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Volume 11
Issue 10
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Biology, Volume 11, Issue 10 (October 2022) – 172 articles

Cover Story (view full-size image): The increased popularity of zebrafish as a research model calls for the refinement of procedures, such as finding the best anaesthetic protocol to use in adult zebrafish in a laboratory setting. The scarce literature available regarding aversion described the most-used anaesthetic (MS222) as aversive to adult zebrafish. Thus, we studied the impact of three different anaesthetic protocols (a combination of propofol with lidocaine, clove oil, and etomidate) and the standard anaesthetic (MS222) on the zebrafish aversion and on cortisol levels. Our results suggested that all the anaesthetic protocols, except for etomidate, were valid candidates to use in a laboratory setting, although none were innocuous. View this paper
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16 pages, 6366 KiB  
Article
Reinvestigation of the Late Devonian Lycopsid Sublepidodendron grabaui from Anhui Province, South China
by Peng Xu, Le Liu and Deming Wang
Biology 2022, 11(10), 1544; https://doi.org/10.3390/biology11101544 - 21 Oct 2022
Viewed by 1602
Abstract
South China displays Devonian strata with well-exposed outcrops and is regarded as a diversity hotspot of Late Devonian lycopsids. The heterosporous lycopsid Sublepidodendron grabaui has been studied for over ten years, with its general morphology, aerial stem anatomy, microsporangiate strobili, and growth architecture [...] Read more.
South China displays Devonian strata with well-exposed outcrops and is regarded as a diversity hotspot of Late Devonian lycopsids. The heterosporous lycopsid Sublepidodendron grabaui has been studied for over ten years, with its general morphology, aerial stem anatomy, microsporangiate strobili, and growth architecture reported. Based on new specimens from Guangde City, Anhui Province, this study provides further knowledge about the megasporangiate strobili and megaspores of S. grabaui. Its slender megasporangiate strobili occur singly or in pairs and occasionally bifurcate in the middle-upper portion. Each megasporophyll consists of a flattened pedicel and an adaxially curved lamina. The lamina forms a downturned heel at the base. Each sessile megasporangium contains at least eight Lagenicula-type megaspores with a small gula. The other observed characteristics of S. grabaui in this study conform to those previously known and are compared to relative coeval taxa. Full article
(This article belongs to the Special Issue Recent Advances in Palaeobotany)
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13 pages, 1176 KiB  
Article
Plant Use Adaptation in Pamir: Sarikoli Foraging in the Wakhan Area, Northern Pakistan
by Muhammad Abdul Aziz, Zahid Ullah, Muhammad Adnan, Renata Sõukand and Andrea Pieroni
Biology 2022, 11(10), 1543; https://doi.org/10.3390/biology11101543 - 21 Oct 2022
Cited by 6 | Viewed by 1713
Abstract
The study recorded the food uses of wild food plants (WFPs) among the Sarikoli diaspora and the dominant Wakhi in Broghil Valley, North Pakistan, to understand their food adaptation, mainly by looking through the lens of food ethnobotanies. A total of 30 participants [...] Read more.
The study recorded the food uses of wild food plants (WFPs) among the Sarikoli diaspora and the dominant Wakhi in Broghil Valley, North Pakistan, to understand their food adaptation, mainly by looking through the lens of food ethnobotanies. A total of 30 participants took part in the study, which included 15 elderly individuals from each ethnic group. Data were gathered through semi-structured interviews. We recorded 29 WFPs, mostly used as cooked vegetables and snacks. The food uses, as well as the local plant nomenclatures, linked to WFPs of the two studied groups were completely homogenized, which could be attributed to the cultural assimilation of the Sarikoli people to Wakhi culture. We found that although traditional knowledge on WFPs has been homogenized, social change in nearby regions is also threatening the traditional knowledge of the two communities, as evidenced by the smaller number of plants reported compared to that of all other field ethnobotanical studies conducted in nearby regions. Moreover, the growth of legal restrictions and sanctions on accessing natural resources are posing serious challenges to cultural resilience in the valley, and the restrictions on cross-border movement in particular are creating challenges for those who have cross-border kinship relationships between the two groups. We suggest specific measures, such as the promotion of food tourism and educational activities, to protect traditional knowledge and bicultural heritage from further erosion in the region. Full article
(This article belongs to the Special Issue Documenting, Assessing, and Celebrating Bio-Cultural Diversities in the Ongoing Global Crisis: New Ways to Foster Citizens' Science?)
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12 pages, 1828 KiB  
Article
Bone Molecular Modifications Induced by Diagenesis Followed-Up for 12 Months
by Guillaume Falgayrac, Raffaele Vitale, Yann Delannoy, Hélène Behal, Guillaume Penel, Cécile Olejnik, Ludovic Duponchel and Thomas Colard
Biology 2022, 11(10), 1542; https://doi.org/10.3390/biology11101542 - 21 Oct 2022
Viewed by 1698
Abstract
After death, diagenesis takes place. Numerous processes occur concomitantly, which makes it difficult to identify the diagenetic processes. The diagenetic processes refer to all processes (chemical or physical) that modify the skeletal remains. These processes are highly variable depending on the environmental factors [...] Read more.
After death, diagenesis takes place. Numerous processes occur concomitantly, which makes it difficult to identify the diagenetic processes. The diagenetic processes refer to all processes (chemical or physical) that modify the skeletal remains. These processes are highly variable depending on the environmental factors (weather, temperature, age, sex, etc.), especially in the early stages. Numerous studies have evaluated bone diagenetic processes over long timescales (~millions of years), but fewer have been done over short timescales (between days and thousands of years). The objective of the study is to assess the early stages of diagenetic processes by Raman microspectroscopy over 12 months. The mineral and organic matrix modifications are monitored through physicochemical parameters. Ribs from six humans were buried in soil. The modifications of bone composition were followed by Raman spectroscopy each month. The decrease in the mineral/organic ratio and carbonate type-B content and the increase in crystallinity reveal that minerals undergo dissolution–recrystallization. The decrease in collagen cross-linking indicates that collagen hydrolysis induces the fragmentation of collagen fibres over 12 months. Full article
(This article belongs to the Special Issue Forensic Anthropology: New Methodological and Theoretical Perspectives in Forensic Human Skeletal Identification and Methods)
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14 pages, 2355 KiB  
Article
Memory Modulation by Exercise in Young Adults Is Related to Lactate and Not Affected by Sex or BDNF Polymorphism
by Juan Arturo Ballester-Ferrer, Alba Roldan, Eduardo Cervelló and Diego Pastor
Biology 2022, 11(10), 1541; https://doi.org/10.3390/biology11101541 - 20 Oct 2022
Cited by 3 | Viewed by 2172
Abstract
Currently, high-intensity interval exercise (HIIE) is on the rise compared to moderate-intensity exercise (MIE) due to its similar benefits for health and performance with low time requirements. Recent studies show how physical exercise can also influence cognitive function, although the optimal dose and [...] Read more.
Currently, high-intensity interval exercise (HIIE) is on the rise compared to moderate-intensity exercise (MIE) due to its similar benefits for health and performance with low time requirements. Recent studies show how physical exercise can also influence cognitive function, although the optimal dose and underlying mechanisms remain unknown. Therefore, in our study, we have compared the effects on visuospatial and declarative memory of different exercise intensities (HIIE vs. MIE), including possible implicated factors such as lactate released after each session and the Brain-Derived Neurotrophic Factor (BDNF) genotype. Thirty-six undergraduate students participated in this study. The HIIE session consisted of a 3 min warm-up, four 2 min sets at 90–95% of the maximal aerobic speed (MAS) with 2 min of passive recovery between sets, and a 3 min cooldown, and the MIE session implies the same total duration of continuous exercise at 60% of the MAS. Better improvements were found after HIIE than MIE on the backward condition of the visuospatial memory test (p = 0.014, ηp2 = 0.17) and the 48 h retention of the declarative memory test (p = 0.04; d = 0.34). No differences were observed in the forward condition of the visuospatial memory test and the 7-day retention of the declarative memory test (p > 0.05). Moreover, non-modifiable parameters such as biological sex and BDNF polymorphism (Val/Val, Val/Met, or Met/Met) did not modulate the cognitive response to exercise. Curiously, the correlational analysis showed associations (p < 0.05) between changes in memory (visuospatial and declarative) and lactate release. In this sense, our results suggest an important role for intensity in improving cognitive function with exercise, regardless of genetic factors such as biological sex or BDNF Val66Met polymorphism. Full article
(This article belongs to the Special Issue New Frontiers of Sport, Exercise and Physical Activity for Health and Human Performance)
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16 pages, 2405 KiB  
Article
A Novel ssDNA Aptamer Targeting Carcinoembryonic Antigen: Selection and Characterization
by Nigara Yunussova, Marzhan Sypabekova, Zhazira Zhumabekova, Bakhyt Matkarimov and Damira Kanayeva
Biology 2022, 11(10), 1540; https://doi.org/10.3390/biology11101540 - 20 Oct 2022
Cited by 3 | Viewed by 2174
Abstract
One of the major causes of a drastically shorter life expectancy and one of the most prevalent diseases in the world today is cancer. Given the data on the rise in cancer cases throughout the world, it is obvious that, despite the diagnostic [...] Read more.
One of the major causes of a drastically shorter life expectancy and one of the most prevalent diseases in the world today is cancer. Given the data on the rise in cancer cases throughout the world, it is obvious that, despite the diagnostic techniques currently being used, there is a pressing need to develop precise and sensitive techniques for early diagnosis of the disease. A high degree of affinity and specificity towards particular targets is maintained by the short nucleic acid molecules known as aptamers. Aptamers outperform antibodies due to their unique benefits, such as their simplicity in synthesis and modification, lack of toxicity, and long-term stability. Utilizing an accurate recognition element and a robust signal transduction mechanism, molecular diagnostics can be extremely sensitive and specific. In this study, development of new single-stranded DNA aptamers against CEA for use in cancer diagnostics was accomplished using SELEX and NGS methods. As a result of 12 iterative SELEX rounds, nine aptamer candidates against CEA were developed. NGS comparative analysis revealed that round twelve had an enriched number of aptamers that were specifically bound, as opposed to round eight. Among the selected nine sequences characterized by bioinformatics analysis and ELONA, an aptamer sequence with the highest specificity and affinity for the target protein was identified and further examined. Aptamer sequence (6) was screened in a concentration-dependent assay, specificity analysis was performed, and its potential secondary and tertiary structures were predicted, which enabled us to test one of the possible putative interactions with CEA. Finally, aptamer sequence (6) labelled with a Cy5 fluorescent tag was used in confocal microscopy to observe its binding towards the CEA expressed in HT-29 human colon adenocarcinoma cell line. Full article
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20 pages, 3234 KiB  
Article
A Non-Stressful Temperature Rise and Greater Food Availability Could Increase Tolerance to Calcium Limitation of Daphnia cf. pulex (Sensu Hebert, 1995) Populations in Cold Soft-Water Lakes
by Eloísa Ramos-Rodríguez, Carmen Pérez-Martínez and José María Conde-Porcuna
Biology 2022, 11(10), 1539; https://doi.org/10.3390/biology11101539 - 20 Oct 2022
Cited by 1 | Viewed by 1266
Abstract
Calcium (Ca) is an important driver of community structure in freshwaters. We examined the combined effects of increased temperatures and variations in food quantity on the tolerance to low Ca of Daphnia pulex. The aim was to predict the impact of climate [...] Read more.
Calcium (Ca) is an important driver of community structure in freshwaters. We examined the combined effects of increased temperatures and variations in food quantity on the tolerance to low Ca of Daphnia pulex. The aim was to predict the impact of climate warming on this keystone zooplanktonic species in cold-climate lakes. We conducted a factorial life-history experiment in a clone of North American Daphnia cf. pulex to analyse the interaction effects of a temperature increase (17.5 °C–21 °C) within their physiological preferred range and expected by climate warming over the next few decades and a narrow Ca gradient (0.25–1.74 mg Ca L−1) under stressful vs. abundant food conditions. We found a striking positive synergistic effect of Ca and temperature on D. pulex reproduction at high food conditions. Although the increase in temperature to 21 °C greatly reduced survival, high energy allocation to reproduction at high food levels allowed the population to succeed in poor Ca (<0.25 mg Ca L−1). Results suggest that climate warming and higher food availability will make the populations of many cold and Ca-limited lakes more tolerant to low Ca levels with higher growth population rates, thereby altering zooplanktonic community structures and inducing potential cascading effects on the food web. Full article
(This article belongs to the Section Ecology)
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16 pages, 3659 KiB  
Article
Nervous System Development and Neuropeptides Characterization in Embryo and Larva: Insights from a Non-Chordate Deuterostome, the Sea Cucumber Apostichopus japonicus
by Yingqiu Zheng, Xiao Cong, Huachen Liu, Yixin Wang, Kenneth B. Storey and Muyan Chen
Biology 2022, 11(10), 1538; https://doi.org/10.3390/biology11101538 - 20 Oct 2022
Cited by 2 | Viewed by 1974
Abstract
Here, we described the complex nervous system at five early developmental stages (blastula, gastrula, auricularia, doliolaria and pentactula) of a holothurian species with highly economic value, Apostichopus japonicus. The results revealed that the nervous system of embryos and larvae is mainly distributed [...] Read more.
Here, we described the complex nervous system at five early developmental stages (blastula, gastrula, auricularia, doliolaria and pentactula) of a holothurian species with highly economic value, Apostichopus japonicus. The results revealed that the nervous system of embryos and larvae is mainly distributed in the anterior apical region, ciliary bands or rings, and the feeding and attachment organs, and that serotonergic immunoreactivity was not observed until the embryo developed into the late gastrula; these are evolutionarily conserved features of echinoderm, hemichordate and protostome larvae. Furthermore, based on available transcriptome data, we reported the neuropeptide precursors profile at different embryonic and larval developmental stages. This analysis showed that 40 neuropeptide precursors present in adult sea cucumbers were also identified at different developmental stages of embryos and larvae, and only four neuropeptide precursors (SWYG precursor 2, GYWKDLDNYVKAHKT precursor, Neuropeptide precursor 14-like precursor, GLRFAmprecursor-like precursor) predicted in adults were absent in embryos and larvae. Combining the quantitative expression of ten specific neuropeptide precursor genes (NPs) by qRT-PCR, we revealed the potential important roles of neuropeptides in embryo development, feeding and attachment in A. japonicus larvae. In conclusion, this work provides novel perspectives on the diverse physiological functions of neuropeptides and contributes to understanding the evolution of neuropeptidergic systems in echinoderm embryos and larvae. Full article
(This article belongs to the Special Issue Molecular Physiology of Marine Invertebrates)
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16 pages, 2331 KiB  
Article
SMART Drumlines Ineffective in Catching White Sharks in the High Energy Capes Region of Western Australia: Acoustic Detections Confirm That Sharks Are Not Always Amenable to Capture
by Stephen M. Taylor, Jason How, Michael J. Travers, Stephen J. Newman, Silas Mountford, Daniela Waltrick, Christopher E. Dowling, Ainslie Denham and Daniel J. Gaughan
Biology 2022, 11(10), 1537; https://doi.org/10.3390/biology11101537 - 20 Oct 2022
Cited by 1 | Viewed by 1683
Abstract
The management of human-shark interactions can benefit from the implementation of effective shark hazard mitigation measures. A Shark-Management-Alert-in-Real-Time (SMART) drumline trial in the Capes region of Western Australia was instigated after several serious incidents involving surfers and white sharks (Carcharodon carcharias). [...] Read more.
The management of human-shark interactions can benefit from the implementation of effective shark hazard mitigation measures. A Shark-Management-Alert-in-Real-Time (SMART) drumline trial in the Capes region of Western Australia was instigated after several serious incidents involving surfers and white sharks (Carcharodon carcharias). The project aimed to determine whether white sharks (target species), which were relocated after capture, remained offshore using satellite and acoustic tagging. Over a 27-month period, 352 fish were caught, 55% of which comprised tiger sharks (Galeocerdo cuvier). Ninety-one percent of animals were released alive in good condition. Only two white sharks were caught; both were relocated ≥ 1 km offshore before release and moved immediately further offshore after capture, remaining predominately in offshore waters for the duration of their 54-day and 186-day tag deployments. Our results confirm that desirable animal welfare outcomes can be achieved using SMART drumlines when response times are minimised. The low target catches and the detection of 24 other tagged white sharks within the study area supported the decision to cease the trial. Our results reiterate there is no simple remedy for dealing with the complexities of shark hazards and reinforce the importance of trialing mitigation measures under local conditions. Full article
(This article belongs to the Special Issue Understanding and Managing Human–Shark Interactions in an Environmentally Aware World)
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12 pages, 1944 KiB  
Article
Revised Annotation and Characterization of Novel Aedes albopictus miRNAs and Their Potential Functions in Dengue Virus Infection
by Azali Azlan, Muhammad Amir Yunus, Mardani Abdul Halim and Ghows Azzam
Biology 2022, 11(10), 1536; https://doi.org/10.3390/biology11101536 - 19 Oct 2022
Viewed by 1251
Abstract
The Asian tiger mosquito, Ae. albopictus, is a highly invasive species that transmits several arboviruses including dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV). Although several studies have identified microRNAs (miRNAs) in Ae. albopictus, it is crucial to extend and improve current [...] Read more.
The Asian tiger mosquito, Ae. albopictus, is a highly invasive species that transmits several arboviruses including dengue (DENV), Zika (ZIKV), and chikungunya (CHIKV). Although several studies have identified microRNAs (miRNAs) in Ae. albopictus, it is crucial to extend and improve current annotations with both the newly improved genome assembly and the increased number of small RNA-sequencing data. We combined our high-depth sequence data and 26 public datasets to re-annotate Ae. albopictus miRNAs and found a total of 72 novel mature miRNAs. We discovered that the expression of novel miRNAs was lower than known miRNAs. Furthermore, compared to known miRNAs, novel miRNAs are prone to expression in a stage-specific manner. Upon DENV infection, a total of 44 novel miRNAs were differentially expressed, and target prediction analysis revealed that miRNA-target genes were involved in lipid metabolism and protein processing in endoplasmic reticulum. Taken together, the miRNA annotation profile provided here is the most comprehensive to date. We believed that this would facilitate future research in understanding virus–host interactions, particularly in the role of miRNAs. Full article
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13 pages, 4736 KiB  
Article
Cmcrf1, a Putative Zn2Cys6 Fungal Transcription Factor, Is Involved in Conidiation, Carotenoid Production, and Fruiting Body Development in Cordyceps militaris
by Ronglin He, Lin Zhang, Jinling Lan, Shengjie Mei and Yu Li
Biology 2022, 11(10), 1535; https://doi.org/10.3390/biology11101535 - 19 Oct 2022
Cited by 3 | Viewed by 1874
Abstract
Cordyceps militaris is a high-value medicinal and edible fungus that produces many bioactive compounds, including carotenoid, and thus, improving the carotenoid productivity of C. militaris will increase its commercial value. However, little is known about the genetic regulatory mechanism of carotenoid biosynthesis in [...] Read more.
Cordyceps militaris is a high-value medicinal and edible fungus that produces many bioactive compounds, including carotenoid, and thus, improving the carotenoid productivity of C. militaris will increase its commercial value. However, little is known about the genetic regulatory mechanism of carotenoid biosynthesis in C. militaris. To further understanding the regulatory mechanism of carotenoid biosynthesis, we performed a large-scale screen of T-DNA insertional mutant library and identified a defective mutant, denoted T111, whose colonies did not change color from white to yellow upon exposure to light. Mutation analysis confirmed that a single T-DNA insertion occurred in the gene encoding a 695-amino-acid putative fungal-specific transcription factor with a predicted Zn2Cys6 binuclear cluster DNA-binding domain found uniquely in fungi. Targeted deletion of this gene, denoted C. militaris carotenogenesis regulatory factor 1 (Cmcrf1), generated the ΔCmcrf1 mutant that exhibited drastically reduced carotenoid biosynthesis and failed to generate fruiting bodies. In addition, the ΔCmcrf1 mutant showed significantly increased conidiation and increased hypersensitivity to cell-wall-perturbing agents compared with the wild-type strain. However, the Cmcrf1 gene did not have an impact on the mycelia growth of C. militaris. These results show that Cmcrf1 is involved in carotenoid biosynthesis and is required for conidiation and fruiting body formation in C. militaris. Full article
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33 pages, 1830 KiB  
Review
Distribution of the Order Lampriformes in the Mediterranean Sea with Notes on Their Biology, Morphology, and Taxonomy
by Marco Albano, Claudio D’Iglio, Nunziacarla Spanò, Jorge Manuel de Oliveira Fernandes, Serena Savoca and Gioele Capillo
Biology 2022, 11(10), 1534; https://doi.org/10.3390/biology11101534 - 19 Oct 2022
Cited by 8 | Viewed by 3065
Abstract
Lampriformes are circumglobally distributed and contain several families of strictly marine bony fishes that have a peculiar morphology. Lampriformes systematics is affected by limitations in biometric, meristic, and molecular data; for this reason, it underwent several rearrangements in the past. This review aimed [...] Read more.
Lampriformes are circumglobally distributed and contain several families of strictly marine bony fishes that have a peculiar morphology. Lampriformes systematics is affected by limitations in biometric, meristic, and molecular data; for this reason, it underwent several rearrangements in the past. This review aimed to describe the biological and ecological characteristics of the order Lampriformes, summarizing the current taxonomy of the group. The main aim was to clarify what is known about the distribution of the order Lampriformes in the Mediterranean Sea, collecting all the scarce and fragmented reports and notes on their occurrence. Knowledge scarcity is due to their solitary nature, in addition to their low to absent economic value. Despite this, the order Lampriformes represents a taxon of high biological and ecological importance. The high depth range of distribution characterizes their lifestyle. In the Mediterranean Sea, four families are present—Lampridae, Lophotidae, Regalecidae, and Trachipteridae—with the following species respectively, Lampris guttatus (Brünnich, 1788), Lophotus lacepede (Giorna, 1809), Regalecus glesne (Ascanius, 1772), Trachipterus arcticus (Brünnich, 1788), T. trachypterus (Gmelin, 1789), and Zu cristatus (Bonelli, 1819). Data deficiencies affect information on this taxon; the present review, which collected all the reports of the Mediterranean Sea, creates a baseline for depicting the biogeography of these rare and important species. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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12 pages, 1612 KiB  
Article
Obesity and Metabolic Traits after High-Fat Diet in Iberian Pigs with Low Birth Weight of Placental Origin
by Ana Heras-Molina, Natalia Yeste, José Luis Pesantez-Pacheco, Susana Astiz, Marta Vazquez-Gomez, Arianna Bettiga, Francesco Trevisani, Consolacion Garcia-Contreras, Sergio Luis-Lima, Anna Bassols, Esteban Porrini and Antonio Gonzalez-Bulnes
Biology 2022, 11(10), 1533; https://doi.org/10.3390/biology11101533 - 19 Oct 2022
Viewed by 1918
Abstract
Intrauterine growth restriction (IUGR) and later obesity and metabolic disorders have classically been associated with maternal malnutrition, but most cases of IUGR are related to placental insufficiency. The current study, using a swine model for IUGR and obesity, aimed to determine the interaction [...] Read more.
Intrauterine growth restriction (IUGR) and later obesity and metabolic disorders have classically been associated with maternal malnutrition, but most cases of IUGR are related to placental insufficiency. The current study, using a swine model for IUGR and obesity, aimed to determine the interaction of birth weight (categorized as low birth weight [LBW] or normal birth-weight [NBW]) and postnatal diet (categorized as maintenance diet [MD] or fattening diet [FD]) on body weight, adiposity and metabolic traits. FD induced higher body weight and adiposity (both p < 0.0001), with higher fructosamine levels (p < 0.005) and a trend toward higher HOMA-β index (p = 0.05). NBW pigs remained heavier than LBW pigs during the early juvenile period (p < 0.005), but there were no differences at later stages. There were no differences in metabolic traits during juvenile development, but there were differences in adulthood, when LBW pigs showed higher glucose and lower insulin levels than NBW pigs (both p < 0.05). These results suggest that (a) FD allows LBW offspring to achieve similar obesity in adulthood as NBW offspring, and (b) glucose metabolism is more compromised in obese LBW than obese NBW pigs. The comparison of our data with previous studies highlights significant differences between offspring with LBW induced by maternal malnutrition or placental insufficiency, which should be considered when studying the condition. Full article
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16 pages, 1540 KiB  
Article
Plasticity in Compensatory Growth to Artificial Defoliation and Light Availability in Four Neotropical Understory and Forest Edge Herb Species
by Jennifer W. C. Sun, M. Rasoul Sharifi and Philip W. Rundel
Biology 2022, 11(10), 1532; https://doi.org/10.3390/biology11101532 - 19 Oct 2022
Viewed by 1204
Abstract
Defoliation from falling branches is a major factor in the survival of understory herbs in tropical rainforests. Experimental studies of defoliation under three levels of light environment compared responses to partial and total defoliation in four species of tropical rainforest understory herbs. We [...] Read more.
Defoliation from falling branches is a major factor in the survival of understory herbs in tropical rainforests. Experimental studies of defoliation under three levels of light environment compared responses to partial and total defoliation in four species of tropical rainforest understory herbs. We predicted that elevated levels of light availability would help compensate for damage to through compensatory growth in both understory and forest edge species and that forest edge species would more effectively compensate under high light conditions than shade-tolerant species from the forest understory All species showed a high tolerance to defoliation under high and intermediate light conditions. Under low-light conditions survival differed dramatically with minimal mortality in forest-edge species compared to high mortality in completely defoliated understory species. Defoliation, and light × defoliation interactions, impacted multiple growth traits in understory species. In contrast, forest-edge species showed no effect of defoliation except on total biomass, and only one light × defoliation interaction was observed. Our results indicate that differences in biomass allocation, leaf ecophysiology, and other growth parameters between forest understory and edge species may be structuring post-damage response in understory and forest edge herbs. Full article
(This article belongs to the Section Ecology)
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20 pages, 6892 KiB  
Article
Machine-Learning-Assisted Analysis of TCR Profiling Data Unveils Cross-Reactivity between SARS-CoV-2 and a Wide Spectrum of Pathogens and Other Diseases
by Georgios K. Georgakilas, Achilleas P. Galanopoulos, Zafeiris Tsinaris, Maria Kyritsi, Varvara A. Mouchtouri, Matthaios Speletas and Christos Hadjichristodoulou
Biology 2022, 11(10), 1531; https://doi.org/10.3390/biology11101531 - 19 Oct 2022
Cited by 1 | Viewed by 1846
Abstract
During the last two years, the emergence of SARS-CoV-2 has led to millions of deaths worldwide, with a devastating socio-economic impact on a global scale. The scientific community’s focus has recently shifted towards the association of the T cell immunological repertoire with COVID-19 [...] Read more.
During the last two years, the emergence of SARS-CoV-2 has led to millions of deaths worldwide, with a devastating socio-economic impact on a global scale. The scientific community’s focus has recently shifted towards the association of the T cell immunological repertoire with COVID-19 progression and severity, by utilising T cell receptor sequencing (TCR-Seq) assays. The Multiplexed Identification of T cell Receptor Antigen (MIRA) dataset, which is a subset of the immunoACCESS study, provides thousands of TCRs that can specifically recognise SARS-CoV-2 epitopes. Our study proposes a novel Machine Learning (ML)-assisted approach for analysing TCR-Seq data from the antigens’ point of view, with the ability to unveil key antigens that can accurately distinguish between MIRA COVID-19-convalescent and healthy individuals based on differences in the triggered immune response. Some SARS-CoV-2 antigens were found to exhibit equal levels of recognition by MIRA TCRs in both convalescent and healthy cohorts, leading to the assumption of putative cross-reactivity between SARS-CoV-2 and other infectious agents. This hypothesis was tested by combining MIRA with other public TCR profiling repositories that host assays and sequencing data concerning a plethora of pathogens. Our study provides evidence regarding putative cross-reactivity between SARS-CoV-2 and a wide spectrum of pathogens and diseases, with M. tuberculosis and Influenza virus exhibiting the highest levels of cross-reactivity. These results can potentially shift the emphasis of immunological studies towards an increased application of TCR profiling assays that have the potential to uncover key mechanisms of cell-mediated immune response against pathogens and diseases. Full article
(This article belongs to the Section Bioinformatics)
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16 pages, 3713 KiB  
Article
Phenotypes of Floral Nectaries in Developmental Mutants of Legumes and What They May Tell about Genetic Control of Nectary Formation
by Andrey Sinjushin
Biology 2022, 11(10), 1530; https://doi.org/10.3390/biology11101530 - 19 Oct 2022
Viewed by 1572
Abstract
The vast majority of angiosperms attracts animal pollinators with the nectar secreted through specialized floral nectaries (FNs). Although there is evidence that principal patterns of regulation of FN development are conserved in large angiosperm clades, these structures are very diverse considering their morphology [...] Read more.
The vast majority of angiosperms attracts animal pollinators with the nectar secreted through specialized floral nectaries (FNs). Although there is evidence that principal patterns of regulation of FN development are conserved in large angiosperm clades, these structures are very diverse considering their morphology and position within a flower. Most data on genetic control of FN formation were obtained in surveys of a model plant species, Arabidopsis thaliana (Brassicaceae). There are almost no data on genetic factors affecting FN development in Leguminosae, the plant family of a high agricultural value and possessing outstandingly diverse flowers. In this work, the morphology of FNs was examined in a set of leguminous species, both wild-type and developmental mutants, by the means of a scanning electron microscopy. Unlike Brassicaceae, FNs in legumes are localized between stamens and a carpel instead of being associated with a certain floral organ. FNs were found stable in most cases of mutants when perianth and/or androecium morphology was affected. However, regulation of FN development by BLADE-ON-PETIOLE-like genes seems to be a shared feature between legumes (at least Pisum) and Arabidopsis. In some legumes, the adaxial developmental program (most probably CYCLOIDEA-mediated) suppresses the FN development. The obtained results neither confirm the role of orthologues of UNUSUAL FLORAL ORGANS and LEAFY in FN development in legumes nor reject it, as two studied pea mutants were homozygous at the weakest alleles of the corresponding loci and possessed FNs similar to those of wild-type. Full article
(This article belongs to the Section Plant Science)
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15 pages, 1341 KiB  
Article
Prevalence of Periodontal Pathogens in Slovak Patients with Periodontitis and Their Possible Aspect of Transmission from Companion Animals to Humans
by Miriam Sondorová, Ján Kučera, Jana Kačírová, Zuzana Krchová Nagyová, Natália Šurín Hudáková, Tomáš Lipták and Marián Maďar
Biology 2022, 11(10), 1529; https://doi.org/10.3390/biology11101529 - 19 Oct 2022
Cited by 2 | Viewed by 1582
Abstract
Oral health and diseases are greatly influenced by oral bacteria. During dysbiosis, bacterial composition changes, which can lead to periodontitis. Periodontitis in humans is associated with periodontal pathogens such as Treponema denticola, Porphyromonas gingivalis, Tannerella forsythia and Aggregatibacter actinomycetemcomitans. Animal-to-human [...] Read more.
Oral health and diseases are greatly influenced by oral bacteria. During dysbiosis, bacterial composition changes, which can lead to periodontitis. Periodontitis in humans is associated with periodontal pathogens such as Treponema denticola, Porphyromonas gingivalis, Tannerella forsythia and Aggregatibacter actinomycetemcomitans. Animal-to-human transmission of some of these pathogens has also been reported. The aim of this study was to evaluate the prevalence of periodontal pathogens in Slovak patients and to assess the possible risk of transmission of these pathogens from animals to their owners. The presence of periodontal pathogens in dental plaque was monitored by PCR. Amplified products were analysed using Sanger sequencing. T. forsythia isolates were assessed for the susceptibility to different antibiotics using the disk diffusion method. In humans, T. denticola, P. gingivalis, T. forsythia and A. actinomycetemcomitans were present in 69.23%, 69.23%, 100% and 84.62%, respectively. Most isolates of T. forsythia were susceptible to amoxicillin-clavulanic acid, clindamycin and moxifloxacin, but they were resistant to metronidazole. The transmission of T. forsythia from animals to their owners was not proven based on sequence analysing. On the other hand, transmission of Porphyromonas gulae was confirmed, but the risk of its involvement in the pathogenesis of periodontitis in humans must be further investigated. Full article
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10 pages, 1782 KiB  
Brief Report
Osmotic Gradient Is a Factor That Influences the Gill Microbiota Communities in Oryzias melastigma
by Keng Po Lai, Delbert Almerick T. Boncan, Lu Yang, Cherry Chi Tim Leung, Jeff Cheuk Hin Ho, Xiao Lin, Ting Fung Chan, Richard Yuen Chong Kong and William Ka Fai Tse
Biology 2022, 11(10), 1528; https://doi.org/10.3390/biology11101528 - 19 Oct 2022
Cited by 3 | Viewed by 1678
Abstract
The fish gill is the first tissue that is exposed to the external media and undergoes continuous osmotic challenges. Recently, our group published an article entitled “Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka” in the [...] Read more.
The fish gill is the first tissue that is exposed to the external media and undergoes continuous osmotic challenges. Recently, our group published an article entitled “Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka” in the journal mSystems (e0004722, 2022), and suggested the possible host-bacterium interaction in the fish gill during osmotic stress. The previous study was performed by the progressive fresh water transfer (i.e., seawater to fresh water transfer via 50% seawater (FW)). Our group hypothesized that osmotic gradient could be a factor that determines the microbiota communities in the gill. The current 16S rRNA metagenomic sequencing study found that the direct transfer (i.e., seawater to fresh water (FWd)) could result in different gill microbiota communities in the same fresh water endpoints. Pseduomonas was the dominant bacteria (more than 55%) in the FWd gill. The Kyoto Encyclopedia of Genes and Genomes and MetaCyc analysis further suggested that the FWd group had enhanced osmosensing pathways, such as the ATP-binding cassette transporters, taurine degradation, and energy-related tricarboxylic acid metabolism compared to the FW group. Full article
(This article belongs to the Special Issue Secondary Metabolites from Microorganisms, or Microorganism-Host Interaction?)
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26 pages, 1932 KiB  
Article
Invasive Urban Mammalian Predators: Distribution and Multi-Scale Habitat Selection
by Kim F. Miller, Deborah J. Wilson, Stephen Hartley, John G. Innes, Neil B. Fitzgerald, Poppy Miller and Yolanda van Heezik
Biology 2022, 11(10), 1527; https://doi.org/10.3390/biology11101527 - 19 Oct 2022
Cited by 5 | Viewed by 1997
Abstract
A barrier to successful ecological restoration of urban green spaces in many cities is invasive mammalian predators. We determined the fine- and landscape-scale habitat characteristics associated with the presence of five urban predators (black and brown rats, European hedgehogs, house mice, and brushtail [...] Read more.
A barrier to successful ecological restoration of urban green spaces in many cities is invasive mammalian predators. We determined the fine- and landscape-scale habitat characteristics associated with the presence of five urban predators (black and brown rats, European hedgehogs, house mice, and brushtail possums) in three New Zealand cities, in spring and autumn, in three green space types: forest fragments, amenity parks, and residential gardens. Season contributed to variations in detections for all five taxa. Rodents were detected least in residential gardens; mice were detected more often in amenity parks. Hedgehogs were detected least in forest fragments. Possums were detected most often in forest fragments and least often in residential gardens. Some of this variation was explained by our models. Proximity of amenity parks to forest patches was strongly associated with presence of possums (positively), hedgehogs (positively), and rats (negatively). Conversely, proximity of residential gardens to forest patches was positively associated with rat presence. Rats were associated with shrub and lower canopy cover and mice with herb layer cover. In residential gardens, rat detection was associated with compost heaps. Successful restoration of biodiversity in these cities needs extensive, coordinated predator control programmes that engage urban residents. Full article
(This article belongs to the Section Conservation Biology and Biodiversity)
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11 pages, 1580 KiB  
Article
MEKK-3 Acts Cooperatively with NSY-1 in SKN-1-Dependent Manner against Oxidative Stress and Aging in Caenorhabditis elegans
by Min Hwang, Chandani Shrestha, Shinwon Kang and Jiyoon Kim
Biology 2022, 11(10), 1526; https://doi.org/10.3390/biology11101526 - 18 Oct 2022
Cited by 2 | Viewed by 1890
Abstract
Oxidative stress resulting from reactive oxygen species and other toxic metabolites is involved in human diseases, and it plays an important role in aging. In Caenorhabditis elegans, SKN-1 is required for protection against oxidative stress and aging. As p38 mitogen-activated protein kinase [...] Read more.
Oxidative stress resulting from reactive oxygen species and other toxic metabolites is involved in human diseases, and it plays an important role in aging. In Caenorhabditis elegans, SKN-1 is required for protection against oxidative stress and aging. As p38 mitogen-activated protein kinase signaling is activated in response to oxidative stress, SKN-1 accumulates in intestinal nuclei and induces phase II detoxification genes. However, NSY-1, a well-known mitogen-activated protein kinase kinase kinase (MAPKKK) of C. elegans, acts as a partial regulator of the SKN-1-induced oxidative stress signaling pathway, suggesting that the regulator for optimal activation of SKN-1 remains unknown. Here, we report a MAPKKK, MEKK-3, as a new regulator required for full activation of SKN-1-mediated resistance against oxidative stress and aging. In RNA-interference-based screening, we found that the simultaneous knockdown of mekk-3 and nsy-1 significantly decreased the oxidative stress resistance and survival of SKN-1 transgenic worms. MEKK-3 was induced in response to oxidative stress. Mechanistic analysis revealed that double knockdown of mekk-3 and nsy-1 completely suppressed the nuclear localization of SKN-1. These results were reproduced in mutant worms in which SKN-1 is constitutively localized to intestinal nuclei. In addition, mekk-3 and nsy-1 were required for optimal induction of SKN-1 target genes such as gcs-1 and trx-1. These data indicate that MEKK-3 plays an essential role in the SKN-1-dependent signaling pathway involved in oxidative stress resistance and longevity by cooperating with NSY-1. Full article
(This article belongs to the Special Issue Genetic and Epigenetic Mechanisms of Longevity and Aging)
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14 pages, 922 KiB  
Review
The Key Element Role of Metallophores in the Pathogenicity and Virulence of Staphylococcus aureus: A Review
by Ghassan Ghssein and Zeinab Ezzeddine
Biology 2022, 11(10), 1525; https://doi.org/10.3390/biology11101525 - 18 Oct 2022
Cited by 16 | Viewed by 2400
Abstract
The ubiquitous bacterium Staphylococcus aureus causes many diseases that sometimes can be fatal due to its high pathogenicity. The latter is caused by the ability of this pathogen to secrete secondary metabolites, enabling it to colonize inside the host causing infection through various [...] Read more.
The ubiquitous bacterium Staphylococcus aureus causes many diseases that sometimes can be fatal due to its high pathogenicity. The latter is caused by the ability of this pathogen to secrete secondary metabolites, enabling it to colonize inside the host causing infection through various processes. Metallophores are secondary metabolites that enable bacteria to sequester metal ions from the surrounding environment since the availability of metal ions is crucial for bacterial metabolism and virulence. The uptake of iron and other metal ions such as nickel and zinc is one of these essential mechanisms that gives this germ its virulence properties and allow it to overcome the host immune system. Additionally, extensive interactions occur between this pathogen and other bacteria as they compete for resources. Staphylococcus aureus has high-affinity metal import pathways including metal ions acquisition, recruitment and metal–chelate complex import. These characteristics give this bacterium the ability to intake metallophores synthesized by other bacteria, thus enabling it to compete with other microorganisms for the limited nutrients. In scarce host conditions, free metal ions are extremely low because they are confined to storage and metabolic molecules, so metal ions are sequestered by metallophores produced by this bacterium. Both siderophores (iron chelating molecules) and staphylopine (wide- spectrum metallophore) are secreted by Staphylococcus aureus giving it infectious properties. The genetic regulation of the synthesis and export together with the import of metal loaded metallophores are well established and are all covered in this review. Full article
(This article belongs to the Special Issue Secondary Metabolites from Microorganisms, or Microorganism-Host Interaction?)
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21 pages, 3207 KiB  
Article
Quantifying Catch Rates, Shark Abundance and Depredation Rate at a Spearfishing Competition on the Great Barrier Reef, Australia
by Adam Smith, Al Songcuan, Jonathan Mitchell, Max Haste, Zachary Schmidt, Glenn Sands and Marcus Lincoln Smith
Biology 2022, 11(10), 1524; https://doi.org/10.3390/biology11101524 - 18 Oct 2022
Cited by 1 | Viewed by 2502
Abstract
We developed and applied a method to quantify spearfisher effort and catch, shark interactions and shark depredation in a boat-based recreational spearfishing competition in the Great Barrier Reef Marine Park in Queensland. Survey questions were designed to collect targeted quantitative data whilst minimising [...] Read more.
We developed and applied a method to quantify spearfisher effort and catch, shark interactions and shark depredation in a boat-based recreational spearfishing competition in the Great Barrier Reef Marine Park in Queensland. Survey questions were designed to collect targeted quantitative data whilst minimising the survey burden of spearfishers. We provide the first known scientific study of shark depredation during a recreational spearfishing competition and the first scientific study of shark depredation in the Great Barrier Reef region. During the two-day spearfishing competition, nine vessels with a total of 33 spearfishers reported a catch of 144 fish for 115 h of effort (1.25 fish per hour). A subset of the catch comprised nine eligible species under competition rules, of which 47 pelagic fish were weighed. The largest fish captured was a 34.4 kg Sailfish (Istiophorus platypterus). The most common species captured and weighed was Spanish Mackerel (Scomberomorus commerson). The total weight of eligible fish was 332 kg and the average weight of each fish was 7.1 kg. During the two-day event, spearfishers functioned as citizen scientists and counted 358 sharks (115 h effort), averaging 3.11 sharks per hour. Grey Reef Sharks (Carcharhinus amblyrhynchos) comprised 64% of sightings. Nine speared fish were fully depredated by sharks as spearfishers attempted to retrieve their catch, which equates to a depredation rate of 5.9%. The depredated fish included four pelagic fish and five reef fish. The shark species responsible were Grey Reef Shark (C. amblyrhynchos) (66%), Bull Shark (Carcharhinus leucas) (11%), Whitetip Reef Shark (Triaenodon obesus) (11%) and Great Hammerhead (Sphyrna mokarran) (11%). There were spatial differences in fish catch, shark sightings and rates of depredation. We developed a report card that compared average catch of fish, sightings of sharks per hour and depredation rate by survey area, which assists recreational fishers and marine park managers to assess spatio-temporal changes. The participating spearfishers can be regarded as experienced (average 18 days a year for average 13.4 years). Sixty percent of interviewees perceived that shark numbers have increased in the past 10 years, 33% indicated no change and 7% indicated shark numbers had decreased. Total fuel use of all vessels was 2819 L and was equivalent to 6.48 tons of greenhouse gas emissions for the competition. Full article
(This article belongs to the Special Issue Understanding and Managing Human–Shark Interactions in an Environmentally Aware World)
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27 pages, 2148 KiB  
Article
Selenium Nanoparticle-Enriched and Potential Probiotic, Lactiplantibacillus plantarum S14 Strain, a Diet Supplement Beneficial for Rainbow Trout
by Francisco Yanez-Lemus, Rubén Moraga, Carlos T. Smith, Paulina Aguayo, Kimberly Sánchez-Alonzo, Apolinaria García-Cancino, Ariel Valenzuela and Víctor L. Campos
Biology 2022, 11(10), 1523; https://doi.org/10.3390/biology11101523 - 18 Oct 2022
Cited by 8 | Viewed by 2168
Abstract
Lactic acid bacteria (LAB), obtained from rainbow trout (Oncorhynchus mykiss) intestine, were cultured in MRS medium and probiotic candidates. Concurrently, producers of elemental selenium nanoparticles (Se0Nps) were selected. Probiotic candidates were subjected to morphological characterization and the following tests: [...] Read more.
Lactic acid bacteria (LAB), obtained from rainbow trout (Oncorhynchus mykiss) intestine, were cultured in MRS medium and probiotic candidates. Concurrently, producers of elemental selenium nanoparticles (Se0Nps) were selected. Probiotic candidates were subjected to morphological characterization and the following tests: antibacterial activity, antibiotic susceptibility, hemolytic activity, catalase, hydrophobicity, viability at low pH, and tolerance to bile salts. Two LAB strains (S4 and S14) satisfied the characteristics of potential probiotics, but only strain S14 reduced selenite to biosynthesize Se0Nps. S14 strain was identified, by 16S rDNA analysis, as Lactiplantibacillus plantarum. Electron microscopy showed Se0Nps on the surface of S14 cells. Rainbow trout diet was supplemented (108 CFU g−1 feed) with Se0Nps-enriched L. plantarum S14 (LABS14-Se0Nps) or L. plantarum S14 alone (LABS14) for 30 days. At days 0, 15, and 30, samples (blood, liver, and dorsal muscle) were obtained from both groups, plus controls lacking diet supplementation. Fish receiving LABS14-Se0Nps for 30 days improved respiratory burst and plasmatic lysozyme, (innate immune response) and glutathione peroxidase (GPX) (oxidative status) activities and productive parameters when compared to controls. The same parameters also improved when compared to fish receiving LABS14, but significant only for plasmatic and muscle GPX. Therefore, Se0Nps-enriched L. plantarum S14 may be a promising alternative for rainbow trout nutritional supplementation. Full article
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16 pages, 3530 KiB  
Article
The Evolutionary Dynamics of the Mitochondrial tRNA in the Cichlid Fish Family
by Yosur G. Fiteha and Mahmoud Magdy
Biology 2022, 11(10), 1522; https://doi.org/10.3390/biology11101522 - 18 Oct 2022
Cited by 2 | Viewed by 1579
Abstract
The mitochondrial transfer RNA genes (tRNAs) attract more attention due to their highly dynamic and rapidly evolving nature. The current study aimed to detect and evaluate the dynamics, characteristic patterns, and variations of mitochondrial tRNAs. The study was conducted in two main parts: [...] Read more.
The mitochondrial transfer RNA genes (tRNAs) attract more attention due to their highly dynamic and rapidly evolving nature. The current study aimed to detect and evaluate the dynamics, characteristic patterns, and variations of mitochondrial tRNAs. The study was conducted in two main parts: first, the published mitogenomic sequences of cichlids mt tRNAs have been filtered. Second, the filtered mitochondrial tRNA and additional new mitogenomes representing the most prevalent Egyptian tilapiine were compared and analyzed. Our results revealed that all 22 tRNAs of cichlids folded into a classical cloverleaf secondary structure with four domains, except for trnSGCU, missing the D domain in all cichlids. When consensus tRNAs were compared, most of the mutations were observed in the trnP at nucleotide levels (substitutions and indels), in contrast to trnLUAA. From a structural perspective, the anticodon loop and T-loop formations were the most conserved structures among all parts of the tRNA in contrast to the A-stem and D-loop formations. The trnW was the lowest polymorphic unneutral tRNA among all cichlids (both the family and the haplotilapiine lineage), in contrast with the neutral trnD that was extremely polymorphic among and within the haplotilapiine lineage species compared to other cichlids species. From a phylogenetic perspective, the trnC was extremely hypervariable and neutral tRNA in both haplotilapiine lineage and cichlids but was unable to report correct phylogenetic signal for the cichlids. In contrast to trnI and trnY, less variable neutral tRNAs that were able to cluster the haplotilapiine lineage and cichlids species as previously reported. By observing the DNA polymorphism in the coding DNA sequences (CDS), the highest affected amino acid by non-synonymous mutations was isoleucine and was equally mutated to valine and vice versa; no correlation between mutations in CDS and tRNAs was statistically found. The current study provides an insight into the mitochondrial tRNA evolution and its effect on the cichlid diversity and speciation model at the maternal level. Full article
(This article belongs to the Special Issue Macro-Ecology, Macro-Evolution and Conservation of Animals and Plants)
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12 pages, 4194 KiB  
Article
Quantifications of Mandibular Trabecular Bone Microstructure Using Cone Beam Computed Tomography for Age Estimation: A Preliminary Study
by Arshiya Tabassum, Mansharan Kaur Chainchel Singh, Norliza Ibrahim, Subramaniam Ramanarayanan and Mohd Yusmiaidil Putera Mohd Yusof
Biology 2022, 11(10), 1521; https://doi.org/10.3390/biology11101521 - 18 Oct 2022
Cited by 2 | Viewed by 1631
Abstract
The aim of this study is two-fold: first, to correlate the values for each of the trabecular bone microstructure (TBM) parameters to the individual’s chronological age and sex, thereby facilitating the assessment of potential age and sex-related changes in trabecular bone microstructure parameters [...] Read more.
The aim of this study is two-fold: first, to correlate the values for each of the trabecular bone microstructure (TBM) parameters to the individual’s chronological age and sex, thereby facilitating the assessment of potential age and sex-related changes in trabecular bone microstructure parameters in the mandible; and second, to quantify the trabecular microstructural parameters in relation to chronological age. Twenty cone-beam computed tomographic (CBCT) scans were retrieved retrospectively from a database of adult patients with ages ranging in age from 22 to 43 years. In the mandible, the volume of interest included the inter-dental space between the second mandibular premolar and the first mandibular molar, as well as the trabecular space beneath and between the apices. Using the AnalyzeDirect 14.0 software, the DICOM images of CBCT scans were pre-processed, transformed, segmented using a novel semi-automatic threshold-guided method, and quantified. In addition, TBM parameters were derived, and statistical analysis was conducted using a Pearson correlation test with two tails. All parameters exhibited no statistically significant differences (p > 0.05) between chronological age and sex. Statistically significant negative correlations were found between Tb. N (r = −0.489), BS/TV (r = −0.527), and chronological age (p = 0.029 and p = 0.017, respectively). Only Tb. N and BS/TV exhibited an inverse relationship with chronological age. Numerous studies have quantified the trabecular architecture of the jaw bones, but none have found a correlation between the quantified trabecular parameters and chronological age. The digital imprints produced by radiographic imaging can serve as biological profiles for data collection. Full article
(This article belongs to the Special Issue Forensic Anthropology: New Methodological and Theoretical Perspectives in Forensic Human Skeletal Identification and Methods)
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21 pages, 12407 KiB  
Article
Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress
by Zhenfan Yu, Dongdong Zhang, Shaobo Hu, Xingyue Liu, Bin Zeng, Wenwen Gao, Yawen He, Huanxue Qin and Xintong Ma
Biology 2022, 11(10), 1520; https://doi.org/10.3390/biology11101520 - 17 Oct 2022
Cited by 5 | Viewed by 1973
Abstract
The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene [...] Read more.
The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene family in almond (Prunus dulcis). In this study, a total of 136 PdAP2/ERF genes were identified from the almond genome, and their protein physicochemical properties were analyzed. The PdAP2/ERF members were divided into five subgroups: AP2, RAV, ERF, DREB, and Soloist. The PdAP2/ERF members in each subgroup had conserved motif types and exon/intron numbers. PdAP2/ERFS members are distributed on eight chromosomes, with 22 pairs of segmental duplications and 28 pairs of tandem duplications. We further explored the colinear relationship between almond and Arabidopsis thaliana, Oryza sativa, Malus domestica, and Prunus persicaAP2/ERF genes and their evolution. The results of cis-acting elements showed that PdAP2/ERF members are widely involved in various processes, such as growth and development, hormone regulation, and stress response. The results based on transcriptome expression patterns showed that PdAP2/ERF genes had significant tissue-specific expression characteristics and were involved in the response of annual dormant branches of almond to low-temperature freezing stress. In addition, the fluorescence quantitative relative expression results of 13 representative PdAP2/ERF genes in four tissues of ‘Wanfeng’ almond and under six low-temperature freezing treatments of annual dormant branches were consistent with the transcriptome results. It is worth noting that the fluorescence quantitative expression level showed that the PdERF24 gene was extremely significant at −30 °C, suggesting that this gene may play an important role in the response of almond dormancy to ultralow temperature freezing stress. Finally, we identified 7424 and 6971 target genes based on AP2 and ERF/DREB DNA-binding sites, respectively. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on PdAP2/ERF genes, including 13 PdAP2/ERF genes, and performed fluorescence quantitative analysis of annual dormant shoots under different low-temperature freezing stress treatments to understand the tolerance of almond dormancy to freezing stress and suggest future improvements. Full article
(This article belongs to the Special Issue Eco-Physiological and Molecular Basis of Stress Tolerance in Plants)
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13 pages, 712 KiB  
Article
Na,K-ATPase Kinetics and Oxidative Stress in Kidneys of Zucker Diabetic Fatty (fa/fa) Rats Depending on the Diabetes Severity—Comparison with Lean (fa/+) and Wistar Rats
by Norbert Vrbjar, Tomas Jasenovec, Marta Kollarova, Denisa Snurikova, Maria Chomova, Dominika Radosinska, Ivana Shawkatova, Lubomira Tothova and Jana Radosinska
Biology 2022, 11(10), 1519; https://doi.org/10.3390/biology11101519 - 17 Oct 2022
Cited by 4 | Viewed by 1373
Abstract
For a better insight into relations between type 2 diabetes mellitus (T2DM) and Na,K-ATPase properties in kidneys, we aimed to characterize two subgroups of ZDF obese (fa/fa) rats, with more and less developed T2DM, and compare them with two controls: lean (fa/+) and [...] Read more.
For a better insight into relations between type 2 diabetes mellitus (T2DM) and Na,K-ATPase properties in kidneys, we aimed to characterize two subgroups of ZDF obese (fa/fa) rats, with more and less developed T2DM, and compare them with two controls: lean (fa/+) and Wistar. Na,K-ATPase enzyme kinetics were estimated by measuring the ATP hydrolysis in the range of NaCl and ATP levels. As Na,K-ATPase is sensitive to oxidative stress, we evaluated selected oxidative stress parameters in kidney homogenates. Our results suggest that thiol–disulfide redox balance in the renal medulla and Na,K-ATPase properties in the renal cortex differ between both controls, while observed measurements in lean (fa/+) rats showed deviation towards the values observed in ZDF (fa/fa) rats. In comparison with both controls, Na,K-ATPase enzyme activity was higher in the renal cortex of ZDF rats independent of diabetes severity. This might be a consequence of increased glucose load in tubular fluid. The increase in lipid peroxidation observed in the renal cortex of ZDF rats was not associated with Na,K-ATPase activity impairment. Regarding the differences between subgroups of ZDF animals, well-developed T2DM (glycemia higher than 10 mmol/L) was associated with a higher ability of Na,K-ATPase to utilize the ATP energy substrate. Full article
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13 pages, 2307 KiB  
Article
Two New Species and Two New Records of the Lichen-Forming Fungal Genus Peltula (Ascomycota: Peltulaceae) from China
by Qiuxia Yang, Jason Hollinger, Steven D. Leavitt and Xinli Wei
Biology 2022, 11(10), 1518; https://doi.org/10.3390/biology11101518 - 17 Oct 2022
Viewed by 1670
Abstract
In this study, two new species, Peltula confusa Q.X. Yang & X.L. Wei, sp. nov., growing in a dry microenvironment within a semi-humid area, and Peltula subpatellata Q.X. Yang & X.L. Wei, sp. nov., occurring in arid and semi-arid regions, are described. In [...] Read more.
In this study, two new species, Peltula confusa Q.X. Yang & X.L. Wei, sp. nov., growing in a dry microenvironment within a semi-humid area, and Peltula subpatellata Q.X. Yang & X.L. Wei, sp. nov., occurring in arid and semi-arid regions, are described. In addition, two species, P. polyspora (Tuck.) Wetmore and P. obscuratula (Nyl.) Poelt ex Egea, are recorded for the first time in China. All four species are described based on morphological, anatomical and molecular data. Peltula confusa is characterized by a lighter, brighter, and more yellowish upper surface than other species of this genus, with discs concentrated in the central part of squamules, and a thick lower cortex. Peltula subpatellata can be distinguished from P. patellata (Bagl.) Swinscow & Krog by its non-thickened and sometimes darkened margins and sometimes the presence of peltate squamules. Phylogenetic analysis based on DNA sequences of four loci (ITS, nrSSU, nrLSU, and RPB2) demonstrates the placement of these species within Peltula, and supports current species delimitations. We suggest that the growth substrate should be considered as an additional characteristic for species delimitation. Full article
(This article belongs to the Special Issue Studies on Species Diversity and Phylogeny of Ascomycota (Fungi))
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19 pages, 4370 KiB  
Article
SNRPD2 Is a Novel Substrate for the Ubiquitin Ligase Activity of the Salmonella Type III Secretion Effector SlrP
by Andrea Bullones-Bolaños, Juan Luis Araujo-Garrido, Jesús Fernández-García, Francisco Romero, Joaquín Bernal-Bayard and Francisco Ramos-Morales
Biology 2022, 11(10), 1517; https://doi.org/10.3390/biology11101517 - 17 Oct 2022
Cited by 3 | Viewed by 1499
Abstract
SlrP is a protein with E3 ubiquitin ligase activity that is translocated by Salmonella enterica serovar Typhimurium into eukaryotic host cells through a type III secretion system. A yeast two-hybrid screen was performed to find new human partners for this protein. Among the [...] Read more.
SlrP is a protein with E3 ubiquitin ligase activity that is translocated by Salmonella enterica serovar Typhimurium into eukaryotic host cells through a type III secretion system. A yeast two-hybrid screen was performed to find new human partners for this protein. Among the interacting proteins identified by this screen was SNRPD2, a core component of the spliceosome. In vitro ubiquitination assays demonstrated that SNRPD2 is a substrate for the catalytic activity of SlrP, but not for other members of the NEL family of E3 ubiquitin ligases, SspH1 and SspH2. The lysine residues modified by this activity were identified by mass spectrometry. The identification of a new ubiquitination target for SlrP is a relevant contribution to the understanding of the role of this Salmonella effector. Full article
(This article belongs to the Section Microbiology)
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18 pages, 2816 KiB  
Review
Was There a Cambrian Explosion on Land? The Case of Arthropod Terrestrialization
by Erik Tihelka, Richard J. Howard, Chenyang Cai and Jesus Lozano-Fernandez
Biology 2022, 11(10), 1516; https://doi.org/10.3390/biology11101516 - 17 Oct 2022
Cited by 4 | Viewed by 5534
Abstract
Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian–Devonian, the fossil record [...] Read more.
Arthropods, the most diverse form of macroscopic life in the history of the Earth, originated in the sea. Since the early Cambrian, at least ~518 million years ago, these animals have dominated the oceans of the world. By the Silurian–Devonian, the fossil record attests to arthropods becoming the first animals to colonize land, However, a growing body of molecular dating and palaeontological evidence suggests that the three major terrestrial arthropod groups (myriapods, hexapods, and arachnids), as well as vascular plants, may have invaded land as early as the Cambrian–Ordovician. These dates precede the oldest fossil evidence of those groups and suggest an unrecorded continental “Cambrian explosion” a hundred million years prior to the formation of early complex terrestrial ecosystems in the Silurian–Devonian. We review the palaeontological, phylogenomic, and molecular clock evidence pertaining to the proposed Cambrian terrestrialization of the arthropods. We argue that despite the challenges posed by incomplete preservation and the scarcity of early Palaeozoic terrestrial deposits, the discrepancy between molecular clock estimates and the fossil record is narrower than is often claimed. We discuss strategies for closing the gap between molecular clock estimates and fossil data in the evolution of early ecosystems on land Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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Correction
Correction: Torres et al. Twentieth-Century Paleoproteomics: Lessons from Venta Micena Fossils. Biology 2022, 11, 1184
by Jesús M. Torres, Concepción Borja, Luis Gibert, Francesc Ribot and Enrique G. Olivares
Biology 2022, 11(10), 1515; https://doi.org/10.3390/biology11101515 - 17 Oct 2022
Cited by 1 | Viewed by 794
Abstract
There was an error in the original publication [...] Full article
(This article belongs to the Special Issue Paleontology in the 21st Century)
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