, Merce Morató, Carme Alomar, Beatriz Rios-Fuster, Maria Valls, Montserrat Compa and Salud Deudero
Biology 2022, 11(11), 1634; https://doi.org/10.3390/biology11111634 - 08 Nov 2022
Cited by 8 | Viewed by 1876
Abstract
Plastic debris is a growing environmental problem on a global scale, as plastics and microplastics (MPs) can be ingested by marine organisms, inducing toxic effects. The aim of this study was to assess MP intake and antioxidant responses in three bioindicator species: red [...] Read more.
Plastic debris is a growing environmental problem on a global scale, as plastics and microplastics (MPs) can be ingested by marine organisms, inducing toxic effects. The aim of this study was to assess MP intake and antioxidant responses in three bioindicator species: red mullet, bogue, and anchovy (Mullus surmuletus, Boops boops, and Engraulis encrasicolus, respectively) for plastic contamination in the Mediterranean Sea. MP intake was assessed in the gastrointestinal tract of the fish. Further, several enzymes from both the liver and brain were analysed. The antioxidant defences, catalase (CAT) and superoxide dismutase (SOD), as well as the detoxifying enzyme glutathione-S-transferase (GST), were measured in both tissues. The acetylcholine esterase (AchE), as an indicator of neuronal damage, was measured in the brain. Malondialdehyde (MDA) was analysed as a marker of oxidative damage in the brain and liver samples. Total MP intake and MP typology differed between the three species, with M. surmuletus showing the lowest intake of MPs, while B. boops showed the highest intake of MPs. An increase in both antioxidant enzymes was evidenced in E. encrasicolus liver activity with respect to MP intake. In brain samples, an increase in CAT activity was found in M. surmuletus and B. boops as a consequence of MP ingestion. SOD activity in the brain increased in B. boops and E. encrasicolus that had ingested MPs. GST activity increased in the liver of M. surmuletus’ and in brains of B. boops that had ingested MPs. The intake of MPs is species related, as well as being inherently linked to the habitat they live in and being able to induce a light activation of species-specific detoxifying and antioxidant mechanisms. Full article
(This article belongs to the Special Issue Effects of Microplastic Pollution on Marine Ecology)
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21 pages, 4325 KiB  
Article
Butterfly Wing Color Pattern Modification Inducers May Act on Chitin in the Apical Extracellular Site: Implications in Morphogenic Signals for Color Pattern Determination
by Joji M. Otaki and Yugo Nakazato
Biology 2022, 11(11), 1620; https://doi.org/10.3390/biology11111620 - 06 Nov 2022
Cited by 3 | Viewed by 3818
Abstract
Butterfly wing color patterns are modified by various treatments, such as temperature shock, injection of chemical inducers, and covering materials on pupal wing tissue. Their mechanisms of action have been enigmatic. Here, we investigated the mechanisms of color pattern modifications using the blue [...] Read more.
Butterfly wing color patterns are modified by various treatments, such as temperature shock, injection of chemical inducers, and covering materials on pupal wing tissue. Their mechanisms of action have been enigmatic. Here, we investigated the mechanisms of color pattern modifications using the blue pansy butterfly Junonia orithya. We hypothesized that these modification-inducing treatments act on the pupal cuticle or extracellular matrix (ECM). Mechanical load tests revealed that pupae treated with cold shock or chemical inducers were significantly less rigid, suggesting that these treatments made cuticle formation less efficient. A known chitin inhibitor, FB28 (fluorescent brightener 28), was discovered to efficiently induce modifications. Taking advantage of its fluorescent character, fluorescent signals from FB28 were observed in live pupae in vivo from the apical extracellular side and were concentrated at the pupal cuticle focal spots immediately above the eyespot organizing centers. It was shown that chemical modification inducers and covering materials worked additively. Taken together, various modification-inducing treatments likely act extracellularly on chitin or other polysaccharides to inhibit pupal cuticle formation or ECM function, which probably causes retardation of morphogenic signals. It is likely that an interactive ECM is required for morphogenic signals for color pattern determination to travel long distances. Full article
(This article belongs to the Section Developmental Biology)
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21 pages, 3438 KiB  
Review
Wide-Field Calcium Imaging of Neuronal Network Dynamics In Vivo
by Angela K. Nietz, Laurentiu S. Popa, Martha L. Streng, Russell E. Carter, Suhasa B. Kodandaramaiah and Timothy J. Ebner
Biology 2022, 11(11), 1601; https://doi.org/10.3390/biology11111601 - 01 Nov 2022
Cited by 12 | Viewed by 6348
Abstract
A central tenet of neuroscience is that sensory, motor, and cognitive behaviors are generated by the communications and interactions among neurons, distributed within and across anatomically and functionally distinct brain regions. Therefore, to decipher how the brain plans, learns, and executes behaviors requires [...] Read more.
A central tenet of neuroscience is that sensory, motor, and cognitive behaviors are generated by the communications and interactions among neurons, distributed within and across anatomically and functionally distinct brain regions. Therefore, to decipher how the brain plans, learns, and executes behaviors requires characterizing neuronal activity at multiple spatial and temporal scales. This includes simultaneously recording neuronal dynamics at the mesoscale level to understand the interactions among brain regions during different behavioral and brain states. Wide-field Ca2+ imaging, which uses single photon excitation and improved genetically encoded Ca2+ indicators, allows for simultaneous recordings of large brain areas and is proving to be a powerful tool to study neuronal activity at the mesoscopic scale in behaving animals. This review details the techniques used for wide-field Ca2+ imaging and the various approaches employed for the analyses of the rich neuronal-behavioral data sets obtained. Also discussed is how wide-field Ca2+ imaging is providing novel insights into both normal and altered neural processing in disease. Finally, we examine the limitations of the approach and new developments in wide-field Ca2+ imaging that are bringing new capabilities to this important technique for investigating large-scale neuronal dynamics. Full article
(This article belongs to the Special Issue New Era in Neuroscience)
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14 pages, 860 KiB  
Review
A Review of Diopatra Ecology: Current Knowledge, Open Questions, and Future Threats for an Ecosystem Engineering Polychaete
by Sarah K. Berke
Biology 2022, 11(10), 1485; https://doi.org/10.3390/biology11101485 - 11 Oct 2022
Cited by 5 | Viewed by 2022
Abstract
A well-known example of marine ecosystem engineering is the annelid genus Diopatra, which builds large tubes in coastal sediments worldwide. Early studies of Diopatra were among the first to recognize the importance of facilitation in ecology, and Diopatra has become a key [...] Read more.
A well-known example of marine ecosystem engineering is the annelid genus Diopatra, which builds large tubes in coastal sediments worldwide. Early studies of Diopatra were among the first to recognize the importance of facilitation in ecology, and Diopatra has become a key marine soft-sediment application of the ecosystem engineering concept. Here, I review our current knowledge of Diopatra ecology, including its natural history, ecosystem engineering effects, and trophic relationships. I particularly explore how human activities are influencing Diopatra in terms of climate change, bait fishing, and species invasions. Most of what we know about Diopatra ecology comes from focal studies of a few species in a few well-known regions. Further evaluating how our current understanding applies to other species and/or other regions will help to refine and deepen our understanding of structure and function in marine systems. Full article
(This article belongs to the Special Issue Diopatra: The Amazing Ecosystem Engineering Polychaetous Annelid)
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19 pages, 5852 KiB  
Article
Preliminary Data about Habitat Use of Subadult and Adult White Sharks (Carcharodon carcharias) in Eastern Australian Waters
by Jessica L. Coxon, Paul A. Butcher, Julia L. Y. Spaet and Justin R. Rizzari
Biology 2022, 11(10), 1443; https://doi.org/10.3390/biology11101443 - 01 Oct 2022
Cited by 4 | Viewed by 2641
Abstract
In eastern Australia, white sharks (Carcharodon carcharias) are targeted in shark control programs, yet the movement of subadults and adults of the eastern Australasian population is poorly understood. To investigate horizontal and vertical movement and habitat use in this region, MiniPAT [...] Read more.
In eastern Australia, white sharks (Carcharodon carcharias) are targeted in shark control programs, yet the movement of subadults and adults of the eastern Australasian population is poorly understood. To investigate horizontal and vertical movement and habitat use in this region, MiniPAT pop-up satellite archival tags were deployed on three larger white sharks (340–388 cm total length) between May 2021 and January 2022. All sharks moved away from the coast after release and displayed a preference for offshore habitats. The upper < 50 m of the water column and temperatures between 14–19 °C were favoured, with a diel pattern of vertical habitat use evident as deeper depths were occupied during the day and shallower depths at night. Horizontal movement consisted of north–south seasonality interspersed with periods of residency. Very little information is available for adult white sharks in eastern Australia and studies like this provide key baseline information for their life history. Importantly, the latitudinal range achieved by white sharks illuminate the necessity for multijurisdictional management to effectively mitigate human-shark interactions whilst supporting conservation efforts of the species. Full article
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25 pages, 1641 KiB  
Review
Lysosomes and Their Role in Regulating the Metabolism of Hematopoietic Stem Cells
by Tasleem Arif
Biology 2022, 11(10), 1410; https://doi.org/10.3390/biology11101410 - 27 Sep 2022
Cited by 4 | Viewed by 3342
Abstract
Hematopoietic stem cells (HSCs) have the capacity to renew blood cells at all stages of life and are largely quiescent at a steady state. It is essential to understand the processes that govern quiescence in HSCs to enhance bone marrow transplantation. It is [...] Read more.
Hematopoietic stem cells (HSCs) have the capacity to renew blood cells at all stages of life and are largely quiescent at a steady state. It is essential to understand the processes that govern quiescence in HSCs to enhance bone marrow transplantation. It is hypothesized that in their quiescent state, HSCs primarily use glycolysis for energy production rather than mitochondrial oxidative phosphorylation (OXPHOS). In addition, the HSC switch from quiescence to activation occurs along a continuous developmental path that is driven by metabolism. Specifying the metabolic regulation pathway of HSC quiescence will provide insights into HSC homeostasis for therapeutic application. Therefore, understanding the metabolic demands of HSCs at a steady state is key to developing innovative hematological therapeutics. Lysosomes are the major degradative organelle in eukaryotic cells. Catabolic, anabolic, and lysosomal function abnormalities are connected to an expanding list of diseases. In recent years, lysosomes have emerged as control centers of cellular metabolism, particularly in HSC quiescence, and essential regulators of cell signaling have been found on the lysosomal membrane. In addition to autophagic processes, lysosomal activities have been shown to be crucial in sustaining quiescence by restricting HSCs access to a nutritional reserve essential for their activation into the cell cycle. Lysosomal activity may preserve HSC quiescence by altering glycolysis-mitochondrial biogenesis. The understanding of HSC metabolism has significantly expanded over the decade, revealing previously unknown requirements of HSCs in both their dividing (active) and quiescent states. Therefore, understanding the role of lysosomes in HSCs will allow for the development of innovative treatment methods based on HSCs to fight clonal hematopoiesis and HSC aging. Full article
(This article belongs to the Special Issue Metabolism of Hematopoietic Stem Cells during Development and Aging)
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12 pages, 1697 KiB  
Article
Evidence of Orientation-Dependent Early States of Prion Protein Misfolded Structures from Single Molecule Force Spectroscopy
by Andrea Raspadori, Valentina Vignali, Anna Murello, Gabriele Giachin, Bruno Samorì, Motomasa Tanaka, Carlos Bustamante, Giampaolo Zuccheri and Giuseppe Legname
Biology 2022, 11(9), 1358; https://doi.org/10.3390/biology11091358 - 16 Sep 2022
Cited by 2 | Viewed by 1962
Abstract
Prion diseases are neurodegenerative disorders characterized by the presence of oligomers and amyloid fibrils. These are the result of protein aggregation processes of the cellular prion protein (PrPC) into amyloidal forms denoted as prions or PrPSc. We employed atomic [...] Read more.
Prion diseases are neurodegenerative disorders characterized by the presence of oligomers and amyloid fibrils. These are the result of protein aggregation processes of the cellular prion protein (PrPC) into amyloidal forms denoted as prions or PrPSc. We employed atomic force microscopy (AFM) for single molecule pulling (single molecule force spectroscopy, SMFS) experiments on the recombinant truncated murine prion protein (PrP) domain to characterize its conformations and potential initial oligomerization processes. Our AFM-SMFS results point to a complex scenario of structural heterogeneity of PrP at the monomeric and dimer level, like other amyloid proteins involved in similar pathologies. By applying this technique, we revealed that the PrP C-terminal domain unfolds in a two-state process. We used two dimeric constructs with different PrP reciprocal orientations: one construct with two sequential PrP in the N- to C-terminal orientation (N-C dimer) and a second one in the C- to C-terminal orientation (C-C dimer). The analysis revealed that the different behavior in terms of unfolding force, whereby the dimer placed C-C dimer unfolds at a higher force compared to the N-C orientation. We propose that the C-C dimer orientation may represent a building block of amyloid fibril formation. Full article
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19 pages, 3639 KiB  
Article
Diversity and Assemblage of Harmful Algae in Homestead Fish Ponds in a Tropical Coastal Area
by Liza Akter, Md. Akram Ullah, Mohammad Belal Hossain, Anu Rani Karmaker, Md. Solaiman Hossain, Mohammed Fahad Albeshr and Takaomi Arai
Biology 2022, 11(9), 1335; https://doi.org/10.3390/biology11091335 - 09 Sep 2022
Cited by 2 | Viewed by 2320
Abstract
Algae are the naturally produced food for fish in any aquatic ecosystem and an indicator of a productive pond. However, excess abundance of harmful algae can have detrimental effects on fish health. In this study, the algal communities of 30 coastal homestead fish [...] Read more.
Algae are the naturally produced food for fish in any aquatic ecosystem and an indicator of a productive pond. However, excess abundance of harmful algae can have detrimental effects on fish health. In this study, the algal communities of 30 coastal homestead fish ponds were investigated to identify the diversity, assemblage and controlling environmental variables of harmful algae from a tropical coastal area. The findings showed that 81 of the 89 genera of identified algae were harmful, with the majority of them being in the classes of Cyanophyceae (50.81%), Chlorophyceae (23.75%), Bacillariophyceae (9.5%), and Euglenophyceae (8.47%). Microcystis spp. alone contributed 28.24% to the total abundance of harmful algae. Significant differences (p < 0.05) in algal abundance were found among the ponds with the highest abundance (470 ± 141.74 × 103 cells L−1) at pond (S25) near agricultural fields and the lowest abundance (109.33 ± 46.91 × 103 cells L−1) at pond (S14) which was lacking sufficient sunlight and nutrients. Diversity indices, e.g., dominance (D), evenness (J′), richness (d) and Shannon diversity index (H′) ranged from 0.17 to 0.44, 0.23 to 0.6, 0.35 to 2.23 and 0.7 to 1.79, respectively, indicating a moderate range of diversity and community stability. Community composition analysis showed the assemblage was dominated by Cyanophyceae, Chlorophyceae and Bacillariophyceae, whereas, multivariate cluster analyses (CA) identified 11 major clusters. To identify the factors controlling their distribution or community assemblages, eight environmental variables (temperature, pH, dissolved oxygen (DO), salinity, transparency, nitrates, phosphates and sulphate) were measured. ANOVA analysis showed that the variables significantly differed (p < 0.05) among the ponds, and canonical correspondence analysis (CCA) demonstrated that DO, nitrates, phosphates, sulphates, salinity and transparency have the most impact on the abundance of algal genera. In addition, analyses with Pearson’s correlation coefficient showed that the abundance of total algae, diversity and community were mainly governed by phosphates and sulphates. These results can be used to identify and control these toxic algal groups in the local aquaculture sector. Full article
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18 pages, 805 KiB  
Article
Primary-like Human Hepatocytes Genetically Engineered to Obtain Proliferation Competence as a Capable Application for Energy Metabolism Experiments in In Vitro Oncologic Liver Models
by Andrea Scheffschick, Jonas Babel, Sebastian Sperling, Julia Nerusch, Natalie Herzog, Daniel Seehofer and Georg Damm
Biology 2022, 11(8), 1195; https://doi.org/10.3390/biology11081195 - 09 Aug 2022
Cited by 2 | Viewed by 2106
Abstract
Non-alcoholic fatty liver disease (NAFLD), characterized by lipid accumulation in the liver, is the most common cause of liver diseases in Western countries. NAFLD is a major risk factor for developing hepatocellular carcinoma (HCC); however, in vitro evaluation of hepatic cancerogenesis fails due [...] Read more.
Non-alcoholic fatty liver disease (NAFLD), characterized by lipid accumulation in the liver, is the most common cause of liver diseases in Western countries. NAFLD is a major risk factor for developing hepatocellular carcinoma (HCC); however, in vitro evaluation of hepatic cancerogenesis fails due to a lack of liver models displaying a proliferation of hepatocytes. Originally designed to overcome primary human hepatocyte (PHH) shortages, upcyte hepatocytes were engineered to obtain continuous proliferation and, therefore, could be a suitable tool for HCC research. We generated upcyte hepatocytes, termed HepaFH3 cells, and compared their metabolic characteristics to HepG2 hepatoma cells and PHHs isolated from resected livers. For displaying NAFLD-related HCCs, we induced steatosis in all liver models. Lipid accumulation, lipotoxicity and energy metabolism were characterized using biochemical assays and Western blot analysis. We showed that proliferating HepaFH3 cells resemble HepG2, both showing a higher glucose uptake rate, lactate levels and metabolic rate compared to PHHs. Confluent HepaFH3 cells displayed some similarities to PHHs, including higher levels of the transaminases AST and ALT compared to proliferating HepaFH3 cells. We recommend proliferating HepaFH3 cells as a pre-malignant cellular model for HCC research, while confluent HepaFH3 cells could serve as PHH surrogates for energy metabolism studies. Full article
(This article belongs to the Section Cancer Biology)
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19 pages, 3026 KiB  
Article
The Use of Reproductive Indicators for Conservation Purposes: The Case Study of Palinurus elephas in Two Fully Protected Areas and Their Surrounding Zones (Central-Western Mediterranean)
by Cristina Porcu, Laura Carugati, Andrea Bellodi, Pierluigi Carbonara, Alessandro Cau, Danila Cuccu, Faustina Barbara Cannea, Martina Francesca Marongiu, Antonello Mulas, Alessandra Padiglia, Noemi Pascale, Paola Pesci and Maria Cristina Follesa
Biology 2022, 11(8), 1188; https://doi.org/10.3390/biology11081188 - 07 Aug 2022
Viewed by 1739
Abstract
In 1990s, the European spiny lobster Palinurus elephas, one of the most commercially important species in the Mediterranean, exhibited a population decline. For this reason, fully protected areas (FPAs) appeared effective in re-establishing natural populations and supporting fishery-management objectives. Here, the reproductive [...] Read more.
In 1990s, the European spiny lobster Palinurus elephas, one of the most commercially important species in the Mediterranean, exhibited a population decline. For this reason, fully protected areas (FPAs) appeared effective in re-establishing natural populations and supporting fishery-management objectives. Here, the reproductive parameters of P. elephas populations in two different FPAs (Su Pallosu and Buggerru, central-western Mediterranean), where a restocking programme was carried out, and in their surrounding commercial zones, were investigated from quantitative and qualitative perspectives. The comparison of fecundity between females collected inside and outside FPAs did not show statistical differences as well as the vitellogenin concentration, which did not vary among eggs of different size classes of females caught inside and outside the FPAs, indicating the same reproductive potential. The study demonstrated a benefit of overexploited populations in terms of enhancement of egg production overtime (15 years for Su Pallosu and 6 years for Buggerru) with a mean egg production 4.25–5.5 times higher at the end of the study than that observed at the beginning of the study. The main driver of eggs production appeared to be size, with larger lobsters more present inside the FPAs than outside. Given these results, the dominant contribution of the two studied FPAs to the regional lobster reproduction is remarkable. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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25 pages, 3456 KiB  
Article
Too Close for Comfort? Isotopic Niche Segregation in New Zealand’s Odontocetes
by Katharina J. Peters, Sarah J. Bury, Bethany Hinton, Emma L. Betty, Déborah Casano-Bally, Guido J. Parra and Karen A. Stockin
Biology 2022, 11(8), 1179; https://doi.org/10.3390/biology11081179 - 05 Aug 2022
Cited by 4 | Viewed by 3956
Abstract
Species occurring in sympatry and relying on similar and limited resources may partition resource use to avoid overlap and interspecific competition. Aotearoa, New Zealand hosts an extraordinarily rich marine megafauna, including 50% of the world’s cetacean species. In this study, we used carbon [...] Read more.
Species occurring in sympatry and relying on similar and limited resources may partition resource use to avoid overlap and interspecific competition. Aotearoa, New Zealand hosts an extraordinarily rich marine megafauna, including 50% of the world’s cetacean species. In this study, we used carbon and nitrogen stable isotopes as ecological tracers to investigate isotopic niche overlap between 21 odontocete (toothed whale) species inhabiting neritic, mesopelagic, and bathypelagic waters. Results showed a clear niche separation for the bathypelagic Gray’s beaked whales (Mesoplodon grayi) and sperm whales (Physeter macrocephalus), but high isotopic niche overlap and potential interspecific competition for neritic and mesopelagic species. For these species, competition could be reduced via temporal or finer-scale spatial segregation or differences in foraging behaviour. This study represents the first insights into the coexistence of odontocetes in a biodiverse hotspot. The data presented here provide a critical baseline to a system already ongoing ecosystem change via ocean warming and subsequent effects on prey abundance and distributions. Full article
(This article belongs to the Special Issue Applications of Stable Isotope Analysis in Ecology)
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24 pages, 2146 KiB  
Review
How Metabolic Rate Relates to Cell Size
by Douglas S. Glazier
Biology 2022, 11(8), 1106; https://doi.org/10.3390/biology11081106 - 25 Jul 2022
Cited by 19 | Viewed by 3910
Abstract
Metabolic rate and its covariation with body mass vary substantially within and among species in little understood ways. Here, I critically review explanations (and supporting data) concerning how cell size and number and their establishment by cell expansion and multiplication may affect metabolic [...] Read more.
Metabolic rate and its covariation with body mass vary substantially within and among species in little understood ways. Here, I critically review explanations (and supporting data) concerning how cell size and number and their establishment by cell expansion and multiplication may affect metabolic rate and its scaling with body mass. Cell size and growth may affect size-specific metabolic rate, as well as the vertical elevation (metabolic level) and slope (exponent) of metabolic scaling relationships. Mechanistic causes of negative correlations between cell size and metabolic rate may involve reduced resource supply and/or demand in larger cells, related to decreased surface area per volume, larger intracellular resource-transport distances, lower metabolic costs of ionic regulation, slower cell multiplication and somatic growth, and larger intracellular deposits of metabolically inert materials in some tissues. A cell-size perspective helps to explain some (but not all) variation in metabolic rate and its body-mass scaling and thus should be included in any multi-mechanistic theory attempting to explain the full diversity of metabolic scaling. A cell-size approach may also help conceptually integrate studies of the biological regulation of cellular growth and metabolism with those concerning major transitions in ontogenetic development and associated shifts in metabolic scaling. Full article
(This article belongs to the Section Cell Biology)
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19 pages, 1813 KiB  
Article
PhIP-Seq Reveals Autoantibodies for Ubiquitously Expressed Antigens in Viral Myocarditis
by Mahima T. Rasquinha, Ninaad Lasrado, Erika Petro-Turnquist, Eric Weaver, Thiagarajan Venkataraman, Daniel Anderson, Uri Laserson, H. Benjamin Larman and Jay Reddy
Biology 2022, 11(7), 1055; https://doi.org/10.3390/biology11071055 - 13 Jul 2022
Cited by 4 | Viewed by 3334
Abstract
Enteroviruses such as group B coxsackieviruses (CVB) are commonly suspected as causes of myocarditis that can lead to dilated cardiomyopathy (DCM), and the mouse model of CVB3 myocarditis is routinely used to understand DCM pathogenesis. Mechanistically, autoimmunity is suspected due to the presence [...] Read more.
Enteroviruses such as group B coxsackieviruses (CVB) are commonly suspected as causes of myocarditis that can lead to dilated cardiomyopathy (DCM), and the mouse model of CVB3 myocarditis is routinely used to understand DCM pathogenesis. Mechanistically, autoimmunity is suspected due to the presence of autoantibodies for select antigens. However, their role continues to be enigmatic, which also raises the question of whether the breadth of autoantibodies is sufficiently characterized. Here, we attempted to comprehensively analyze the autoantibody repertoire using Phage ImmunoPrecipitation Sequencing (PhIP-Seq), a versatile and high-throughput platform, in the mouse model of CVB3 myocarditis. First, PhIP-Seq analysis using the VirScan library revealed antibody reactivity only to CVB3 in the infected group but not in controls, thus validating the technique in this model. Second, using the mouse peptide library, we detected autoantibodies to 32 peptides from 25 proteins in infected animals that are ubiquitously expressed and have not been previously reported. Third, by using ELISA as a secondary assay, we confirmed antibody reactivity in sera from CVB3-infected animals to cytochrome c oxidase assembly factor 4 homolog (COA4) and phosphoinositide-3-kinase adaptor protein 1 (PIK3AP1), indicating the specificity of antibody detection by PhIP-Seq technology. Fourth, we noted similar antibody reactivity patterns in CVB3 and CVB4 infections, suggesting that the COA4- and PIK3AP1-reactive antibodies could be common to multiple CVB infections. The specificity of the autoantibodies was affirmed with influenza-infected animals that showed no reactivity to any of the antigens tested. Taken together, our data suggest that the autoantibodies identified by PhIP-Seq may have relevance to CVB pathogenesis, with a possibility that similar reactivity could be expected in human DCM patients. Full article
(This article belongs to the Special Issue Immunology and Immunotherapy in Cardiovascular Disease)
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18 pages, 3785 KiB  
Article
A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes
by Reza Halabian and Wojciech Makałowski
Biology 2022, 11(7), 1032; https://doi.org/10.3390/biology11071032 - 08 Jul 2022
Cited by 5 | Viewed by 2409
Abstract
As one of the major structural constituents, mobile elements comprise more than half of the human genome, among which Alu, L1, and SVA elements are still active and continue to generate new offspring. One of the major characteristics of L1 and SVA [...] Read more.
As one of the major structural constituents, mobile elements comprise more than half of the human genome, among which Alu, L1, and SVA elements are still active and continue to generate new offspring. One of the major characteristics of L1 and SVA elements is their ability to co-mobilize adjacent downstream sequences to new loci in a process called 3′ DNA transduction. Transductions influence the structure and content of the genome in different ways, such as increasing genome variation, exon shuffling, and gene duplication. Moreover, given their mutagenicity capability, 3′ transductions are often involved in tumorigenesis or in the development of some diseases. In this study, we analyzed 3202 genomes sequenced at high coverage by the New York Genome Center to catalog and characterize putative 3′ transduced segments mediated by L1s and SVAs. Here, we present a genome-wide map of inter/intrachromosomal 3′ transduction variants, including their genomic and functional location, length, progenitor location, and allelic frequency across 26 populations. In total, we identified 7103 polymorphic L1s and 3040 polymorphic SVAs. Of these, 268 and 162 variants were annotated as high-confidence L1 and SVA 3′ transductions, respectively, with lengths that ranged from 7 to 997 nucleotides. We found specific loci within chromosomes X, 6, 7, and 6_GL000253v2_alt as master L1s and SVAs that had yielded more transductions, among others. Together, our results demonstrate the dynamic nature of transduction events within the genome and among individuals and their contribution to the structural variations of the human genome. Full article
(This article belongs to the Section Genetics and Genomics)
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12 pages, 1025 KiB  
Review
Roles of Natriuretic Peptides and the Significance of Neprilysin in Cardiovascular Diseases
by Hitoshi Nakagawa and Yoshihiko Saito
Biology 2022, 11(7), 1017; https://doi.org/10.3390/biology11071017 - 06 Jul 2022
Cited by 6 | Viewed by 3497
Abstract
Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) activate the guanylyl cyclase A receptor (GC-A), which synthesizes the second messenger cGMP in a wide variety of tissues and cells. C-type natriuretic peptide (CNP) activates the cGMP-producing guanylyl cyclase B receptor (GC-B) in [...] Read more.
Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) activate the guanylyl cyclase A receptor (GC-A), which synthesizes the second messenger cGMP in a wide variety of tissues and cells. C-type natriuretic peptide (CNP) activates the cGMP-producing guanylyl cyclase B receptor (GC-B) in chondrocytes, endothelial cells, and possibly smooth muscle cells, cardiomyocytes, and cardiac fibroblasts. The development of genetically modified mice has helped elucidate the physiological roles of natriuretic peptides via GC-A or GC-B. These include the hormonal effects of ANP/BNP in the vasculature, autocrine effects of ANP/BNP in cardiomyocytes, and paracrine effects of CNP in the vasculature and cardiomyocytes. Neprilysin (NEP) is a transmembrane neutral endopeptidase that degrades the three natriuretic peptides. Recently, mice overexpressing NEP, specifically in cardiomyocytes, revealed that local cardiac NEP plays a vital role in regulating natriuretic peptides in the heart tissue. Since NEP inhibition is a clinically accepted approach for heart failure treatment, the physiological roles of natriuretic peptides have regained attention. This article focuses on the physiological roles of natriuretic peptides elucidated in mice with GC-A or GC-B deletion, the significance of NEP in natriuretic peptide metabolism, and the long-term effects of angiotensin receptor-neprilysin inhibitor (ARNI) on cardiovascular diseases. Full article
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12 pages, 2779 KiB  
Article
Desert Ants Learn to Avoid Pitfall Traps While Foraging
by Adi Bar, Chen Marom, Nikol Zorin, Tomer Gilad, Aziz Subach, Susanne Foitzik and Inon Scharf
Biology 2022, 11(6), 897; https://doi.org/10.3390/biology11060897 - 10 Jun 2022
Cited by 4 | Viewed by 2031
Abstract
Central-place foragers, such as social insects or nesting birds, repeatedly use the same routes from and to their nests when foraging for food. Such species forage more efficiently after accumulating experience. We examined, here, a relatively neglected aspect of such an improvement with [...] Read more.
Central-place foragers, such as social insects or nesting birds, repeatedly use the same routes from and to their nests when foraging for food. Such species forage more efficiently after accumulating experience. We examined, here, a relatively neglected aspect of such an improvement with experience—the avoidance of pitfall traps. Similar pits are built by antlions, which co-occur with the ants, but they also resemble other natural obstacles. We used the desert ant Cataglyphis niger, common in sandy habitats, and allowed it to forage for three successive runs for a food reward. Ant workers discovered food more slowly and in smaller numbers when pits were in their path. Pit presence also led to longer tracks by ants and slower movement. However, with experience, the ants fell into such pits less often and reached the food more quickly. To understand how past conditions affect current behavior, we investigated whether removing or adding pits led to a different result to that with a constant number of pits. Workers adjusted their behavior immediately when conditions changed. The only carryover effect was the longer tracks crossed by workers after pit removal, possibly resulting from the mismatch between the past and current conditions. Finally, the workers were more likely to fall into pits that were closer to the nest than those that were further away. This is a good example of the advantage that ambush predators can derive from ambushing their prey in specific locations. Full article
(This article belongs to the Section Behavioural Biology)
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20 pages, 5642 KiB  
Article
The Two Domains of the Avian Double-β-Defensin AvBD11 Have Different Ancestors, Common with Potential Monodomain Crocodile and Turtle Defensins
by Nicolas Guyot, Céline Landon and Philippe Monget
Biology 2022, 11(5), 690; https://doi.org/10.3390/biology11050690 - 30 Apr 2022
Cited by 3 | Viewed by 2112
Abstract
Beta-defensins are an essential group of cysteine-rich host-defence peptides involved in vertebrate innate immunity and are generally monodomain. Among bird defensins, the avian β-defensin 11 (AvBD11) is unique because of its peculiar structure composed of two β-defensin domains. The reasons for the appearance [...] Read more.
Beta-defensins are an essential group of cysteine-rich host-defence peptides involved in vertebrate innate immunity and are generally monodomain. Among bird defensins, the avian β-defensin 11 (AvBD11) is unique because of its peculiar structure composed of two β-defensin domains. The reasons for the appearance of such ‘polydefensins’ during the evolution of several, but not all branches of vertebrates, still remain an open question. In this study, we aimed at exploring the origin and evolution of the bird AvBD11 using a phylogenetic approach. Although they are homologous, the N- and C-terminal domains of AvBD11 share low protein sequence similarity and possess different cysteine spacing patterns. Interestingly, strong variations in charge properties can be observed on the C-terminal domain depending on bird species but, despite this feature, no positive selection was detected on the AvBD11 gene (neither on site nor on branches). The comparison of AvBD11 protein sequences in different bird species, however, suggests that some amino acid residues may have undergone convergent evolution. The phylogenetic tree of avian defensins revealed that each domain of AvBD11 is distant from ovodefensins (OvoDs) and may have arisen from different ancestral defensins. Strikingly, our phylogenetic analysis demonstrated that each domain of AvBD11 has common ancestors with different putative monodomain β-defensins from crocodiles and turtles and are even more closely related with these reptilian defensins than with their avian paralogs. Our findings support that AvBD11′s domains, which differ in their cysteine spacing and charge distribution, do not result from a recent internal duplication but most likely originate from a fusion of two different ancestral genes or from an ancestral double-defensin arisen before the Testudines-Archosauria split. Full article
(This article belongs to the Special Issue Avian Evolution: From the Perspective of Developmental Biology)
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19 pages, 3432 KiB  
Article
Self-DNA Exposure Induces Developmental Defects and Germline DNA Damage Response in Caenorhabditis elegans
by Marcello Germoglio, Adele Adamo, Guido Incerti, Fabrizio Cartenì, Silvia Gigliotti, Aurora Storlazzi and Stefano Mazzoleni
Biology 2022, 11(2), 262; https://doi.org/10.3390/biology11020262 - 08 Feb 2022
Cited by 7 | Viewed by 2779
Abstract
All organisms, from bacteria to mammals, sense and respond to foreign nucleic acids to fight infections in order to survive and preserve genome integrity across generations. The innate immune system is an evolutionarily conserved defence strategy. Complex organisms have developed various cellular processes [...] Read more.
All organisms, from bacteria to mammals, sense and respond to foreign nucleic acids to fight infections in order to survive and preserve genome integrity across generations. The innate immune system is an evolutionarily conserved defence strategy. Complex organisms have developed various cellular processes to respond to and recognise not only infections, i.e., pathogen-associated molecular patterns (PAMPs), but also to sense injury and tissue dysfunctions, i.e., damage-associated molecular patterns (DAMPs). Mis-localized self-DNA can be sensed as DAMP by specific DNA-sensing pathways, and self-DNA chronic exposure can be detrimental to the organisms. Here, we investigate the effects of dietary delivered self-DNA in the nematode Caenorhabditis elegans. The hermaphrodite worms were fed on Escherichia coli genomic libraries: a C. elegans library (self) and a legume (Medicago truncatula) library (non-self). We show that the self-library diet affects embryogenesis, larval development and gametogenesis. DNA damage and activation of p53/CEP-1-dependent apoptosis occur in gonadal germ cells. Studies of self-DNA exposure in this model organism were not pursued up to now. The genetic tractability of C. elegans will help to identify the basic molecular pathways involved in such mechanisms. The specificity of the adverse effects associated with a self-DNA enriched diet suggests applications in biological pest control approaches. Full article
(This article belongs to the Section Developmental Biology)
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20 pages, 3870 KiB  
Article
Zoonotic Visceral Leishmaniasis: New Insights on Innate Immune Response by Blood Macrophages and Liver Kupffer Cells to Leishmania infantum Parasites
by Armanda Viana Rodrigues, Ana Valério-Bolas, Graça Alexandre-Pires, Maria Aires Pereira, Telmo Nunes, Dário Ligeiro, Isabel Pereira da Fonseca and Gabriela Santos-Gomes
Biology 2022, 11(1), 100; https://doi.org/10.3390/biology11010100 - 09 Jan 2022
Cited by 3 | Viewed by 3323
Abstract
L. infantum is the aetiological agent of zoonotic visceral leishmaniasis (ZVL), a disease that affects humans and dogs. Leishmania parasites are well adapted to aggressive conditions inside the phagolysosome and can control the immune activation of macrophages (MØs). Although MØs are highly active [...] Read more.
L. infantum is the aetiological agent of zoonotic visceral leishmaniasis (ZVL), a disease that affects humans and dogs. Leishmania parasites are well adapted to aggressive conditions inside the phagolysosome and can control the immune activation of macrophages (MØs). Although MØs are highly active phagocytic cells with the capacity to destroy pathogens, they additionally comprise the host cells for Leishmania infection, replication, and stable establishment in the mammal host. The present study compares, for the first time, the innate immune response to L. infantum infection of two different macrophage lineages: the blood macrophages and the liver macrophages (Kupffer cells, KC). Our findings showed that L. infantum takes advantage of the natural predisposition of blood-MØs to phagocyte pathogens. However, parasites rapidly subvert the mechanisms of MØs immune activation. On the other hand, KCs, which are primed for immune tolerance, are not extensively activated and can overcome the dormancy induced by the parasite, exhibiting a selection of immune mechanisms, such as extracellular trap formation. Altogether, KCs reveal a different pattern of response in contrast with blood-MØs when confronting L. infantum parasites. In addition, KCs response appears to be more efficient in managing parasite infection, thus contributing to the ability of the liver to naturally restrain Leishmania dissemination. Full article
(This article belongs to the Section Immunology)
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17 pages, 3678 KiB  
Article
Development of an SNP Assay for Marker-Assisted Selection of Soil-Borne Rhizoctonia solani AG-2-2-IIIB Resistance in Sugar Beet
by Samathmika Ravi, Mahdi Hassani, Bahram Heidari, Saptarathi Deb, Elena Orsini, Jinquan Li, Christopher M. Richards, Lee W. Panella, Subhashini Srinivasan, Giovanni Campagna, Giuseppe Concheri, Andrea Squartini and Piergiorgio Stevanato
Biology 2022, 11(1), 49; https://doi.org/10.3390/biology11010049 - 29 Dec 2021
Cited by 7 | Viewed by 3486
Abstract
Rhizoctonia solani, causing Rhizoctonia crown and root rot, is a major risk to sugar beet (Beta vulgaris L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection is a priority of breeding programs. We report the identification of a single-nucleotide [...] Read more.
Rhizoctonia solani, causing Rhizoctonia crown and root rot, is a major risk to sugar beet (Beta vulgaris L.) cultivation. The development of resistant varieties accelerated by marker-assisted selection is a priority of breeding programs. We report the identification of a single-nucleotide polymorphism (SNP) marker linked to Rhizoctonia resistance using restriction site-associated DNA (RAD) sequencing of two geographically discrete sets of plant materials with different degrees of resistance/susceptibility to enable a wider selection of superior genotypes. The variant calling pipeline utilized SAMtools for variant calling and the resulting raw SNPs from RAD sequencing (15,988 and 22,439 SNPs) were able to explain 13.40% and 25.45% of the phenotypic variation in the two sets of material from different sources of origin, respectively. An association analysis was carried out independently on both the datasets and mutually occurring significant SNPs were filtered depending on their contribution to the phenotype using principal component analysis (PCA) biplots. To provide a ready-to-use marker for the breeding community, a systematic molecular validation of significant SNPs distributed across the genome was undertaken to combine high-resolution melting, Sanger sequencing, and rhAmp SNP genotyping. We report that RsBv1 located on Chromosome 6 (9,000,093 bp) is significantly associated with Rhizoctonia resistance (p < 0.01) and able to explain 10% of the phenotypic disease variance. The related SNP assay is thus ready for marker-assisted selection in sugar beet breeding for Rhizoctonia resistance. Full article
(This article belongs to the Special Issue Crop Improvement Now and Beyond)
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15 pages, 5984 KiB  
Article
Precise Dose of Folic Acid Supplementation Is Essential for Embryonic Heart Development in Zebrafish
by Xuhui Han, Bingqi Wang, Dongxu Jin, Kuang Liu, Hongjie Wang, Liangbiao Chen and Yao Zu
Biology 2022, 11(1), 28; https://doi.org/10.3390/biology11010028 - 26 Dec 2021
Cited by 9 | Viewed by 4705
Abstract
Folic acid, one of the 13 essential vitamins, plays an important role in cardiovascular development. Mutations in folic acid synthesis gene 5,10-methylenetetrahydrofolate reductase (MTHFR) is associated with the occurrence of congenital heart disease. However, the mechanisms underlying the regulation of cardiac [...] Read more.
Folic acid, one of the 13 essential vitamins, plays an important role in cardiovascular development. Mutations in folic acid synthesis gene 5,10-methylenetetrahydrofolate reductase (MTHFR) is associated with the occurrence of congenital heart disease. However, the mechanisms underlying the regulation of cardiac development by mthfr gene are poorly understood. Here, we exposed zebrafish embryos to excessive folate or folate metabolism inhibitors. Moreover, we established a knock-out mutant of mthfr gene in zebrafish by using CRISPR/Cas9. The zebrafish embryos of insufficient or excessive folic acid and mthfr−/− mutant all gave rise to early pericardial edema and cardiac defect at 3 days post fertilization (dpf). Furthermore, the folic acid treated embryos showed abnormal movement at 5 dpf. The expression levels of cardiac marker genes hand2, gata4, and nppa changed in the abnormality of folate metabolism embryos and mthfr−/− mutant, and there is evidence that they are related to the change of methylation level caused by the change of folate metabolism. In conclusion, our study provides a novel model for the in-depth study of MTHFR gene and folate metabolism. Furthermore, our results reveal that folic acid has a dose-dependent effect on early cardiac development. Precise dosage of folic acid supplementation is crucial for the embryonic development of organisms. Full article
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17 pages, 3607 KiB  
Article
Soil Fungal Diversity of the Aguarongo Andean Forest (Ecuador)
by Ernesto F. Delgado, Adrián T. Valdez, Sergio A. Covarrubias, Solveig Tosi and Lidia Nicola
Biology 2021, 10(12), 1289; https://doi.org/10.3390/biology10121289 - 07 Dec 2021
Cited by 9 | Viewed by 3874
Abstract
Fungi represent an essential component of ecosystems, functioning as decomposers and biotrophs, and they are one of the most diverse groups of Eukarya. In the tropics, many species are unknown. In this work, high-throughput DNA sequencing was used to discover the biodiversity of [...] Read more.
Fungi represent an essential component of ecosystems, functioning as decomposers and biotrophs, and they are one of the most diverse groups of Eukarya. In the tropics, many species are unknown. In this work, high-throughput DNA sequencing was used to discover the biodiversity of soil fungi in the Aguarongo forest reserve, one of the richest biodiversity hotspots in Ecuador. The rDNA metabarcoding analysis revealed the presence of seven phyla: Ascomycota, Basidiomycota, Mortierellomycota, Mucoromycota, Glomeromycota, Chytridiomycota, and Monoblepharomycota. A total of 440 identified species were recorded. They mainly belonged to Ascomycota (263) and Basidiomycota (127). In Mortierellomycota, 12 species were recorded, among which Podila verticillata is extremely frequent and represents the dominant species in the entire mycobiota of Aguarongo. The present research provides the first account of the entire soil mycobiota in the Aguarongo forest, where many fungal species exist that have strong application potential in agriculture, bioremediation, chemical, and the food industry. The Aguarongo forest hides a huge number of unknown fungal species that could be assessed, and its protection is of the utmost importance. Full article
(This article belongs to the Special Issue Diversity of Soil Fungal Communities)
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25 pages, 1364 KiB  
Review
Cell-Based Neuroprotection of Retinal Ganglion Cells in Animal Models of Optic Neuropathies
by Yue Hu, Lynn Michelle Grodzki, Susanne Bartsch and Udo Bartsch
Biology 2021, 10(11), 1181; https://doi.org/10.3390/biology10111181 - 15 Nov 2021
Cited by 4 | Viewed by 2879
Abstract
Retinal ganglion cells (RGCs) comprise a heterogenous group of projection neurons that transmit visual information from the retina to the brain. Progressive degeneration of these cells, as it occurs in inflammatory, ischemic, traumatic or glaucomatous optic neuropathies, results in visual deterioration and is [...] Read more.
Retinal ganglion cells (RGCs) comprise a heterogenous group of projection neurons that transmit visual information from the retina to the brain. Progressive degeneration of these cells, as it occurs in inflammatory, ischemic, traumatic or glaucomatous optic neuropathies, results in visual deterioration and is among the leading causes of irreversible blindness. Treatment options for these diseases are limited. Neuroprotective approaches aim to slow down and eventually halt the loss of ganglion cells in these disorders. In this review, we have summarized preclinical studies that have evaluated the efficacy of cell-based neuroprotective treatment strategies to rescue retinal ganglion cells from cell death. Intraocular transplantations of diverse genetically nonmodified cell types or cells engineered to overexpress neurotrophic factors have been demonstrated to result in significant attenuation of ganglion cell loss in animal models of different optic neuropathies. Cell-based combinatorial neuroprotective approaches represent a potential strategy to further increase the survival rates of retinal ganglion cells. However, data about the long-term impact of the different cell-based treatment strategies on retinal ganglion cell survival and detailed analyses of potential adverse effects of a sustained intraocular delivery of neurotrophic factors on retina structure and function are limited, making it difficult to assess their therapeutic potential. Full article
(This article belongs to the Special Issue Glaucoma – Pathophysiology and Therapeutic Options)
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19 pages, 4806 KiB  
Article
Inflammatory Response Modulation by Vitamin C in an MPTP Mouse Model of Parkinson’s Disease
by Francesco De Nuccio, Antonia Cianciulli, Chiara Porro, Marianna Kashyrina, Melania Ruggiero, Rosa Calvello, Alessandro Miraglia, Giuseppe Nicolardi, Dario Domenico Lofrumento and Maria Antonietta Panaro
Biology 2021, 10(11), 1155; https://doi.org/10.3390/biology10111155 - 09 Nov 2021
Cited by 16 | Viewed by 3294
Abstract
Vitamin C (Vit C) is anutrient present in many foods, particularly citrus fruits, green vegetables, tomatoes, and potatoes. Vit C is studied for its applications in the prevention and management of different pathologies, including neurodegenerative diseases. Neuroinflammation is a defense mechanism activated by [...] Read more.
Vitamin C (Vit C) is anutrient present in many foods, particularly citrus fruits, green vegetables, tomatoes, and potatoes. Vit C is studied for its applications in the prevention and management of different pathologies, including neurodegenerative diseases. Neuroinflammation is a defense mechanism activated by a stimulus or an insult that is aimed at the preservation of the brain by promoting tissue repair and removing cellular debris; however, persistent inflammatory responses are detrimental and may lead to the pathogenesis and progression of neurodegenerative diseases like Parkinson’s disease (PD) and Alzheimer’s disease. PD is one of the most common chronic progressive neurodegenerative disorders, and oxidative stress is one of the most important factors involved in its pathogenesis and progression.Due to this, research on antioxidant and anti-inflammatory compounds is an important target for counteracting neurodegenerative diseases, including PD. In the central nervous system, the presence of Vit C in the brain is higher than in other body districts, but why and how this occurs is still unknown. In this research, Vit C, with its anti-inflammatory and anti-oxidative properties, is studied to better understand its contribution to brain protection; in particular, we have investigated the neuroprotective effects of Vit C in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced animal model of PD and its role in the modulation of neuroinflammation. First, we observed that Vit C significantly decreased the MPTP-induced loss of tyrosine hydroxylase (TH)-positive dopaminergic neuronal cells in the substantia nigra, as well as microglial cell activation and astrogliosis. Furthermore, gait and spontaneous locomotor activity, evaluated by an automated treadmill and the Open Field test, respectively, were partially ameliorated by Vit C treatment in MPTP-intoxicated animals. In relation to neuroinflammation, results show that Vit C reduced the protein and mRNA expression of inflammatory cytokines such as IL-6, TLR4, TNF-α, iNOS, and CD40, while anti-inflammatory proteins such as IL-10, CD163, TGF-β, and IL-4 increased. Interestingly, we show for the first time that Vit C reduces neuroinflammation by modulating microglial polarization and astrocyte activation. Moreover, Vit C was able to reduce NLRP3 activation, which is linked to the pathogenesis of many inflammatory diseases, including neuroinflammatory disorders. In conclusion, our study provides evidence that Vit C may represent a new promising dietary supplement for the prevention and alleviation of the inflammatory cascade of PD, thus contributing to neuroprotection. Full article
(This article belongs to the Section Neuroscience)
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23 pages, 489 KiB  
Review
Borreliae Part 2: Borrelia Relapsing Fever Group and Unclassified Borrelia
by Giusto Trevisan, Marina Cinco, Sara Trevisini, Nicola di Meo, Maurizio Ruscio, Patrizia Forgione and Serena Bonin
Biology 2021, 10(11), 1117; https://doi.org/10.3390/biology10111117 - 29 Oct 2021
Cited by 15 | Viewed by 3894
Abstract
Borreliae of the relapsing fever group (RFG) are heterogenous and can be divided mainly into three groups according to vectors, namely the soft-tick-borne relapsing fever (STBRF) Borreliae, the hard-tick-borne relapsing fever (HTBRF) Borreliae, the louse-borne relapsing fever (LBRF) Borreliae, and [...] Read more.
Borreliae of the relapsing fever group (RFG) are heterogenous and can be divided mainly into three groups according to vectors, namely the soft-tick-borne relapsing fever (STBRF) Borreliae, the hard-tick-borne relapsing fever (HTBRF) Borreliae, the louse-borne relapsing fever (LBRF) Borreliae, and the avian relapsing fever ones. With respect to the geographical distribution, the STBRF Borreliae are further subdivided into Old World and New World strains. Except for the Avian relapsing fever group Borreliae, which cause avian spirochetosis, all the others share infectivity in humans. They are indeed the etiological agent of both endemic and epidemic forms of relapsing fever, causing high spirochaetemia and fever. Vectors are primarily soft ticks of Ornithodoros spp. in the STBRF group; hard ticks, notably Ixodes sp., Amblyomma sp., Dermacentor sp., and Rhipicephalus sp., in the HTBRF group; and the louse pediculus humanus humanus in the TBRF one. A recent hypothesis was supported for a common ancestor of RFG Borreliae, transmitted at the beginning by hard-body ticks. Accordingly, STBRF Borreliae switched to use soft-bodied ticks as a vector, which was followed by the use of lice by Borrelia recurrentis. There are also new candidate species of Borreliae, at present unclassified, which are also described in this review. Full article
(This article belongs to the Special Issue Advances in the Biology of Leptospira, Borrelia and Other Spirochetes)
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10 pages, 279 KiB  
Article
Comparison of the Mineral and Nutraceutical Profiles of Elephant Garlic (Allium ampeloprasum L.) Grown in Organic and Conventional Fields of Valdichiana, a Traditional Cultivation Area of Tuscany, Italy
by Stefano Loppi, Riccardo Fedeli, Giulia Canali, Massimo Guarnieri, Stefano Biagiotti and Andrea Vannini
Biology 2021, 10(10), 1058; https://doi.org/10.3390/biology10101058 - 18 Oct 2021
Cited by 12 | Viewed by 3152
Abstract
In the Valdichiana area (Tuscany, Italy) an ancient native landrace of elephant garlic (Allium ampeloprasum L.), locally known as “Aglione della Valdichiana”, has long been cultivated. The aim of this study was to check whether there are differences in the mineral and [...] Read more.
In the Valdichiana area (Tuscany, Italy) an ancient native landrace of elephant garlic (Allium ampeloprasum L.), locally known as “Aglione della Valdichiana”, has long been cultivated. The aim of this study was to check whether there are differences in the mineral and nutraceutical profiles of the Aglione della Valdichiana cultivated conventionally and organically. Based on the analysis by ICP-MS of a wide array of major, minor, essential, and non-essential trace elements as well as rare earth elements, and the evaluation of the content of polyphenols, flavonoids, antioxidants, soluble proteins, soluble sugars, and starch, as well as the weight and water content, it was concluded that differences in the mineral and nutraceutical profiles of organically and conventionally grown bulbs were very limited. Only a statistically (p < 0.05) higher concentration of Cd (+2620%), Co (+113%), Mn (+55%), Rb (+180%), and Sb (+180%), as well as glucose (+37%) in conventionally cultivated bulbs emerged. Cadmium was the only element slightly higher than in the “reference plant,” but with a negligible risk (three orders of magnitude lower) for human health based on consumption. It is concluded that we failed to find evidence of healthier food or a higher nutraceutical quality for organically cultivated elephant garlic. Full article
(This article belongs to the Section Plant Science)
11 pages, 2681 KiB  
Article
Gut Microbiota Cannot Compensate the Impact of (quasi) Aposymbiosis in Blattella germanica
by Maria Muñoz-Benavent, Amparo Latorre, Ester Alemany-Cosme, Jesús Marín-Miret, Rebeca Domínguez-Santos, Francisco J. Silva, Rosario Gil and Carlos García-Ferris
Biology 2021, 10(10), 1013; https://doi.org/10.3390/biology10101013 - 09 Oct 2021
Cited by 6 | Viewed by 1941
Abstract
Blattella germanica presents a very complex symbiotic system, involving the following two kinds of symbionts: the endosymbiont Blattabacterium and the gut microbiota. Although the role of the endosymbiont has been fully elucidated, the function of the gut microbiota remains unclear. The study of [...] Read more.
Blattella germanica presents a very complex symbiotic system, involving the following two kinds of symbionts: the endosymbiont Blattabacterium and the gut microbiota. Although the role of the endosymbiont has been fully elucidated, the function of the gut microbiota remains unclear. The study of the gut microbiota will benefit from the availability of insects deprived of Blattabacterium. Our goal is to determine the effect of the removal (or, at least, the reduction) of the endosymbiont population on the cockroach’s fitness, in a normal gut microbiota community. For this purpose, we treated our cockroach population, over several generations, with rifampicin, an antibiotic that only affects the endosymbiont during its extracellular phase, and decreases its amount in the following generation. As rifampicin also affects gut bacteria that are sensitive to this antibiotic, the treatment was performed during the first 12 days of the adult stage, which is the period when the endosymbiont infects the oocytes and lacks bacteriocyte protection. We found that after this antibiotic treatment, the endosymbiont population remained extremely reduced and only the microbiota was able to recover, although it could not compensate for the endosymbiont role, and the host’s fitness was drastically affected. This accomplished reduction, however, is not homogenous and requires further study to develop stable quasi-aposymbiotic cockroaches. Full article
(This article belongs to the Section Microbiology)
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17 pages, 1508 KiB  
Review
Plasticity in Cervical Motor Circuits following Spinal Cord Injury and Rehabilitation
by John R. Walker and Megan Ryan Detloff
Biology 2021, 10(10), 976; https://doi.org/10.3390/biology10100976 - 28 Sep 2021
Cited by 9 | Viewed by 4047
Abstract
Neuroplasticity is a robust mechanism by which the central nervous system attempts to adapt to a structural or chemical disruption of functional connections between neurons. Mechanical damage from spinal cord injury potentiates via neuroinflammation and can cause aberrant changes in neural circuitry known [...] Read more.
Neuroplasticity is a robust mechanism by which the central nervous system attempts to adapt to a structural or chemical disruption of functional connections between neurons. Mechanical damage from spinal cord injury potentiates via neuroinflammation and can cause aberrant changes in neural circuitry known as maladaptive plasticity. Together, these alterations greatly diminish function and quality of life. This review discusses contemporary efforts to harness neuroplasticity through rehabilitation and neuromodulation to restore function with a focus on motor recovery following cervical spinal cord injury. Background information on the general mechanisms of plasticity and long-term potentiation of the nervous system, most well studied in the learning and memory fields, will be reviewed. Spontaneous plasticity of the nervous system, both maladaptive and during natural recovery following spinal cord injury is outlined to provide a baseline from which rehabilitation builds. Previous research has focused on the impact of descending motor commands in driving spinal plasticity. However, this review focuses on the influence of physical therapy and primary afferent input and interneuron modulation in driving plasticity within the spinal cord. Finally, future directions into previously untargeted primary afferent populations are presented. Full article
(This article belongs to the Special Issue Pathophysiology of Spinal Cord Injury (SCI))
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9 pages, 2170 KiB  
Article
Antibacterial Activity of Ikarugamycin against Intracellular Staphylococcus aureus in Bovine Mammary Epithelial Cells In Vitro Infection Model
by Shamsaldeen Ibrahim Saeed, Erkihun Aklilu, Khalid M. Mohammedsalih, Adewole A. Adekola, Ahmed Elmontaser Mergani, Maizan Mohamad and Nor Fadhilah Kamaruzzaman
Biology 2021, 10(10), 958; https://doi.org/10.3390/biology10100958 - 25 Sep 2021
Cited by 8 | Viewed by 3443
Abstract
Staphylococcus aureus is an ubiquitous and versatile pathogen associated with a wide range of diseases. In animals, this bacterium is one of the causative agents of bovine mastitis, responsible for huge economic losses in the dairy industry. Besides the development of antibiotic resistance, [...] Read more.
Staphylococcus aureus is an ubiquitous and versatile pathogen associated with a wide range of diseases. In animals, this bacterium is one of the causative agents of bovine mastitis, responsible for huge economic losses in the dairy industry. Besides the development of antibiotic resistance, the intracellular survival of S. aureus within udder cells has rendered many antibiotics ineffective, leading to therapeutic failure. Our study therefore aims to investigate the in vitro bactericidal activity of ikarugamycin (IKA) against intracellular S. aureus using a bovine mammary epithelial cells (Mac-T cells) infection model and determine the cytotoxic effect. Minimum inhibitory concentration (MIC) was used to determine the antibacterial activity of IKA, and Mac-T cells were infected with S. aureus using gentamicin protection assay. IKA intracellular antibacterial activity assays were used to determine the bactericidal activity of IKA against intracellular S. aureus. The cytotoxicity of IKA against Mac-T cells was evaluated using the resazurin assay. We showed that, S. aureus is susceptible to IKA with a MIC value of 0.6 μg/mL. IKA at 4 × MIC and 8 × MIC have bactericidal activity by reducing 3 and 5 logs10 CFU/mL of S. aureus in the first six-hour of treatment respectively. In addition, IKA demonstrated intracellular killing activity by killing 90% of intracellular S. aureus at 5 μg/mL. This level is comparatively lower than 9.2 μg/mL determined as the half-maximal inhibitory concentration (IC50) of IKA required to kill 50% of Mac-T cells, highlighting a lower concentration required for bactericidal effect compared to the cytotoxic effect. The study highlighted that importance of IKA as a potential antibiotic candidate to be explored for the in vivo efficacy in treating S. aureus mastitis. Full article
(This article belongs to the Section Microbiology)
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19 pages, 1495 KiB  
Review
Peripheral Immune Dysfunction: A Problem of Central Importance after Spinal Cord Injury
by Marisa A. Jeffries and Veronica J. Tom
Biology 2021, 10(9), 928; https://doi.org/10.3390/biology10090928 - 17 Sep 2021
Cited by 16 | Viewed by 5187
Abstract
Individuals with spinal cord injuries (SCI) exhibit increased susceptibility to infection, with pneumonia consistently ranking as a leading cause of death. Despite this statistic, chronic inflammation and concurrent immune suppression have only recently begun to be explored mechanistically. Investigators have now identified numerous [...] Read more.
Individuals with spinal cord injuries (SCI) exhibit increased susceptibility to infection, with pneumonia consistently ranking as a leading cause of death. Despite this statistic, chronic inflammation and concurrent immune suppression have only recently begun to be explored mechanistically. Investigators have now identified numerous changes that occur in the peripheral immune system post-SCI, including splenic atrophy, reduced circulating lymphocytes, and impaired lymphocyte function. These effects stem from maladaptive changes in the spinal cord after injury, including plasticity within the spinal sympathetic reflex circuit that results in exaggerated sympathetic output in response to peripheral stimulation below injury level. Such pathological activity is particularly evident after a severe high-level injury above thoracic spinal cord segment 6, greatly increasing the risk of the development of sympathetic hyperreflexia and subsequent disrupted regulation of lymphoid organs. Encouragingly, studies have presented evidence for promising therapies, such as modulation of neuroimmune activity, to improve regulation of peripheral immune function. In this review, we summarize recent publications examining (1) how various immune functions and populations are affected, (2) mechanisms behind SCI-induced immune dysfunction, and (3) potential interventions to improve SCI individuals’ immunological function to strengthen resistance to potentially deadly infections. Full article
(This article belongs to the Special Issue Pathophysiology of Spinal Cord Injury (SCI))
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11 pages, 907 KiB  
Article
Clinical Significance of the Head-Up Tilt Test in Improving Prognosis in Patients with Possible Neurally Mediated Syncope
by Kengo Ayabe, Tomoyoshi Komiyama, Misaki Hasegawa, Tetsuri Sakai, Masahiro Morise, Susumu Sakama, Atsuhiko Yagishita, Mari Amino, Yuji Ikari and Koichiro Yoshioka
Biology 2021, 10(9), 919; https://doi.org/10.3390/biology10090919 - 15 Sep 2021
Cited by 4 | Viewed by 3101
Abstract
Syncope is commonly encountered in daily clinical practice. Depending on its etiology (benign or life-threatening conditions or environmental triggers), syncope can be neurally mediated (reflex), cardiac, or orthostatic. Furthermore, neurologic disease can cause symptoms that mimic syncope. However, there is limited research on [...] Read more.
Syncope is commonly encountered in daily clinical practice. Depending on its etiology (benign or life-threatening conditions or environmental triggers), syncope can be neurally mediated (reflex), cardiac, or orthostatic. Furthermore, neurologic disease can cause symptoms that mimic syncope. However, there is limited research on neurally mediated syncope (NMS), which is considered a benign disorder, and close follow-ups are rarely performed. NMS can cause serious clinical events, including severe trauma and car accidents. The head-up tilt test (HUTT) is the gold standard for diagnosing NMS; however, its clinical significance remains unknown, and its relevance to NMS prognosis requires further research. This retrospective study aimed to assess the clinical significance of the HUTT for NMS. We reviewed the charts of 101 patients who underwent HUTT at Tokai University Hospital in Japan between January 2016 and March 2019. During the HUTT, 72 patients (69.2%) experienced syncope. Patients were followed up for 886.1 ± 457.7 days (interquartile range: 518–1293 days). The syncope recurrence rate was 16.9%; however, no significant difference was observed between the two groups (HUTT positive vs. negative) (13.8% vs. 18.1%, p = 0.772). Four of 29 (13.9%) and two of 72 (2.8%) patients in the negative and positive HUTT groups, respectively, experienced cardiac events (p = 0.019). Negative HUTT results may assist in anticipating unexpected clinical events within a few years. A negative HUTT result may allow us to reconsider the NMS diagnosis based on clinical information. Close outpatient follow-up of patients with negative HUTT results is warranted. Full article
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15 pages, 1227 KiB  
Article
Genome Analysis of Acinetobacter lwoffii Strains Isolated from Permafrost Soils Aged from 15 Thousand to 1.8 Million Years Revealed Their Close Relationships with Present-Day Environmental and Clinical Isolates
by Andrey L. Rakitin, Alexandra Y. Ermakova, Alexey V. Beletsky, Mayya Petrova, Andrey V. Mardanov and Nikolai V. Ravin
Biology 2021, 10(9), 871; https://doi.org/10.3390/biology10090871 - 04 Sep 2021
Cited by 7 | Viewed by 3797
Abstract
Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. Acinetobacter lwoffii [...] Read more.
Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. Acinetobacter lwoffii is a typical soil bacterium that has been increasingly reported as hospital pathogens associated with bacteremia. In order to identify the specific genetic characteristics of ancient permafrost-conserved strains of A. lwoffii and their differences from present-day clinical isolates, we carried out a genome-wide analysis of five strains of A. lwoffii isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not identify chromosomal genetic determinants that distinguish permafrost strains from clinical A. lwoffii isolates and strains from other natural habitats. Phylogenetic analysis based on whole genome sequences showed that permafrost strains do not form a separate cluster and some of them are most closely related to clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal transfer of genetic material. Comparison of plasmids of modern and permafrost strains showed that plasmids from the modern strains are enriched with antibiotic resistance genes, while the content of genes for resistance to heavy metals and arsenic is nearly the same. The thawing of permafrost caused by global warming could release new potentially pathogenic strains of Acinetobacter. Full article
(This article belongs to the Special Issue Microbial Diversity and Microbial Resistance)
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12 pages, 860 KiB  
Review
SnoRNA in Cancer Progression, Metastasis and Immunotherapy Response
by Jildou van der Werf, Chue Vin Chin and Nicholas Ian Fleming
Biology 2021, 10(8), 809; https://doi.org/10.3390/biology10080809 - 20 Aug 2021
Cited by 31 | Viewed by 4702
Abstract
Small nucleolar RNA (snoRNA) were one of our earliest recognised classes of non-coding RNA, but were largely ignored by cancer investigators due to an assumption that their activities were confined to the nucleolus. However, as full genome sequences have become available, many new [...] Read more.
Small nucleolar RNA (snoRNA) were one of our earliest recognised classes of non-coding RNA, but were largely ignored by cancer investigators due to an assumption that their activities were confined to the nucleolus. However, as full genome sequences have become available, many new snoRNA genes have been identified, and multiple studies have shown their functions to be diverse. The consensus now is that many snoRNA are dysregulated in cancers, are differentially expressed between cancer types, stages and metastases, and they can actively modify disease progression. In addition, the regulation of the snoRNA class is dominated by the cancer-supporting mTOR signalling pathway, and they may have particular significance to immune cell function and anti-tumour immune responses. Given the recent advent of therapeutics that can target RNA molecules, snoRNA have robust potential as drug targets, either solely or in the context of immunotherapies. Full article
(This article belongs to the Special Issue The Role of Non-coding RNA in Tumor Progression and Metastasis)
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