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Volume 11
Issue 5
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Biology, Volume 11, Issue 5 (May 2022) – 179 articles

Cover Story (view full-size image): Fossils of dinosaurs other than birds are at least 66 million years old. Many organic compounds have survived fossilization and can still be detected. This review article describes the discoveries of organic molecules in dinosaur fossils up to date along with the analytical methods used for their characterization. Organic compounds detected in dinosaurs include protoporphyrin IX, heme, biliverdin, melanin, collagens, and keratins. Difficulties in unambiguously confirming the presence of organic compounds in these fossils are discussed. View this paper
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28 pages, 6541 KiB  
Article
Integrated Expression Analysis of Small RNA, Degradome and Microarray Reveals Complex Regulatory Action of miRNA during Prolonged Shade in Swarnaprabha Rice
by Madhusmita Panigrahy, Kishore Chandra Sekhar Panigrahi, Yugandhar Poli, Aman Ranga and Neelofar Majeed
Biology 2022, 11(5), 798; https://doi.org/10.3390/biology11050798 - 23 May 2022
Cited by 4 | Viewed by 3189
Abstract
Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small [...] Read more.
Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade. Full article
(This article belongs to the Topic Advances in Environmental Biotechnology (AEB))
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14 pages, 4801 KiB  
Article
An Insight Based on Computational Analysis of the Interaction between the Receptor-Binding Domain of the Omicron Variants and Human Angiotensin-Converting Enzyme 2
by Ismail Celik, Magda H. Abdellattif and Trina Ekawati Tallei
Biology 2022, 11(5), 797; https://doi.org/10.3390/biology11050797 - 23 May 2022
Cited by 10 | Viewed by 2073
Abstract
Concerns have been raised about the high number of mutations in the spike protein of the new emergence of the highly transmissible Omicron variant (B.1.1529 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This variant’s extraordinary ability to evade antibodies would significantly [...] Read more.
Concerns have been raised about the high number of mutations in the spike protein of the new emergence of the highly transmissible Omicron variant (B.1.1529 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This variant’s extraordinary ability to evade antibodies would significantly impair the current vaccination program. This present study aimed to computationally analyze the interaction between the receptor-binding domain (RBD) in the spike protein of Omicron variants and human angiotensin-converting enzyme 2 (hACE2). The docking results indicated that Omicron BA.2 has exceptionally strong interactions with hACE2 in comparison to Omicron BA.1, Delta, and wild-type, as indicated by various parameters such as salt bridge, hydrogen bond, and non-bonded interactions. The results of the molecular dynamics simulation study corroborate these findings, indicating that Omicron BA.2 has a strong and stable interaction with hACE2. This study provides insight into the development of an effective intervention against this variant. Full article
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24 pages, 2787 KiB  
Systematic Review
Detection of the Synthetic Cannabinoids AB-CHMINACA, ADB-CHMINACA, MDMB-CHMICA, and 5F-MDMB-PINACA in Biological Matrices: A Systematic Review
by Elisabet Navarro-Tapia, Jana Codina, Víctor José Villanueva-Blasco, Óscar García-Algar and Vicente Andreu-Fernández
Biology 2022, 11(5), 796; https://doi.org/10.3390/biology11050796 - 23 May 2022
Cited by 6 | Viewed by 3523
Abstract
New synthetic cannabinoids (SCs) are emerging rapidly and continuously. Biological matrices are key for their precise detection to link toxicity and symptoms to each compound and concentration and ascertain consumption trends. The objective of this study was to determine the best human biological [...] Read more.
New synthetic cannabinoids (SCs) are emerging rapidly and continuously. Biological matrices are key for their precise detection to link toxicity and symptoms to each compound and concentration and ascertain consumption trends. The objective of this study was to determine the best human biological matrices to detect the risk-assessed compounds provided by The European Monitoring Centre for Drugs and Drug Addiction: AB-CHMINACA, ADB-CHMNACA, MDMB-CHMICA, and 5F-MDMB-PINACA. We carried out a systematic review covering 2015 up to the present date, including original articles assessing detection in antemortem human biological matrices with detailed validation information of the technique. In oral fluid and blood, SC parent compounds were found in oral fluid and blood at low concentrations and usually with other substances; thus, the correlation between SCs concentrations and severity of symptoms could rarely be established. When hair is used as the biological matrix, there are difficulties in excluding passive contamination when evaluating chronic consumption. Detection of metabolites in urine is complex because it requires prior identification studies. LC-MS/MS assays were the most widely used approaches for the selective identification of SCs, although the lack of standard references and the need for revalidation with the continuous emergence of new SCs are limiting factors of this technique. A potential solution is high-resolution mass spectrometry screening, which allows for non-targeted detection and retrospective data interrogation. Full article
(This article belongs to the Special Issue Last Updates on Biomarkers of Exposure to Psychoactive Substances in Humans)
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11 pages, 1280 KiB  
Article
GJB2 Is a Major Cause of Non-Syndromic Hearing Impairment in Senegal
by Yacouba Dia, Samuel Mawuli Adadey, Jean Pascal Demba Diop, Elvis Twumasi Aboagye, Seydi Abdoul Ba, Carmen De Kock, Cheikh Ahmed Tidjane Ly, Oluwafemi Gabriel Oluwale, Andrea Regina Gnilane Sène, Pierre Diaga Sarr, Bay Karim Diallo, Rokhaya Ndiaye Diallo and Ambroise Wonkam
Biology 2022, 11(5), 795; https://doi.org/10.3390/biology11050795 - 23 May 2022
Cited by 4 | Viewed by 1902
Abstract
This study aimed to investigate GJB2 (MIM: 121011) and GJB6 (MIM: 604418) variants associated with familial non-syndromic hearing impairment (HI) in Senegal. We investigated a total of 129 affected and 143 unaffected individuals from 44 multiplex families by segregating autosomal recessive non-syndromic HI, [...] Read more.
This study aimed to investigate GJB2 (MIM: 121011) and GJB6 (MIM: 604418) variants associated with familial non-syndromic hearing impairment (HI) in Senegal. We investigated a total of 129 affected and 143 unaffected individuals from 44 multiplex families by segregating autosomal recessive non-syndromic HI, 9 sporadic HI cases of putative genetic origin, and 148 control individuals without personal or family history of HI. The DNA samples were screened for GJB2 coding-region variants and GJB6-D3S1830 deletions. The mean age at the medical diagnosis of the affected individuals was 2.93 ± 2.53 years [range: 1–15 years]. Consanguinity was present in 40 out of 53 families (75.47%). Variants in GJB2 explained HI in 34.1% (n = 15/44) of multiplex families. A bi-allelic pathogenic variant, GJB2: c.94C>T: p.(Arg32Cys) accounted for 25% (n = 11/44 families) of familial cases, of which 80% (n = 12/15) were consanguineous. Interestingly, the previously reported “Ghanaian” founder variant, GJB2: c.427C>T: p.(Arg143Trp), accounted for 4.5% (n = 2/44 families) of the families investigated. Among the normal controls, the allele frequency of GJB2: c.94C>T and GJB2: c.427C>T was estimated at 1% (2/148 ∗ 2) and 2% (4/148 ∗ 2), respectively. No GJB6-D3S1830 deletion was identified in any of the HI patients. This is the first report of a genetic investigation of HI in Senegal, and suggests that GJB2: c.94C>T: p.(Arg32Cys) and GJB2: c.427C>T: p.(Arg143Trp) should be tested in clinical practice for congenital HI in Senegal. Full article
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6 pages, 383 KiB  
Communication
Tolerance of Rodents to an Intravenous Bolus Injection of Sodium Nitrate in a High Concentration
by Rachel Katz-Brull
Biology 2022, 11(5), 794; https://doi.org/10.3390/biology11050794 - 23 May 2022
Viewed by 1555
Abstract
Nitrate, the inorganic anion NO3−, is found in many foods and is an endogenous mammalian metabolite, which is supplied mostly through the diet. Although much is known about the safety of sodium nitrate when given per os, methodological safety [...] Read more.
Nitrate, the inorganic anion NO3−, is found in many foods and is an endogenous mammalian metabolite, which is supplied mostly through the diet. Although much is known about the safety of sodium nitrate when given per os, methodological safety data on intravenous bolus injection of sodium nitrate to rodents are lacking. Recently, we have proposed a new use for nitrate, as a contrast agent for magnetic resonance imaging that will be metal free and leave no traces in the body and the environment further to the imaging examination. It was shown that a stable isotope-labelled analog of this ion (15NO3−), in a sodium nitrate solution form and hyperpolarized state, produces a high magnetic resonance signal with prolonged visibility. Therefore, sodium nitrate was targeted for further preclinical development in this context. In the absence of methodological safety data on the potential effects of a high concentration sodium nitrate bolus intravenous injection into rodents, we carried out such an investigation in mice and rats (n = 12 of each, 6 males and 6 females in each group, altogether 24 animals). We show here that an intravenous bolus administration of sodium nitrate at a concentration of 150 mM and a dose of 51 mg/Kg does not lead to adverse effects in mice and rats. This is the first investigation of the tolerance of rodents to an intravenous injection of sodium nitrate. Full article
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11 pages, 2648 KiB  
Article
Presence of Protease Inhibitor 9 and Granzyme B in Healthy and Pathological Human Corneas
by Stanislava Reinstein Merjava, Jan Kossl, Ales Neuwirth, Pavlina Skalicka, Zuzana Hlinomazova, Vladimir Holan and Katerina Jirsova
Biology 2022, 11(5), 793; https://doi.org/10.3390/biology11050793 - 23 May 2022
Cited by 1 | Viewed by 1536
Abstract
The aim of this study was to find out whether protease inhibitor 9 (PI-9) and granzyme B (GrB) molecules that contribute to immune response and the immunological privilege of various tissues are expressed in healthy and pathological human corneas. [...] Read more.
The aim of this study was to find out whether protease inhibitor 9 (PI-9) and granzyme B (GrB) molecules that contribute to immune response and the immunological privilege of various tissues are expressed in healthy and pathological human corneas. Using cryosections, cell imprints of control corneoscleral discs, we showed that PI-9 was expressed particularly in the endothelium, the superficial and suprabasal epithelium of healthy corneas, limbus, and conjunctiva. GrB was localized in healthy corneal and conjunctival epithelium, while the endothelium showed weak immunostaining. The expression of PI-6 and GrB was confirmed by qRT-PCR. Increased expression levels of the PI-9 and GrB genes were determined when the corneas were cultured with proinflammatory cytokines. Fluorescent and enzymatic immunohistochemistry of pathological corneal explants (corneal melting and herpes virus keratitis) showed pronounced PI-9, GrB, human leucocyte antigen (HLA)-DR, and leukocyte-common antigen (CD45) signals localized in multicellular stromal infiltrates and inflammatory cells scattered in the corneal stroma. We conclude that increased expression of the PI-9 and GrB proteins under pathological conditions and their upregulation in an inflammatory environment indicate their participation in immune response of the cornea during the inflammatory process. Full article
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17 pages, 1433 KiB  
Review
PPAR Alpha as a Metabolic Modulator of the Liver: Role in the Pathogenesis of Nonalcoholic Steatohepatitis (NASH)
by Simona Todisco, Anna Santarsiero, Paolo Convertini, Giulio De Stefano, Michele Gilio, Vito Iacobazzi and Vittoria Infantino
Biology 2022, 11(5), 792; https://doi.org/10.3390/biology11050792 - 23 May 2022
Cited by 27 | Viewed by 5980
Abstract
The strong relationship between metabolic alterations and non-alcoholic steatohepatitis (NASH) suggests a pathogenic interplay. However, many aspects have not yet been fully clarified. Nowadays, NASH is becoming the main cause of liver-associated morbidity and mortality. Therefore, an effort to understand the mechanisms underlying [...] Read more.
The strong relationship between metabolic alterations and non-alcoholic steatohepatitis (NASH) suggests a pathogenic interplay. However, many aspects have not yet been fully clarified. Nowadays, NASH is becoming the main cause of liver-associated morbidity and mortality. Therefore, an effort to understand the mechanisms underlying the pathogenesis of NASH is critical. Among the nuclear receptor transcription factors, peroxisome-proliferator-activated receptor alpha (PPARα) is highly expressed in the liver, where it works as a pivotal transcriptional regulator of the intermediary metabolism. In this context, PPARα’s function in regulating the lipid metabolism is essential for proper liver functioning. Here, we review metabolic liver genes under the control of PPARα and discuss how this aspect can impact the inflammatory condition and pathogenesis of NASH. Full article
(This article belongs to the Special Issue Antitumor and Metabolic Effects Mediated by PPARs)
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14 pages, 2376 KiB  
Article
Effects of Bacillus subtilis T6-1 on the Rhizosphere Microbial Community Structure of Continuous Cropping Poplar
by Junkang Sui, Qianqian Yu, Kai Yang, Jiayi Yang, Chenyu Li and Xunli Liu
Biology 2022, 11(5), 791; https://doi.org/10.3390/biology11050791 - 23 May 2022
Cited by 6 | Viewed by 1961
Abstract
The continuous cropping obstacles in poplar cultivation cause declines in wood yield and serious soil-borne diseases, mainly because of structural alterations in the microbial community and the aggregation of pathogenic fungi. Bacillus subtilis T6-1, isolated from poplar rhizospheric soil, has strong antagonistic effects [...] Read more.
The continuous cropping obstacles in poplar cultivation cause declines in wood yield and serious soil-borne diseases, mainly because of structural alterations in the microbial community and the aggregation of pathogenic fungi. Bacillus subtilis T6-1, isolated from poplar rhizospheric soil, has strong antagonistic effects on poplar pathogens. We aimed to investigate the effects of B. subtilis T6-1 on the structure of the microbial community in the poplar rhizosphere. Poplar seedlings were replanted in three successive generations of soil. The diameter at breast height, plant height, and the number of culturable bacteria of the poplars inoculated with T6-1 exceeded those in the non-inoculated control group. qPCR analysis revealed that the total abundance of T6-1 bacteria in the treated poplars was remarkably higher in contrast to that in the control group. Illumina MiSeq sequencing was employed to track the alterations in diversity and structure of the total microbial community in the poplar rhizosphere inoculated with B. subtilis T6-1. Fungal diversity and abundance in the T6-1 rhizosphere were remarkably lower in contrast with those in the control rhizosphere. The proportion of Bacillus sp. in the total bacterial community in the T6-1 and control groups was 3.04% and 2.38%, respectively, while those of the Rhizoctonia sp. was 2.02% and 5.82%, respectively. In conclusion, B. subtilis T6-1 has the potential to serve as a microbial agent, enhancing the structure of the rhizosphere microbial community as well as promoting tree growth in poplar cultivation. Full article
(This article belongs to the Collection Plant Growth-Promoting Bacteria: Mechanisms and Applications)
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12 pages, 1926 KiB  
Article
Restoring Genetic Resource through In Vitro Culturing Testicular Cells from the Cryo-Preserved Tissue of the American Shad (Alosa sapidissima)
by Hong-Yan Xu, Xiao-You Hong, Chao-Yue Zhong, Xu-Ling Wu and Xin-Ping Zhu
Biology 2022, 11(5), 790; https://doi.org/10.3390/biology11050790 - 22 May 2022
Cited by 1 | Viewed by 2109
Abstract
Germ cells, as opposed to somatic cells, can transmit heredity information between generations. Cryopreservation and in vitro culture of germ cells are key techniques for genetic resource preservation and cellular engineering breeding. In this study, two types of cryopreserved samples, namely testis pieces [...] Read more.
Germ cells, as opposed to somatic cells, can transmit heredity information between generations. Cryopreservation and in vitro culture of germ cells are key techniques for genetic resource preservation and cellular engineering breeding. In this study, two types of cryopreserved samples, namely testis pieces and testicular cells of American shad, were comparatively analyzed for cell viability. The results showed that the cell viability of the cryopreserved testis pieces was much higher than that of the cryopreserved testicular cells. The viability of cells from the cryopreserved testis pieces ranged from 65.2 ± 2.2 (%) to 93.8 ± 0.6 (%), whereas the viability of the dissociated cells after cryopreservation was 38.5 ± 0.8 (%) to 87.1 ± 2.6 (%). Intriguingly, the testicular cells from the post-thaw testicular tissue could be cultured in vitro. Likewise, most of the cultured cells exhibited germ cell properties and highly expressed Vasa and PCNA protein. This study is the first attempt to effectively preserve and culture the male germ cells through freezing tissues in the American shad. The findings of this study would benefit further investigations on genetic resource preservation and other manipulations of germ cells in a commercially and ecologically important fish species. Full article
(This article belongs to the Special Issue Aquatic Biodiversity and Conservation Biology)
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13 pages, 559 KiB  
Article
Modelling 5-km Running Performance on Level and Hilly Terrains in Recreational Runners
by Onécimo Ubiratã Medina Melo, Marcus Peikriszwili Tartaruga, Edilson Fernando de Borba, Daniel Boullosa, Edson Soares da Silva, Rodrigo Torma Bernardo, Renan Coimbra, Henrique Bianchi Oliveira, Rodrigo Gomes da Rosa and Leonardo Alexandre Peyré-Tartaruga
Biology 2022, 11(5), 789; https://doi.org/10.3390/biology11050789 - 22 May 2022
Cited by 3 | Viewed by 2109
Abstract
Incline and level running on treadmills have been extensively studied due to their different cardiorespiratory and biomechanical acute responses. However, there are no studies examining the performance determinants of outdoor running on hilly terrains. We aimed to investigate the influence of anthropometrics, muscle [...] Read more.
Incline and level running on treadmills have been extensively studied due to their different cardiorespiratory and biomechanical acute responses. However, there are no studies examining the performance determinants of outdoor running on hilly terrains. We aimed to investigate the influence of anthropometrics, muscle strength, and cardiorespiratory and gait spatiotemporal parameters during level (0%) and inclined (+7%) running on performance in level and hilly 5-km races. Twenty male recreational runners completed two 5-km outdoor running tests (0% vs. +7% and −7%), and two submaximal (10 km·h−1) and incremental treadmill tests at 0 and 7% slopes, after complete laboratory evaluations. The velocity at maximal oxygen consumption (VO2max) evaluated at 7% incline and level treadmill running were the best performance predictors under both hilly (R2 = 0.72; p < 0.05) and level (R2 = 0.85; p < 0.01) conditions, respectively. Inclusion of ventilatory and submaximal heart rate data improved the predictive models up to 100%. Conversely, none of the parameters evaluated in one condition contributed to the other condition. The spatiotemporal parameters and the runners’ strength levels were not associated to outdoor performances. These results indicate that the vVO2max evaluated at similar slopes in the lab can be used to predict 5-km running performances on both level and hilly terrains. 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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12 pages, 3403 KiB  
Review
Receptor Activity Modifying Protein RAMP Sub-Isoforms and Their Functional Differentiation, Which Regulates Functional Diversity of Adrenomedullin
by Takayuki Shindo, Megumu Tanaka, Akiko Kamiyoshi, Yuka Ichikawa-Shindo, Hisaka Kawate and Takayuki Sakurai
Biology 2022, 11(5), 788; https://doi.org/10.3390/biology11050788 - 21 May 2022
Cited by 3 | Viewed by 2386
Abstract
AM knockout (AM-/-) and RAMP2 knockout (RAMP2-/-) proved lethal for mice due to impaired embryonic vascular development. Although most vascular endothelial cell-specific RAMP2 knockout (E-RAMP2-/-) mice also died during the perinatal period, a few E-RAMP2-/- mice reached adulthood. Adult E-RAMP2-/- mice developed spontaneous [...] Read more.
AM knockout (AM-/-) and RAMP2 knockout (RAMP2-/-) proved lethal for mice due to impaired embryonic vascular development. Although most vascular endothelial cell-specific RAMP2 knockout (E-RAMP2-/-) mice also died during the perinatal period, a few E-RAMP2-/- mice reached adulthood. Adult E-RAMP2-/- mice developed spontaneous organ damage associated with vascular injury. In contrast, adult RAMP3 knockout (RAMP3-/-) mice showed exacerbated postoperative lymphedema with abnormal lymphatic drainage. Thus, RAMP2 is essential for vascular development and homeostasis and RAMP3 is essential for lymphatic vessel function. Cardiac myocyte-specific RAMP2 knockout mice showed early onset of heart failure as well as abnormal mitochondrial morphology and function, whereas RAMP3-/- mice exhibited abnormal cardiac lymphatics and a delayed onset of heart failure. Thus, RAMP2 is essential for maintaining cardiac mitochondrial function, while RAMP3 is essential for cardiac lymphangiogenesis. Transplantation of cancer cells into drug-inducible vascular endothelial cell-specific RAMP2 knockout mice resulted in enhanced metastasis to distant organs, whereas metastasis was suppressed in RAMP3-/- mice. RAMP2 suppresses cancer metastasis by maintaining vascular homeostasis and inhibiting vascular inflammation and pre-metastatic niche formation, while RAMP3 promotes cancer metastasis via malignant transformation of cancer-associated fibroblasts. Focusing on the diverse physiological functions of AM and the functional differentiation of RAMP2 and RAMP3 may lead to the development of novel therapeutic strategies. Full article
(This article belongs to the Special Issue Cardiac Peptides-Current Physiology, Pathophysiology, Biochemistry, Molecular Biology, and Clinical Application)
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14 pages, 1828 KiB  
Article
Assessment of MicroRNAs Associated with Tumor Purity by Random Forest Regression
by Dong-Yeon Nam and Je-Keun Rhee
Biology 2022, 11(5), 787; https://doi.org/10.3390/biology11050787 - 21 May 2022
Cited by 2 | Viewed by 2163
Abstract
Tumor purity refers to the proportion of tumor cells in tumor tissue samples. This value plays an important role in understanding the mechanisms of the tumor microenvironment. Although various attempts have been made to predict tumor purity, attempts to predict tumor purity using [...] Read more.
Tumor purity refers to the proportion of tumor cells in tumor tissue samples. This value plays an important role in understanding the mechanisms of the tumor microenvironment. Although various attempts have been made to predict tumor purity, attempts to predict tumor purity using miRNAs are still lacking. We predicted tumor purity using miRNA expression data for 16 TCGA tumor types using random forest regression. In addition, we identified miRNAs with high feature-importance scores and examined the extent of the change in predictive performance using informative miRNAs. The predictive performance obtained using only 10 miRNAs with high feature importance was close to the result obtained using all miRNAs. Furthermore, we also found genes targeted by miRNAs and confirmed that these genes were mainly related to immune and cancer pathways. Therefore, we found that the miRNA expression data could predict tumor purity well, and the results suggested the possibility that 10 miRNAs with high feature importance could be used as potential markers to predict tumor purity and to help improve our understanding of the tumor microenvironment. Full article
(This article belongs to the Topic miRNAs in Pathophysiology of Disease)
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15 pages, 2506 KiB  
Article
Mapping the Mountains of Giants: Anthropometric Data from the Western Balkans Reveal a Nucleus of Extraordinary Physical Stature in Europe
by Pavel Grasgruber, Bojan Mašanović, Stipan Prce, Stevo Popović, Fitim Arifi, Duško Bjelica, Dominik Bokůvka, Jan Cacek, Ivan Davidović, Jovan Gardašević, Eduard Hrazdíra, Sylva Hřebíčková, Pavlína Ingrová, Predrag Potpara, Nikola Stračárová, Gregor Starc and Nataša Mihailović
Biology 2022, 11(5), 786; https://doi.org/10.3390/biology11050786 - 21 May 2022
Cited by 1 | Viewed by 10836 | Correction
Abstract
The inhabitants of the Dinaric Alps (former Yugoslavia and Albania) have long been known as people of impressive body height, but after World War II, there was a critical lack of data related to this phenomenon. This anthropological synthesis includes the measurements of [...] Read more.
The inhabitants of the Dinaric Alps (former Yugoslavia and Albania) have long been known as people of impressive body height, but after World War II, there was a critical lack of data related to this phenomenon. This anthropological synthesis includes the measurements of 47,158 individuals (24,642 males and 22,516 females) from the period 2010–2018 and describes detailed regional differences in male stature in the Western Balkans. According to these data, young men from Montenegro (182.9 cm) are currently the tallest 18-year-olds in the world, surpassing their Dutch peers (182.4 cm), and 18-year-old boys from Dalmatia are even taller (183.7 cm) at a regional level. A continuous belt of extraordinary height means (>184 cm) stretches from the Adriatic coast of Dalmatia through Herzegovina to the central part of Montenegro. This article summarizes all the key socio-economic, nutritional, and genetic data, and offers possible explanations for this anthropological phenomenon. Since the remarkable height of the Dinaric populations cannot be connected with any commonly known environmental factor, the most probable hypothesis is genetic and links these physical characteristics with the local founder effect of Y haplogroup I-M170. Furthermore, given that both the level of socio-economic development and dietary protein quality are still sub-optimal, the local upward trend in body height has the potential to continue in the future. Full article
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14 pages, 1991 KiB  
Article
Gut Microbiome Suffers from Hematopoietic Stem Cell Transplantation in Childhood and Its Characteristics Are Positively Associated with Intra-Hospital Physical Exercise
by Simona Ugrayová, Peter Švec, Ivan Hric, Sára Šardzíková, Libuša Kubáňová, Adela Penesová, Jaroslava Adamčáková, Petra Pačesová, Júlia Horáková, Alexandra Kolenová, Katarína Šoltys, Martin Kolisek and Viktor Bielik
Biology 2022, 11(5), 785; https://doi.org/10.3390/biology11050785 - 21 May 2022
Cited by 3 | Viewed by 2726
Abstract
Gut microbiome impairment is a serious side effect of cancer treatment. The aim of this study was to identify the effects of hematopoietic stem cell transplantation (HSCT) treatment on gut microbiota composition in children with acute lymphoblastic leukemia (ALL). Fecal microbiotas were categorized [...] Read more.
Gut microbiome impairment is a serious side effect of cancer treatment. The aim of this study was to identify the effects of hematopoietic stem cell transplantation (HSCT) treatment on gut microbiota composition in children with acute lymphoblastic leukemia (ALL). Fecal microbiotas were categorized using specific primers targeting the V1–V3 region of 16S rDNA in eligible pediatric ALL patients after HSCT (n = 16) and in healthy controls (Ctrl, n = 13). An intra-hospital exercise program was also organized for child patients during HSCT treatment. Significant differences in gut microbiota composition were observed between ALL HSCT and Ctrl with further negative effects. Plasma C-reactive protein correlated positively with the pathogenic bacteria Enterococcus spp. and negatively with beneficial bacteria Butyriccocus spp. or Akkermansia spp., respectively (rs = 0.511, p = 0.05; rs = −0.541, p = 0.04; rs = −0.738, p = 0.02). Bacterial alpha diversity correlated with the exercise training characteristics. Therefore, specific changes in the microbiota of children were associated with systemic inflammation or the ability to exercise physically during HSCT treatment. Full article
(This article belongs to the Special Issue Gut Microbiome in Health and Disease)
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11 pages, 479 KiB  
Article
Tooth Cementum Thickness as a Method of Age Estimation in the Forensic Context
by Emanuela Gualdi-Russo, Ilaria Saguto, Paolo Frisoni, Margherita Neri and Natascia Rinaldo
Biology 2022, 11(5), 784; https://doi.org/10.3390/biology11050784 - 21 May 2022
Cited by 5 | Viewed by 2285
Abstract
Estimating age at death is a key element in the process of human identification of skeletal remains. The interest in dental cementum stems from its increase in thickness throughout life and, at the same time, from the fact it should not be affected [...] Read more.
Estimating age at death is a key element in the process of human identification of skeletal remains. The interest in dental cementum stems from its increase in thickness throughout life and, at the same time, from the fact it should not be affected by remodeling processes. Since the age assessment is particularly difficult in adults when using traditional anthropological methods on the skeleton, we tested a dental method based on maximum cementum thickness and developed new regression equations. We microscopically analyzed the histological sections of dental roots from a sample of 108 permanent teeth with known age and sex. Age at the time of dental extraction was in the range of 18–84 years. Our findings show that there were no differences in thickness between sexes, dental arch, and mono- and pluriradicular teeth. Separate regression equations were developed for individuals in the whole age range and individuals under 45 years. The equations were then tested on a hold-out sample from the same Mediterranean population demonstrating higher reliability for the equation developed for those under 45. Conversely, due to the increased error in age estimation in individuals over 45, this method should be used with caution in the forensic context when skeletal remains presumably belong to elderly individuals. Full article
(This article belongs to the Section Medical Biology)
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8 pages, 304 KiB  
Article
Associations between Fat Mass and Fat Free Mass with Physical Fitness in Adolescent Girls: A 3-Year Longitudinal Study
by Mario Kasović, Ana Oreški, Tomáš Vespalec, Marta Gimunová and Lovro Štefan
Biology 2022, 11(5), 783; https://doi.org/10.3390/biology11050783 - 21 May 2022
Cited by 4 | Viewed by 1829
Abstract
The main purpose of the study was to examine the longitudinal associations between fat mass and fat free mass with health-related physical fitness. Two-hundred and forty 15-year old adolescent girls were measured at the baseline and after a period of 3 years (17 [...] Read more.
The main purpose of the study was to examine the longitudinal associations between fat mass and fat free mass with health-related physical fitness. Two-hundred and forty 15-year old adolescent girls were measured at the baseline and after a period of 3 years (17 years). Health-related physical fitness included the following tests: (1) explosive power of the lower extremities (standing broad jump); (2) muscle endurance of the trunk (sit-ups in 60 s); (3) flexibility (sit-and-reach test); (4) muscle endurance of the lower extremities (squats in 60 s); (5) aerobic endurance (the 800 m run test); and (6) speed endurance (the 400 m running test). Fat mass and fat free mass were assessed using the bioelectrical impedance method. Longitudinal associations were analyzed with linear mixed model estimates. After adjusting for body mass index, fat mass was negatively associated with standing broad jump (β = −1.13, p < 0.001), sit-ups in 60 s (β = −0.27, p < 0.001), and squats in 60 s (β = −0.27, p < 0001), while positive associations with the 800 m running test (β = 0.02, p < 0.001) and the 400 m running test (β = 0.02, p < 0.001) were observed. On the other hand, fat free mass was positively associated with standing broad jump (β = 1.14, p < 0.001), sit-ups in 60 s (β = 0.28, p < 0.001), and squats in 60 s (β = 0.28, p < 0001), while the 800 m running test (β = −0.02, p < 0.001) and the 400 m running test (β = −0.02, p < 0.001) exhibited negative associations. This study shows that fat mass and fat free mass components are longitudinally, but oppositely associated with health-related physical fitness in adolescent girls. Full article
(This article belongs to the Special Issue New Frontiers of Sport, Exercise and Physical Activity for Health and Human Performance)
18 pages, 2970 KiB  
Article
Molecular Characterization and Expression Analysis of Putative Class C (Glutamate Family) G Protein-Coupled Receptors in Ascidian Styela clava
by Jin Zhang, Bo Dong and Likun Yang
Biology 2022, 11(5), 782; https://doi.org/10.3390/biology11050782 - 20 May 2022
Cited by 2 | Viewed by 2444
Abstract
In this study, we performed the genome-wide domain analysis and sequence alignment on the genome of Styela clava, and obtained a repertoire of 204 putative GPCRs, which exhibited a highly reduced gene number compared to vertebrates and cephalochordates. In this repertoire, six [...] Read more.
In this study, we performed the genome-wide domain analysis and sequence alignment on the genome of Styela clava, and obtained a repertoire of 204 putative GPCRs, which exhibited a highly reduced gene number compared to vertebrates and cephalochordates. In this repertoire, six Class C GPCRs, including four metabotropic glutamate receptors (Sc-GRMs), one calcium-sensing receptor (Sc-CaSR), and one gamma-aminobutyric acid (GABA) type B receptor 2-like (Sc-GABABR2-like) were identified, with the absence of type 1 taste and vomeronasal receptors. All the Sc-GRMs and Sc-CaSR contained the typical “Venus flytrap” and cysteine-rich domains required for ligand binding and subsequent propagation of conformational changes. In swimming larvae, Sc-grm3 and Sc-casr were mainly expressed at the junction of the sensory vesicle and tail nerve cord while the transcripts of Sc-grm4, Sc-grm7a, and Sc-grm7b appeared at the anterior trunk, which suggested their important functions in neurotransmission. The high expression of these Class C receptors at tail-regression and metamorphic juvenile stages hinted at their potential involvement in regulating metamorphosis. In adults, the transcripts were highly expressed in several peripheral tissues, raising the possibility that S. clava Class C GPCRs might function as neurotransmission modulators peripherally after metamorphosis. Our study systematically characterized the ancestral chordate Class C GPCRs to provide insights into the origin and evolution of these receptors in chordates and their roles in regulating physiological and morphogenetic changes relevant to the development and environmental adaption. Full article
(This article belongs to the Special Issue Molecular Physiology of Marine Invertebrates)
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23 pages, 7155 KiB  
Article
Human Adipose-Derived Stem Cells Combined with Nano-Hydrogel Promote Functional Recovery after Spinal Cord Injury in Rats
by Jianping Li, Zhisheng Ji, Yu Wang, Tiantian Li, Jinghua Luo, Jun Li, Xueshuang Shi, Liming Li, Liumin He and Wutian Wu
Biology 2022, 11(5), 781; https://doi.org/10.3390/biology11050781 - 20 May 2022
Cited by 12 | Viewed by 2771
Abstract
The treatment of spinal cord injury aims to reconstruct the fiber connection and restore the interrupted neural pathways. Adipose mesenchymal stem cells (ADSCs) can promote the recovery of motor functions in spinal cord injury. However, poor survival of ADSCs and leakage outside of [...] Read more.
The treatment of spinal cord injury aims to reconstruct the fiber connection and restore the interrupted neural pathways. Adipose mesenchymal stem cells (ADSCs) can promote the recovery of motor functions in spinal cord injury. However, poor survival of ADSCs and leakage outside of the injury site after local transplantation reduce the number of cells, which seriously attenuates the cumulative effect. We performed heterotopic transplantation on rats with severe spinal cord injury using human ADSCs loaded within self-assembly hydrogel RADA16-RGD (R: arginine; A: alanine; D: aspartic acid; G: glycine). Our results indicate that the combined transplantation of human ADSCs with RADA16-RGD improved the survival of ADSCs at the injured site. The inflammatory reaction was inhibited, with improved survival of the neurons and increased residual area of nerve fibers and myelin protein. The functional behaviors were promoted, as determined by the Basso, Beattie, and Bresnahan (BBB) locomotor rating scale score and electrophysiological measurements. ADSCs can promote the repair of spinal cord injury. This study provides new ideas for the treatment of spinal cord injury. Full article
(This article belongs to the Special Issue Neurodegenerative Diseases: Molecular Mechanisms and Therapeutic Applications)
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21 pages, 2992 KiB  
Article
Ocean Acidification Alleviates Dwarf Eelgrass (Zostera noltii) Lipid Landscape Remodeling under Warming Stress
by Bernardo Duarte, Tiago Repolho, José Ricardo Paula, Isabel Caçador, Ana Rita Matos and Rui Rosa
Biology 2022, 11(5), 780; https://doi.org/10.3390/biology11050780 - 20 May 2022
Cited by 5 | Viewed by 2095
Abstract
Coastal seagrass meadows provide a variety of essential ecological and economic services, including nursery grounds, sediment stabilization, nutrient cycling, coastal protection, and blue carbon sequestration. However, these ecosystems are highly threatened by ongoing climatic change. This study was aimed to understand how the [...] Read more.
Coastal seagrass meadows provide a variety of essential ecological and economic services, including nursery grounds, sediment stabilization, nutrient cycling, coastal protection, and blue carbon sequestration. However, these ecosystems are highly threatened by ongoing climatic change. This study was aimed to understand how the dwarf eelgrass Zostera noltii leaf lipid landscapes are altered under predicted ocean warming (+4 °C) and hypercapnic (ΔpH 0.4) conditions. Warming and hypercapnic conditions were found to induce a severe reduction in the leaf total fatty acid, though the combined treatment substantially alleviated this depletion. The lipid discrimination revealed a significant increase in the relative monogalactosyldiacylglycerol (MGDG) content in both hypercapnic and warming conditions, allied to plastidial membrane stabilization mechanisms. Hypercapnia also promoted enhanced phosphatidylglycerol (PG) leaf contents, a mechanism often associated with thylakoid reinvigoration. In addition to changing the proportion of storage, galacto- and phospholipids, the tested treatments also impacted the FA composition of all lipid classes, with warming exposure leading to decreases in polyunsaturated fatty acids (PUFAs); however, the combination of both stress conditions alleviated this effect. The observed galactolipid and phospholipid PUFA decreases are compatible with a homeoviscous adaptation, allowing for the maintenance of membrane stability by counteracting excessive membrane fluidity. Neutral lipid contents were substantially increased under warming conditions, especially in C18 fatty acids (C18), impairing their use as substrates for fatty acylated derivatives essential for maintaining the osmotic balance of cells. An analysis of the phospholipid and galactolipid fatty acid profiles as a whole revealed a higher degree of discrimination, highlighting the higher impact of warming and the proposed stress alleviation effect induced by increased water-dissolved CO2 availability. Still, it is essential to remember that the pace at which the ocean is warming can overcome the ameliorative capacity induced by higher CO2 availability, leaving seagrasses under severe heat stress beyond their lipid remodeling capacity. Full article
(This article belongs to the Special Issue Impacts of Climate Change on the Marine Biota: From Molecules to Ecosystems)
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16 pages, 104925 KiB  
Article
Structural and Functional Aspects of the Spleen in Molly Fish Poecilia sphenops (Valenciennes, 1846): Synergistic Interactions of Stem Cells, Neurons, and Immune Cells
by Ramy K. A. Sayed, Giacomo Zaccone, Gioele Capillo, Marco Albano and Doaa M. Mokhtar
Biology 2022, 11(5), 779; https://doi.org/10.3390/biology11050779 - 20 May 2022
Cited by 17 | Viewed by 4308
Abstract
In fish, the spleen is the prime secondary lymphoid organ. It has a role in the induction of adaptive immune responses, in addition to its significance in the elimination of immune complexes. This study was conducted on 18 randomly obtained adult molly fish [...] Read more.
In fish, the spleen is the prime secondary lymphoid organ. It has a role in the induction of adaptive immune responses, in addition to its significance in the elimination of immune complexes. This study was conducted on 18 randomly obtained adult molly fish (Poecilia sphenops) of both sexes using histological, immunohistochemical, and ultrastructural studies to highlight the cellular components of the spleen and their potential role in the immune system. The spleen of molly fish was characterized by the presence of well-distinct melanomacrophage centers, and other basic structures present in higher vertebrates including red and white pulps, blood vessels, and ellipsoids. Some mitotic cells could also be identified in the red pulp. Mast cells with characteristic metachromatic granules could be seen among the splenic cells. Rodlet cells were randomly distributed in the spleen and were also observed around the ellipsoids. The white pulp of the spleen expressed APG5. The expressions were well distinct in the melanomacrophages, leukocytes, and macrophages. Myostatin was expressed in leukocytes and epithelial reticular cells. IL-1β showed immunoreactivity in monocytes and macrophages around the ellipsoids. NF-κB and TGF-β were expressed in macrophages and epithelial reticular cells. Nrf2 expression was detected in stem cells and rodlet cells. Sox-9 had a higher expression in epithelial reticular cells and stem cells. The high frequency of immune cells in the spleen confirmed its role in the regulation of both innate and adaptive immunity, cell proliferation, and apoptosis. Full article
(This article belongs to the Special Issue Advances in Fish Immunology and Vaccination during the Past and in Recent Years)
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13 pages, 1870 KiB  
Article
Genomic and Phenotypic Insights into the Potential of Bacillus subtilis YB-15 Isolated from Rhizosphere to Biocontrol against Crown Rot and Promote Growth of Wheat
by Wen Xu, Qian Yang, Xia Xie, Paul H. Goodwin, Xiaoxu Deng, Jie Zhang, Runhong Sun, Qi Wang, Mingcong Xia, Chao Wu and Lirong Yang
Biology 2022, 11(5), 778; https://doi.org/10.3390/biology11050778 - 20 May 2022
Cited by 10 | Viewed by 2091
Abstract
Fusarium crown rot caused by Fusarium pseudograminearum is one of the most devastating diseases of wheat worldwide causing major yield and economic losses. In this study, strain YB-15 was isolated from soil of wheat rhizosphere and classified as Bacillus subtilis by average nucleotide [...] Read more.
Fusarium crown rot caused by Fusarium pseudograminearum is one of the most devastating diseases of wheat worldwide causing major yield and economic losses. In this study, strain YB-15 was isolated from soil of wheat rhizosphere and classified as Bacillus subtilis by average nucleotide identity analysis. It significantly reduced Fusarium crown rot with a control efficacy of 81.50% and significantly improved the growth of wheat seedlings by increasing root and shoot fresh weight by 11.4% and 4.2%, respectively. Reduced Fusarium crown rot may have been due to direct antagonism by the production of β-1, 3-glucanase, amylase, protease and cellulase, or by the ability of B. subtilis YB-15 to induce defense-related enzyme activities of wheat seedlings, both alone and in seedlings infected with F. pseudograminearum. Improved plant growth may be related to the ability of B. subtilis YB-15 to secrete indole acetic acid and siderophores, as well as to solubilize phosphorus. In addition, the genome of strain YB-15 was determined, resulting in a complete assembled circular genome of 4,233,040 bp with GC content of 43.52% consisting of 4207 protein-encoding genes. Sequencing the B. subtilis YB-15 genome further revealed genes for encoding carbohydrate-active enzymes, biosynthesis of various secondary metabolites, nutrient acquisition, phytohormone production, chemotaxis and motility, which could explain the potential of strain YB-15 to be plant growth-promoting bacteria and biological control agent. B. subtilis YB-15 appears to be a promising biocontrol agent against Fusarium crown rot as well as for wheat growth promotion. Full article
(This article belongs to the Section Microbiology)
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13 pages, 1130 KiB  
Article
SMMDA: Predicting miRNA-Disease Associations by Incorporating Multiple Similarity Profiles and a Novel Disease Representation
by Bo-Ya Ji, Liang-Rui Pan, Ji-Ren Zhou, Zhu-Hong You and Shao-Liang Peng
Biology 2022, 11(5), 777; https://doi.org/10.3390/biology11050777 - 20 May 2022
Cited by 1 | Viewed by 1580
Abstract
Increasing evidence has suggested that microRNAs (miRNAs) are significant in research on human diseases. Predicting possible associations between miRNAs and diseases would provide new perspectives on disease diagnosis, pathogenesis, and gene therapy. However, considering the intrinsic time-consuming and expensive cost of traditional Vitro [...] Read more.
Increasing evidence has suggested that microRNAs (miRNAs) are significant in research on human diseases. Predicting possible associations between miRNAs and diseases would provide new perspectives on disease diagnosis, pathogenesis, and gene therapy. However, considering the intrinsic time-consuming and expensive cost of traditional Vitro studies, there is an urgent need for a computational approach that would allow researchers to identify potential associations between miRNAs and diseases for further research. In this paper, we presented a novel computational method called SMMDA to predict potential miRNA-disease associations. In particular, SMMDA first utilized a new disease representation method (MeSHHeading2vec) based on the network embedding algorithm and then fused it with Gaussian interaction profile kernel similarity information of miRNAs and diseases, disease semantic similarity, and miRNA functional similarity. Secondly, SMMDA utilized a deep auto-coder network to transform the original features further to achieve a better feature representation. Finally, the ensemble learning model, XGBoost, was used as the underlying training and prediction method for SMMDA. In the results, SMMDA acquired a mean accuracy of 86.68% with a standard deviation of 0.42% and a mean AUC of 94.07% with a standard deviation of 0.23%, outperforming many previous works. Moreover, we also compared the predictive ability of SMMDA with different classifiers and different feature descriptors. In the case studies of three common Human diseases, the top 50 candidate miRNAs have 47 (esophageal neoplasms), 48 (breast neoplasms), and 48 (colon neoplasms) are successfully verified by two other databases. The experimental results proved that SMMDA has a reliable prediction ability in predicting potential miRNA-disease associations. Therefore, it is anticipated that SMMDA could be an effective tool for biomedical researchers. Full article
(This article belongs to the Special Issue Intelligent Computing in Biology and Medicine)
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15 pages, 1986 KiB  
Article
Functional, Antioxidant, and Anti-Inflammatory Properties of Cricket Protein Concentrate (Gryllus assimilis)
by María Fernanda Quinteros, Jenny Martínez, Alejandra Barrionuevo, Marcelo Rojas and Wilman Carrillo
Biology 2022, 11(5), 776; https://doi.org/10.3390/biology11050776 - 20 May 2022
Cited by 9 | Viewed by 3373
Abstract
Edible insects can represent an alternative to obtain high-quality proteins with positive biological properties for human consumption. Cricket flour (Gryllus assimilis) was used to obtain cricket protein concentrate (CPC) using pHs (10.0 and 12.0) of extraction and pHs (3.0, 4.0, 5.0, [...] Read more.
Edible insects can represent an alternative to obtain high-quality proteins with positive biological properties for human consumption. Cricket flour (Gryllus assimilis) was used to obtain cricket protein concentrate (CPC) using pHs (10.0 and 12.0) of extraction and pHs (3.0, 4.0, 5.0, and 6.0) of isoelectric precipitation (pI). Protein content, water and oil absorption capacity, protein solubility, antioxidant, and anti-inflammatory activities were determined. In addition, the protein profile was characterized by electrophoresis and the in vitro CPC digestibility was evaluated. Cricket flour presented 45.75% of protein content and CPC 12–5.0 presented a value of 71.16% protein content using the Dumas method. All samples were more soluble at pH 9.0 and 12.0. CPC 12–3.0 presented a percentage of water-binding capacity (WBC) of 41.25%. CPC 12–6.0 presented a percentage of oil-binding capacity (OBC) of 72.93%. All samples presented a high antioxidant and anti-inflammatory activity. CPC 12–4.0 presented a value FRAP of 70,034 umol trolox equivalents (TE)/g CPC, CPC 12–6.0 presented a value ABTS of 124,300 umol TE/g CPC and CPC 10–3.0 presented a DPPH value of 68,009 umol TE/g CPC. CPC 10–6.0 and CPC 12–6.0 presented high anti-inflammatory activity, with values of 93.55% and 93.15% of protection, respectively. CPCs can be used as functional ingredients in the food industry for their excellent functional and biological properties. Full article
(This article belongs to the Special Issue Food Chemical Composition and Antioxidant Capacity)
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13 pages, 1816 KiB  
Article
A Novel Ensemble Learning-Based Computational Method to Predict Protein-Protein Interactions from Protein Primary Sequences
by Jie Pan, Shiwei Wang, Changqing Yu, Liping Li, Zhuhong You and Yanmei Sun
Biology 2022, 11(5), 775; https://doi.org/10.3390/biology11050775 - 19 May 2022
Cited by 2 | Viewed by 1743
Abstract
Protein–protein interactions (PPIs) are crucial for understanding the cellular processes, including signal cascade, DNA transcription, metabolic cycles, and repair. In the past decade, a multitude of high-throughput methods have been introduced to detect PPIs. However, these techniques are time-consuming, laborious, and always suffer [...] Read more.
Protein–protein interactions (PPIs) are crucial for understanding the cellular processes, including signal cascade, DNA transcription, metabolic cycles, and repair. In the past decade, a multitude of high-throughput methods have been introduced to detect PPIs. However, these techniques are time-consuming, laborious, and always suffer from high false negative rates. Therefore, there is a great need of new computational methods as a supplemental tool for PPIs prediction. In this article, we present a novel sequence-based model to predict PPIs that combines Discrete Hilbert transform (DHT) and Rotation Forest (RoF). This method contains three stages: firstly, the Position-Specific Scoring Matrices (PSSM) was adopted to transform the amino acid sequence into a PSSM matrix, which can contain rich information about protein evolution. Then, the 400-dimensional DHT descriptor was constructed for each protein pair. Finally, these feature descriptors were fed to the RoF classifier for identifying the potential PPI class. When exploring the proposed model on the Yeast, Human, and Oryza sativa PPIs datasets, it yielded excellent prediction accuracies of 91.93, 96.35, and 94.24%, respectively. In addition, we also conducted numerous experiments on cross-species PPIs datasets, and the predictive capacity of our method is also very excellent. To further access the prediction ability of the proposed approach, we present the comparison of RoF with four powerful classifiers, including Support Vector Machine (SVM), Random Forest (RF), K-nearest Neighbor (KNN), and AdaBoost. We also compared it with some existing superiority works. These comprehensive experimental results further confirm the excellent and feasibility of the proposed approach. In future work, we hope it can be a supplemental tool for the proteomics analysis. Full article
(This article belongs to the Special Issue Intelligent Computing in Biology and Medicine)
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15 pages, 1972 KiB  
Article
Functional Characterization and Whole-Genome Analysis of an Aflatoxin-Degrading Rhodococcus pyridinivorans Strain
by Dun Deng, Jiahong Tang, Zhichang Liu, Zhimei Tian, Min Song, Yiyan Cui, Ting Rong, Huijie Lu, Miao Yu, Jinbao Li, Rui Pang and Xianyong Ma
Biology 2022, 11(5), 774; https://doi.org/10.3390/biology11050774 - 19 May 2022
Cited by 3 | Viewed by 2297
Abstract
Aflatoxin B1 (AFB1) is one of the most toxic, naturally occurring carcinogen compounds and is produced by specific strains of fungi. Crop contamination with AFB1 can cause huge economic losses and serious health problems. Many studies have examined the [...] Read more.
Aflatoxin B1 (AFB1) is one of the most toxic, naturally occurring carcinogen compounds and is produced by specific strains of fungi. Crop contamination with AFB1 can cause huge economic losses and serious health problems. Many studies have examined the microbiological degradation of AFB1, especially the use of efficient AFB1-degrading microorganisms, to control AFB1 contamination. Here, we reported the identification of a new Rhodococcus pyridinivorans strain (4-4) that can efficiently degrade AFB1 (degradation rate 84.9%). The extracellular component of this strain showed the strongest capacity to degrade AFB1 (degradation rate 83.7%). The effects of proteinase K, SDS, temperature, pH, incubation time, and AFB1 concentration on the AFB1 degradation ability of the extracellular component were investigated. We sequenced the complete genome of this strain, encoding 5246 protein-coding genes and 169 RNA genes on a circular chromosome and two plasmids. Comparative genomic analysis revealed high homology with other Rhodococcus strains with high AFB1-degradation ability. Further proteomic analyses of this strain identified a total of 723 proteins in the extracellular component, including multiple potential AFB1-degrading enzymes, along with enzymes that are reported to response to AFB1 treatment. Overall, the results demonstrate that R. pyridinivorans 4-4 would be an excellent candidate for the biodegradation and detoxification of AFB1 contamination. Full article
(This article belongs to the Section Microbiology)
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11 pages, 2174 KiB  
Article
Echinococcosis Is Associated with the Increased Prevalence of Intestinal Blastocystis Infection in Tibetans and Host Susceptibility to the Blastocystis in Mice
by Yang Zou, Yu-Gui Wang, Zhong-Li Liu, Ai-Jiang Guo, Xiao-Lu Li, Zhi-Qi Shi, Xing-Quan Zhu, Xiu-Min Han and Shuai Wang
Biology 2022, 11(5), 773; https://doi.org/10.3390/biology11050773 - 18 May 2022
Cited by 1 | Viewed by 1657
Abstract
Blastocystis is a common human intestinal protozoan parasite. Little is known about its prevalence in echinococcosis. This study tested whether Echinococcus multilocularis infection would increase host susceptibility to Blastocystis. A total of 114 fecal samples (68 hydatid disease patients and 46 healthy [...] Read more.
Blastocystis is a common human intestinal protozoan parasite. Little is known about its prevalence in echinococcosis. This study tested whether Echinococcus multilocularis infection would increase host susceptibility to Blastocystis. A total of 114 fecal samples (68 hydatid disease patients and 46 healthy people) were collected from Tibetans in the Qinghai province in China. The presence of Blastocystis was identified by sequencing of the small subunit (SSU) rRNA gene. Balb/c mice were co-infected with Blastocystis and E. multilocularis and tested for host susceptibility to Blastocystis. The overall Blastocystis prevalence was 12.3%; 16.2% in the patients and 4.4% in healthy people (p < 0.05). Sequence analysis identified three known Blastocystis genotypes, including ST1, ST2, and ST3, and one unknown genotype. Experimental dual infection significantly reduced mouse survival rate (20%), induced more severe signs, and increased intestinal damages with a higher intestinal colonization level of Blastocystis. The mouse model showed that E. multilocularis infection increases host susceptibility to Blastocystis. Our study shows a significantly higher prevalence of Blastocystis in patients with liver echinococcosis and reveals that non-intestinal E. multilocularis infection increases host susceptibility to the Blastocystis. Our results highlight that E. multilocularis infection is associated with Blastocystis. These findings remind us that more attention should be paid to the gut health of the patients with a helminth infection during clinical patient care. Full article
(This article belongs to the Special Issue Blastocystis in Health and Disease)
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12 pages, 3016 KiB  
Article
Expression and Role of β3-Adrenergic Receptor during the Differentiation of 3T3-L1 Preadipocytes into Adipocytes
by Amir Roshanzadeh, Anil Kumar Yadav, Sai-Prasad Pydi, Takefumi Kimura and Byeong-Churl Jang
Biology 2022, 11(5), 772; https://doi.org/10.3390/biology11050772 - 18 May 2022
Cited by 4 | Viewed by 3159
Abstract
β3-adrenergic receptor (β3-AR) is expressed predominantly in mature white and brown/beige adipocytes. Although the lipolytic and thermogenic role of β3-AR in brown/beige adipocytes is well defined, the adipogenic role of β3-AR in white adipocytes remains unclear at present. In this study, we investigated [...] Read more.
β3-adrenergic receptor (β3-AR) is expressed predominantly in mature white and brown/beige adipocytes. Although the lipolytic and thermogenic role of β3-AR in brown/beige adipocytes is well defined, the adipogenic role of β3-AR in white adipocytes remains unclear at present. In this study, we investigated the expression and function of β3-AR in differentiating 3T3-L1 cells, murine white preadipocytes. Of note, the expression of β3-AR at the protein and mRNA levels was highly induced in a time-dependent manner during 3T3-L1 preadipocyte differentiation. Interestingly, the results of the pharmacological inhibition study demonstrated the roles of p38 MAPK and PKC in the induction of β3-AR expression in differentiating 3T3-L1 cells. Knockdown of β3-AR led to less lipid accumulation and triglyceride (TG) content during 3T3-L1 preadipocyte differentiation with no cytotoxicity. Furthermore, knockdown of β3-AR resulted in a decrease in not only expression levels of CCAAT/enhancer-binding protein-α (C/EBP-α), peroxisome proliferator-activated receptor-γ (PPAR-γ), fatty acid synthase (FASN), perilipin A, and leptin but also phosphorylation levels of signal transducer and activator of transcription-5 (STAT-5) during 3T3-L1 preadipocyte differentiation. In summary, these results demonstrate firstly that β3-AR expression is highly up-regulated in p38 MAPK and PKC-dependent manners, and the up-regulated β3-AR plays a crucial role in lipid accumulation in differentiating 3T3-L1 cells, which is mediated through control of expression and phosphorylation levels of C/EBP-α, PPAR-γ, STAT-5, FASN, and perilipin A. Full article
(This article belongs to the Special Issue Infection, Inflammation and Cancer)
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14 pages, 678 KiB  
Article
De Novo Transcriptome of the Flagellate Isochrysis galbana Identifies Genes Involved in the Metabolism of Antiproliferative Metabolites
by Gennaro Riccio, Kevin A. Martinez, Adrianna Ianora and Chiara Lauritano
Biology 2022, 11(5), 771; https://doi.org/10.3390/biology11050771 - 18 May 2022
Cited by 6 | Viewed by 2485
Abstract
Haptophytes are important primary producers in the oceans, and among the phylum Haptophyta, the flagellate Isochrysis galbana has been found to be rich in high-value compounds, such as lipids, carotenoids and highly branched polysaccharides. In the present work, I. galbana was cultured and [...] Read more.
Haptophytes are important primary producers in the oceans, and among the phylum Haptophyta, the flagellate Isochrysis galbana has been found to be rich in high-value compounds, such as lipids, carotenoids and highly branched polysaccharides. In the present work, I. galbana was cultured and collected at both stationary and exponential growth phases. A transcriptomic approach was used to analyze the possible activation of metabolic pathways responsible for bioactive compound synthesis at the gene level. Differential expression analysis of samples collected at the exponential versus stationary growth phase allowed the identification of genes involved in the glycerophospholipid metabolic process, the sterol biosynthetic process, ADP-ribose diphosphatase activity and others. I. galbana raw extracts and fractions were tested on specific human cancer cells for possible antiproliferative activity. The most active fractions, without affecting normal cells, were fractions enriched in nucleosides (fraction B) and triglycerides (fraction E) for algae collected in the exponential growth phase and fraction E for stationary phase samples. Overall, transcriptomic and bioactivity data confirmed the activation of metabolic pathways involved in the synthesis of bioactive compounds giving new insights on possible Isochrysis applications in the anticancer sector. Full article
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31 pages, 3787 KiB  
Article
Amanita Section Phalloideae Species in the Mediterranean Basin: Destroying Angels Reviewed
by Pablo Alvarado, Antonia Gasch-Illescas, Sylvie Morel, Magda Bou Dagher-Kharrat, Gabriel Moreno, José Luis Manjón, Xavier Carteret, Jean-Michel Bellanger, Sylvie Rapior, Matteo Gelardi and Pierre-Arthur Moreau
Biology 2022, 11(5), 770; https://doi.org/10.3390/biology11050770 - 18 May 2022
Cited by 5 | Viewed by 6415
Abstract
In Europe, amatoxin-containing mushrooms are responsible for most of the deadly poisonings caused by macrofungi. The present work presents a multidisciplinary revision of the European species of Amanita sect. Phalloideae based on morphology, phylogeny, epidemiology, and biochemistry of amatoxins and phallotoxins. Five distinct [...] Read more.
In Europe, amatoxin-containing mushrooms are responsible for most of the deadly poisonings caused by macrofungi. The present work presents a multidisciplinary revision of the European species of Amanita sect. Phalloideae based on morphology, phylogeny, epidemiology, and biochemistry of amatoxins and phallotoxins. Five distinct species of this section have been identified in Europe to date: A. phalloides, A. virosa, A. verna, the recently introduced North American species A. amerivirosa, and A. vidua sp. nov., which is a new name proposed for the KOH-negative Mediterranean species previously described as A. verna or A. decipiens by various authors. Epitypes or neotypes are selected for species lacking suitable reference collections, namely A. verna and A. virosa. Three additional taxa, Amanita decipiens, A. porrinensis, and A. virosa var. levipes are here considered later heterotypic synonyms of A. verna, A. phalloides, and A. amerivirosa, respectively. Full article
(This article belongs to the Special Issue Molecular Characterization of Fungi)
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21 pages, 2664 KiB  
Article
Characterization of Microbial Shifts during the Production and Ripening of Raw Ewe Milk-Derived Idiazabal Cheese by High-Throughput Sequencing
by Gorka Santamarina-García, Igor Hernández, Gustavo Amores and Mailo Virto
Biology 2022, 11(5), 769; https://doi.org/10.3390/biology11050769 - 18 May 2022
Cited by 4 | Viewed by 2758
Abstract
In this study, we used high-throughput sequencing technologies (sequencing of V3–V4 hypervariable regions of 16S rRNA gene) to investigate for the first time the microbiota of Latxa ewe raw milk and the bacterial shifts that occur during the production and ripening of Idiazabal [...] Read more.
In this study, we used high-throughput sequencing technologies (sequencing of V3–V4 hypervariable regions of 16S rRNA gene) to investigate for the first time the microbiota of Latxa ewe raw milk and the bacterial shifts that occur during the production and ripening of Idiazabal cheese. Results revealed several bacterial genera not reported previously in raw ewe milk and cheese, such as Buttiauxella and Obesumbacterium. Both the cheese making and ripening processes had a significant impact on bacterial communities. Overall, the growth of lactic acid bacteria (LAB) (Lactococcus, Lactobacillus, Leuconostoc, Enterococcus, Streptococcus and Carnobacterium) was promoted, whereas that of non-desirable and environmental bacteria was inhibited (such as Pseudomonas and Clostridium). However, considerable differences were observed among producers. It is noteworthy that the starter LAB (Lactococcus) predominated up to 30 or 60 days of ripening and then, the growth of non-starter LAB (Lactobacillus, Leuconostoc, Enterococcus and Streptococcus) was promoted. Moreover, in some cases, bacteria related to the production of volatile compounds (such as Hafnia, Brevibacterium and Psychrobacter) also showed notable abundance during the first few weeks of ripening. Overall, the results of this study enhance our understanding of microbial shifts that occur during the production and ripening of a raw ewe milk-derived cheese (Idiazabal), and could indicate that the practices adopted by producers have a great impact on the microbiota and final quality of this cheese. Full article
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