Biology

22 pages, 5365 KiB

Open AccessArticle

Artificial Plantation Responses to Periodic Submergence in Massive Dam and Reservoir Riparian Zones: Changes in Soil Properties and Bacterial Community Characteristics

by Jiajia Li, Lijuan Li, Muhammad Arif, Dongdong Ding, Xin Hu, Jie Zheng, Zhongxun Yuan and Changxiao Li

Biology 2021, 10(8), 819; https://doi.org/10.3390/biology10080819 - 23 Aug 2021

Cited by 19 | Viewed by 2668

Abstract

Plant and microbiome interactions are necessary for plant nutrient acquisition. However, relatively little is known about the responses of roots, bulk, and rhizosphere soil microbial communities in different artificial vegetation types (woody and herbaceous) in riparian areas of massive dams and reservoirs. Therefore, [...] Read more.

Plant and microbiome interactions are necessary for plant nutrient acquisition. However, relatively little is known about the responses of roots, bulk, and rhizosphere soil microbial communities in different artificial vegetation types (woody and herbaceous) in riparian areas of massive dams and reservoirs. Therefore, this study aims to assess such responses at elevations of 165–170 m a.s.l. in the riparian zones of the Three Gorges Dam Reservoir, China. The samples were collected containing the rhizosphere soil, bulk soil, and roots of herbaceous and woody vegetation at different emergence stages in 2018. Then, all the samples were analyzed to quantify the soil properties, bacterial community characteristics, and their interaction in the early and late emergence phases. In different periods, the weight of dominant soil bacteria, including Proteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Cyanobacteria, was higher, and their composition was different in the rhizosphere, bulk soil, and endophytes. Moreover, the soil co-occurrence networks indicated that the weight of soil physical properties was higher than chemical properties in the early emergence stage. In contrast, the weight of chemical properties was relatively higher in the late emergence stage. Furthermore, the richness and diversity of the bacterial community were mainly affected by soil organic matter. This study suggests that these herbaceous and woody vegetation are suitable for planting in reservoir areas affected by hydrology and human disturbance in light of soil nutrients and soil microbial communities, respectively. Additionally, these results provide valuable information to inoculate the soil with key microbiota members by applying fertilizers, potentially improving plant health and soil production. Full article

(This article belongs to the Special Issue Biodiversity Patterns)

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22 pages, 4215 KiB

Open AccessArticle

Phosphorus-Induced Adaptation Mechanisms of Rye Grown on Post-Flotation Copper Tailings

by Piotr Stępień, Krzysztof Gediga and Zofia Spiak

Biology 2021, 10(8), 818; https://doi.org/10.3390/biology10080818 - 23 Aug 2021

Cited by 1 | Viewed by 2162

Abstract

Although a considerable effort has been made over the last decades to develop cost-effective phytotechnologies as an alternative to conventional techniques for the management of contaminated lands, successful revegetation of the tailings still represents a major challenge. Here, we evaluate the potential of [...] Read more.

Although a considerable effort has been made over the last decades to develop cost-effective phytotechnologies as an alternative to conventional techniques for the management of contaminated lands, successful revegetation of the tailings still represents a major challenge. Here, we evaluate the potential of rye (Secale cereale L.) for growth and survival on the tailings after copper (Cu) ore processing. Four rye varieties were cultivated in a pot experiment on the post-flotation sediment with increasing phosphorus (P) doses (22, 44, 66, 88, and 110 mg·kg⁻¹). The resistance of the studied rye genotypes to stress was assessed by observing the growth and development of plants, determining the dry mass accumulation, the Cu and P uptake and content, and a number of physiological parameters related mainly to P mobilisation. Exposure of tested rye varieties to high Cu concentrations in the tailings did not result in any significant plant mortality, with the intracellular Cu concentrations being below the critical toxic level. In contrast, the low availability of P due to alkaline properties of the tailings and the mechanisms involved in the mobilisation of sparingly soluble forms of this element (i.e., H⁺-ATPase-driven proton efflux in roots and organic acid exudation), were identified as main factor determining the level of tolerance. The efficiency of the photosynthetic activity was a key determinant for the P-mobilising capacity of rye. We further showed that rye varieties with more primitive genetic background might be potentially more suitable for growth on the post-flotation copper tailings. The results provide important and novel knowledge that will certainly support future works in developing strategies for successful revitalisation of degraded lands. Full article

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12 pages, 2768 KiB

Open AccessArticle

Proteolyzed Variant of IgG with Free C-Terminal Lysine as a Biomarker of Prostate Cancer

by Anna Lokshin, Lyudmila M. Mikhaleva, Eugene I. Goufman, Marina N. Boltovskaya, Natalia B. Tikhonova, Irina I. Stepanova, Alexandr A. Stepanov, Natalia V. Potoldykova, Andrey Z. Vinarov, Paul Stemmer and Vasily Iakovlev

Biology 2021, 10(8), 817; https://doi.org/10.3390/biology10080817 - 23 Aug 2021

Cited by 3 | Viewed by 1862

Abstract

The differential diagnosis of prostate cancer is problematic due to the lack of markers with high diagnostic accuracy. We previously demonstrated the increased binding of IgG to human plasminogen (PLG) in plasma of patients with prostate cancer (PC) compared to healthy controls. Heavy [...] Read more.

The differential diagnosis of prostate cancer is problematic due to the lack of markers with high diagnostic accuracy. We previously demonstrated the increased binding of IgG to human plasminogen (PLG) in plasma of patients with prostate cancer (PC) compared to healthy controls. Heavy and light chains of PLG (PLG-H and PLG-L) were immobilized on 96-well plates and the binding of IgG to PLG-H and PLG-L was analyzed in serum from 30 prostate cancer (PC) patients, 30 patients with benign prostatic hyperplasia (BPH) and 30 healthy controls using enzyme-linked immunosorbent assay (ELISA). Our results demonstrate that IgG from PC sera bind to PLG-H but not to PLG-L. This interaction occurred through the free IgG C-terminal lysine (Lys) that becomes exposed as a result of IgG conformational changes associated with proteolysis. Circulating levels of modified IgG with exposed C-terminal Lys (IgG-Lys) were significantly higher in PC patients than in healthy controls and in BPH. We used Receiver Operating Characteristic (ROC) analysis to calculate the sensitivity (SN) and specificity (SP) of circulating IgG-Lys for differentiating PC from BPH as 77% and 90%, respectively. The area under the curve (AUC) was 0.87. We demonstrated that the diagnostic accuracy of circulating levels of IgG-Lys is much higher than diagnostic accuracy of total PSA (tPSA). Full article

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15 pages, 2594 KiB

Open AccessArticle

Gene Flow and Diversification in Himalopsyche martynovi Species Complex (Trichoptera: Rhyacophilidae) in the Hengduan Mountains

by Xi-Ling Deng, Adrien Favre, Emily Moriarty Lemmon, Alan R. Lemmon and Steffen U. Pauls

Biology 2021, 10(8), 816; https://doi.org/10.3390/biology10080816 - 23 Aug 2021

Cited by 3 | Viewed by 2480

Abstract

The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). [...] Read more.

The Hengduan Mountains are one of the most species-rich mountainous areas in the world. The origin and evolution of such a remarkable biodiversity are likely to be associated with geological or climatic dynamics, as well as taxon-specific biotic processes (e.g., hybridization, polyploidization, etc.). Here, we investigate the mechanisms fostering the diversification of the endemic Himalopsyche martynovi complex, a poorly known group of aquatic insects. We used multiple allelic datasets generated from 691 AHE loci to reconstruct species and RaxML phylogenetic trees. We selected the most reliable phylogenetic tree to perform network and gene flow analyses. The phylogenetic reconstructions and network analysis identified three clades, including H. epikur, H. martynovi sensu stricto and H. cf. martynovi. Himalopsyche martynovi sensu stricto and H. cf. martynovi present an intermediate morphology between H. epikur and H. viteceki, the closest known relative to the H. martynovi-complex. The gene flow analysis revealed extensive gene flow among these lineages. Our results suggest that H. viteceki and H. epikur are likely to have contributed to the evolution of H. martynovi sensu stricto and H. cf. martynovi via gene flow, and thus, our study provides insights in the diversification process of a lesser-known ecological group, and hints at the potential role of gene flow in the emergence of biological novelty in the Hengduan Mountains. Full article

(This article belongs to the Special Issue Biological Novelty as Source of Biodiversity in Mountains)

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14 pages, 2248 KiB

Open AccessArticle

Comprehensive Utilization of Immature Honey Pomelo Fruit for the Production of Value-Added Compounds Using Novel Continuous Phase Transition Extraction Technology

by Guo Liu, Tao Hou, Shenglan Guo, Hongyu Lin, Meng Chen, Jianyin Miao, Xiaojuan Liu, Yahui Huang, Yong Cao, Yaqi Lan and Mingyue Song

Biology 2021, 10(8), 815; https://doi.org/10.3390/biology10080815 - 23 Aug 2021

Cited by 2 | Viewed by 3063

Abstract

The immature honey pomelo fruit (IPF) is a huge agro-industrial by-product generated during pomelo planting. Although IPF is rich in nutrients, more than 95% of IPF is discarded annually, which causes resource waste and a serious environmental problem. Here, we report a novel [...] Read more.

The immature honey pomelo fruit (IPF) is a huge agro-industrial by-product generated during pomelo planting. Although IPF is rich in nutrients, more than 95% of IPF is discarded annually, which causes resource waste and a serious environmental problem. Here, we report a novel continuous phase transition extraction technology (CPTE) to improve the comprehensive utilization of IPF by sequentially generating high value products and solve pollution problems related to their disposal. First, essential oil was successively extracted by CPTE at a yield of 1.12 ± 0.36%, in which 43 species were identified. Second, naringin extraction parameters were optimized using the response surface methodology (RSM), resulting in a maximum extraction rate of 99.47 ± 0.15%. Finally, pectin was extracted at a yield of 20.23 ± 0.66%, which is similar to the contents of commercial pectin. In conclusion, this study suggested that IPF was an excellent potential substrate for the production of value-added components by CPTE. Full article

(This article belongs to the Special Issue Functional Foods: Bioactivity, Bioavailability, and Biological Characteristics)

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14 pages, 1691 KiB

Open AccessArticle

Breast Cancer Mortality in the Americas and Australasia over the Period 1980–2017 with Predictions for 2025

by Cezary Wojtyla, Paola Bertuccio, Michal Ciebiera and Carlo La Vecchia

Biology 2021, 10(8), 814; https://doi.org/10.3390/biology10080814 - 23 Aug 2021

Cited by 7 | Viewed by 2106

Abstract

Substantial progress has been made in the diagnosis, management, and treatment of breast cancer over the last decades. This has affected mortality rates but has also led to inequality in epidemiological trends between different regions of the world. We extracted death certification data [...] Read more.

Substantial progress has been made in the diagnosis, management, and treatment of breast cancer over the last decades. This has affected mortality rates but has also led to inequality in epidemiological trends between different regions of the world. We extracted death certification data for breast cancer from the World Health Organization database. We analyzed trends in breast cancer mortality in selected countries from America, Asia, and Oceania over the 1980–2017 period and predicted numbers of deaths and rates for 2025. In North America, we observed decreased breast cancer mortality, reaching a rate of about 13/100,000 women in 2017. In Latin American countries, breast cancer mortality rates did not consistently decrease. The highest decreases in mortality were observed in Australia. Mortality trends in Asian countries remained among the lowest globally. We have predicted decreased mortality from breast cancer in 2025 for most of the analyzed countries. The epidemiological situation regarding breast cancer mortality is expected to change in the coming years. Advancements in diagnosis and treatment of breast cancer must be extended in various areas of the world to obtain global control of breast cancer mortality. Full article

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18 pages, 2216 KiB

Open AccessReview

Volumetric Properties of Four-Stranded DNA Structures

by Tigran V. Chalikian and Robert B. Macgregor, Jr.

Biology 2021, 10(8), 813; https://doi.org/10.3390/biology10080813 - 22 Aug 2021

Cited by 7 | Viewed by 2489

Abstract

Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. [...] Read more.

Four-stranded non-canonical DNA structures including G-quadruplexes and i-motifs have been found in the genome and are thought to be involved in regulation of biological function. These structures have been implicated in telomere biology, genomic instability, and regulation of transcription and translation events. To gain an understanding of the molecular determinants underlying the biological role of four-stranded DNA structures, their biophysical properties have been extensively studied. The limited libraries on volume, expansibility, and compressibility accumulated to date have begun to provide insights into the molecular origins of helix-to-coil and helix-to-helix conformational transitions involving four-stranded DNA structures. In this article, we review the recent progress in volumetric investigations of G-quadruplexes and i-motifs, emphasizing how such data can be used to characterize intra-and intermolecular interactions, including solvation. We describe how volumetric data can be interpreted at the molecular level to yield a better understanding of the role that solute–solvent interactions play in modulating the stability and recognition events of nucleic acids. Taken together, volumetric studies facilitate unveiling the molecular determinants of biological events involving biopolymers, including G-quadruplexes and i-motifs, by providing one more piece to the thermodynamic puzzle describing the energetics of cellular processes in vitro and, by extension, in vivo. Full article

(This article belongs to the Special Issue Pressure Perturbation Approach in Biochemistry and Structural Biology. In memoriam of Dr. Gaston Hui Bon Hoa)

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15 pages, 6847 KiB

Open AccessArticle

Polyculture of Juvenile Dog Conch Laevistrombus canarium Reveals High Potentiality in Integrated Multitrophic Aquaculture (IMTA)

by Yung-Cheng Chang, Chia-Huan Ma, Hung-Tai Lee and Te-Hua Hsu

Biology 2021, 10(8), 812; https://doi.org/10.3390/biology10080812 - 22 Aug 2021

Cited by 4 | Viewed by 2793

Abstract

Laevistrombus canarium, also known as dog conch, is a marine gastropod mollusk widely distributed in the Indo-Pacific region. It is an economically crucial species; however, its population has been declining due to overfishing and overexploitation. In this study, the suitable salinity for [...] Read more.

Laevistrombus canarium, also known as dog conch, is a marine gastropod mollusk widely distributed in the Indo-Pacific region. It is an economically crucial species; however, its population has been declining due to overfishing and overexploitation. In this study, the suitable salinity for juvenile L. canarium was between 20 and 35‰. Diatoms and biological detritus by using flow-water from the fish pool were the most favorable diets for newly metamorphosed and 10 mm juveniles. In the polyculture experiment, L. canarium was cultured with whiteleg shrimp, tilapia, small abalone, purple sea urchin, and collector urchin. Better growth was found in all co-culture groups except with whiteleg shrimp. We also found that the polyculture system with or without substrates significantly affected the growth of juveniles. Additionally, we observed that water temperature was the most crucial factor for growth and survival; a water temperature of less than 10 °C might cause the death of L. canarium. We have proposed a novel polyculture and water-flow method for mass production of L. canarium and evaluated the feasibility and benefits of polyculture with other species. The findings from this work reveal the potentiality of L. canarium in integrated multitrophic aquaculture (IMTA) and its implication for aquaculture and resource restoration. Full article

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15 pages, 2487 KiB

Open AccessArticle

Polyploidy Improves Photosynthesis Regulation within the Ranunculus auricomus Complex (Ranunculaceae)

by Fuad Bahrul Ulum, Franz Hadacek and Elvira Hörandl

Biology 2021, 10(8), 811; https://doi.org/10.3390/biology10080811 - 21 Aug 2021

Cited by 10 | Viewed by 2530

Abstract

Polyploidy has substantially contributed to successful plant evolution, and is often connected to a higher resilience to environmental stress. We test the hypothesis that polyploids tolerate light stress better than diploids. The Ranunculus auricomus complex comprises diploid (2x), tetraploid (4x), and hexaploid (6x) [...] Read more.

Polyploidy has substantially contributed to successful plant evolution, and is often connected to a higher resilience to environmental stress. We test the hypothesis that polyploids tolerate light stress better than diploids. The Ranunculus auricomus complex comprises diploid (2x), tetraploid (4x), and hexaploid (6x) cytotypes, the former of which occur in shaded habitats and the latter more in open, sun-exposed habitats in Central Europe. In this study, we experimentally explored the effects of ploidy and photoperiod extension on the efficiency of photosystem II in the three cytotypes in climate growth chambers. Quantum yields and various coefficients that can be calculated from light curve, Kautsky curve, and fluorescent transient OJIP experiments provided support for the hypothesis that, in comparison to diploids, the improved regulation of excess light by more efficient photochemical and non-chemical quenching in polyploids might have facilitated the adaptation to unshaded habitats. We suggest how lower stress levels in reproductive tissues of polyploids might have favored asexual reproduction. Full article

(This article belongs to the Section Plant Science)

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20 pages, 651 KiB

Open AccessReview

Overview of Poultry Management as a Key Factor for Solving Food and Nutritional Security with a Special Focus on Chicken Breeding in East African Countries

by Lenox Omondi Pius, Péter Strausz and Szilvia Kusza

Biology 2021, 10(8), 810; https://doi.org/10.3390/biology10080810 - 20 Aug 2021

Cited by 14 | Viewed by 7293

Abstract

The focus of this review is to offer an overview of food and nutritional security, to identify associated constraints, and propose possible alternative solutions for improving the East African poultry sub-sector in the pursuit of food security, focusing on chicken breeding. To better [...] Read more.

The focus of this review is to offer an overview of food and nutritional security, to identify associated constraints, and propose possible alternative solutions for improving the East African poultry sub-sector in the pursuit of food security, focusing on chicken breeding. To better understand the prospects of the poultry industry, we highlighted and combined confirming evidence of the phenotypic variability and genetic diversity of East African chicken genetic resources using both morphological and molecular tools, as well as performance traits. Furthermore, this work gives a detailed indication of what would be lost if indigenous chicken populations are left to suffer the ongoing massive genetic erosions due to various factors, not limited to indiscriminate crossbreeding. Previous and recent attempts to improve the productivity of indigenous chicken are highlighted, and possible future breeding plans and areas of immediate research are suggested as well. This review concludes that under the prevailing conditions, the village chicken production system appears to be the most imperious production system that needs to be extensively developed ; however, for the sustainability of the industry, the proposed improvement strategies should create a permanent balance between the competing needs of genetic improvement and the genetic diversity of the indigenous chicken genetic resource. Full article

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

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12 pages, 860 KiB

Open AccessEditor’s ChoiceReview

SnoRNA in Cancer Progression, Metastasis and Immunotherapy Response

by Jildou van der Werf, Chue Vin Chin and Nicholas Ian Fleming

Biology 2021, 10(8), 809; https://doi.org/10.3390/biology10080809 - 20 Aug 2021

Cited by 31 | Viewed by 4767

Abstract

Small nucleolar RNA (snoRNA) were one of our earliest recognised classes of non-coding RNA, but were largely ignored by cancer investigators due to an assumption that their activities were confined to the nucleolus. However, as full genome sequences have become available, many new [...] Read more.

Small nucleolar RNA (snoRNA) were one of our earliest recognised classes of non-coding RNA, but were largely ignored by cancer investigators due to an assumption that their activities were confined to the nucleolus. However, as full genome sequences have become available, many new snoRNA genes have been identified, and multiple studies have shown their functions to be diverse. The consensus now is that many snoRNA are dysregulated in cancers, are differentially expressed between cancer types, stages and metastases, and they can actively modify disease progression. In addition, the regulation of the snoRNA class is dominated by the cancer-supporting mTOR signalling pathway, and they may have particular significance to immune cell function and anti-tumour immune responses. Given the recent advent of therapeutics that can target RNA molecules, snoRNA have robust potential as drug targets, either solely or in the context of immunotherapies. Full article

(This article belongs to the Special Issue The Role of Non-coding RNA in Tumor Progression and Metastasis)

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16 pages, 2146 KiB

Open AccessArticle

Increased CD3⁺, CD8⁺, or FoxP3⁺ T Lymphocyte Infiltrations Are Associated with the Pathogenesis of Colorectal Cancer but Not with the Overall Survival of Patients

by Ana Margarida Barbosa, Olga Martinho, Rosete Nogueira, Juliana Campos, Liliana Lobo, Henrique Pinto, Adhemar Longatto-Filho, António G. Castro, Sandra F. Martins and Egídio Torrado

Biology 2021, 10(8), 808; https://doi.org/10.3390/biology10080808 - 20 Aug 2021

Cited by 8 | Viewed by 2103

Abstract

Tumor-infiltrating lymphocytes include heterogeneous populations of T lymphocytes that play crucial roles in the tumor immune response; importantly, their presence in the tumor tissue may predict clinical outcomes. Therefore, we herein studied the prognostic significance of the presence and location of CD3⁺ [...] Read more.

Tumor-infiltrating lymphocytes include heterogeneous populations of T lymphocytes that play crucial roles in the tumor immune response; importantly, their presence in the tumor tissue may predict clinical outcomes. Therefore, we herein studied the prognostic significance of the presence and location of CD3⁺, CD8⁺, and FoxP3⁺ T lymphocytes in colorectal cancer samples. In the intratumor analysis, our data did not reveal any association between lymphocyte infiltrations with clinical or pathological data. However, in the tumor margins, we found that the presence of high infiltrations of CD3⁺, CD8⁺, or FoxP3⁺ T lymphocytes were associated with TNM stages I-II (p = 0.021, p = 0.022, and p = 0.012, respectively) and absence of lymph node metastases (p = 0.010, p = 0.003, and p = 0.004, respectively). Despite these associations with good prognostic indicators, we were not able to find any statistically significant alterations in the overall survival of the patients, even though high infiltrations of FoxP3⁺ T lymphocytes in the tumor margins resulted in an increased overall survival of 14 months. Taken together, these data show that the presence of CD3⁺, CD8⁺, or FoxP3⁺T lymphocyte infiltrates in the tumor margins are associated with the pathogenesis of CRC, but only high Foxp3⁺ T lymphocyte infiltrations in the tumor invasive margins are inclined to indicate favorable prognosis. Full article

(This article belongs to the Section Cancer Biology)

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12 pages, 4309 KiB

Open AccessArticle

Free Amino Acids Profile and Expression Analysis of Core Genes Involved in Branched-Chain Amino Acids Metabolism during Fruit Development of Longan (Dimocarpus longan Lour.) Cultivars with Different Aroma Types

by Wenshun Hu, Baiyu Wang, Muhammad Moaaz Ali, Xiuping Chen, Jisen Zhang, Shaoquan Zheng and Faxing Chen

Biology 2021, 10(8), 807; https://doi.org/10.3390/biology10080807 - 20 Aug 2021

Cited by 11 | Viewed by 2324

Abstract

Amino acids are important component of fruit nutrition and quality. In this study, three longan cultivars, including non-aroma types ‘Shixia’ (SX), ‘Lidongben’ (LDB), and strong aroma type ‘Xiangcui’ (XC), were selected to analyze free amino acids (FAAs) variations at six distinct growth stages [...] Read more.

Amino acids are important component of fruit nutrition and quality. In this study, three longan cultivars, including non-aroma types ‘Shixia’ (SX), ‘Lidongben’ (LDB), and strong aroma type ‘Xiangcui’ (XC), were selected to analyze free amino acids (FAAs) variations at six distinct growth stages (S1–S6). The genome-wide identification and expression analysis of genes related to the branched-chain amino acids (BCAA) synthesis pathway were carried out. Results showed that 36 FAAs were identified, and the total FAAs content ranged from 2601.0 to 9073.5 mg/kg, which increased drastically with fruit development until ripening. L-glutamic acid (Glu), L-alanine (Ala), L-arginine (Arg), γ-Aminobutyric acid (GABA), L-aspartic acid (Asp), L-leucine (Leu), hydroxyl-proline (Hypro), and L-serine (Ser) were the predominant FAAs (1619.9–7213.9 mg/kg) in pulp, accounting for 62.28–92.05% of the total amino acids. During the period of rapid fruit expansion (S2–S4), the aroma of XC changed from light to strong, and the contents of L-alanine (Ala) and L-leucine (Leu) were significantly higher than those of SX and LDB. Furthermore, a total of two 2-isopropyl malate synthase (IPMS), two 3-isopropyl malate dehydrogenase (IPMD), and 16 BCAA transferase (BCAT) genes were identified. The expression levels of DilBCAT1, -6, and -9 genes in XC were significantly higher than those in SX and LDB, while DilBCAT16 in XC was lower. The content of Leu was negatively correlated with the expression of DilBCAT1, -6, and -9 in three varieties, but positively correlated with DilBCAT16, indicating that these four genes may be responsible for the different synthesis and degradation of Leu among cultivars. Full article

(This article belongs to the Section Plant Science)

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17 pages, 2431 KiB

Open AccessArticle

Effect of Extender, Storage Time and Temperature on Kinetic Parameters (CASA) on Bull Semen Samples

by Aitor Fernandez-Novo, Sergio Santos-Lopez, Clara Barrajon-Masa, Patricia Mozas, Eduardo de Mercado, Elisa Caceres, Aizic Garrafa, Juan V. Gonzalez-Martin, Natividad Perez-Villalobos, Agustín Oliet, Susana Astiz and Sonia S. Perez-Garnelo

Biology 2021, 10(8), 806; https://doi.org/10.3390/biology10080806 - 20 Aug 2021

Cited by 11 | Viewed by 2680

Abstract

CASA kinetic parameters are often evaluated in a diagnostic centre. How storage conditions affect ejaculates up to evaluation is unclear. We assessed, in 25 commercial bulls electroejaculated in the field, the impact of time until evaluation (0–2 h, 4–6 h, and 24 h [...] Read more.

CASA kinetic parameters are often evaluated in a diagnostic centre. How storage conditions affect ejaculates up to evaluation is unclear. We assessed, in 25 commercial bulls electroejaculated in the field, the impact of time until evaluation (0–2 h, 4–6 h, and 24 h post-ejaculation), holding temperature (5 °C vs. room temperature), and extender (AndroMed^®, BIOXcell^® or INRA96^®) on CASA kinetic parameters. Total and progressive motility, VCL, VAP, VCL, ALH, BCF, STR, LIN, and WOB were assessed. CASA kinetic parameters were preserved for up to 4–6 h post-ejaculation, except for AndroMed^®. Regardless of extender or temperature, motility decreased from 4–6 h up to 24 h, with the best values obtained with BIOXcell^® at 5 °C. Our results suggest that BIOXcell^® can preserve sperm motility for up to 6 h, either at 5 °C or room temperature, and also INRA96^® at room temperature, with motility assessments and the percentage of the most rapid sperms being the lowest with INRA96^® at 5 °C. The kinetic parameters decreased when analyses were performed at 24 h. Therefore, we suggest evaluating seminal quality as soon as possible, before 6 h after collection. These results help to fix adequate protocols for the short-term storage and shipment of bovine semen collected under field conditions. Full article

(This article belongs to the Special Issue Animal Reproductive Physiology)

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21 pages, 975 KiB

Open AccessReview

Natural Pest Regulation and Its Compatibility with Other Crop Protection Practices in Smallholder Bean Farming Systems

by Baltazar J. Ndakidemi, Ernest R. Mbega, Patrick A. Ndakidemi, Philip C. Stevenson, Steven R. Belmain, Sarah E. J. Arnold and Victoria C. Woolley

Biology 2021, 10(8), 805; https://doi.org/10.3390/biology10080805 - 20 Aug 2021

Cited by 6 | Viewed by 3730

Abstract

Common bean (Phaseolus vulgaris) production and storage are limited by numerous constraints. Insect pests are often the most destructive. However, resource-constrained smallholders in sub-Saharan Africa (SSA) often do little to manage pests. Where farmers do use a control strategy, it typically [...] Read more.

Common bean (Phaseolus vulgaris) production and storage are limited by numerous constraints. Insect pests are often the most destructive. However, resource-constrained smallholders in sub-Saharan Africa (SSA) often do little to manage pests. Where farmers do use a control strategy, it typically relies on chemical pesticides, which have adverse effects on the wildlife, crop pollinators, natural enemies, mammals, and the development of resistance by pests. Nature-based solutions —in particular, using biological control agents with sustainable approaches that include biopesticides, resistant varieties, and cultural tools—are alternatives to chemical control. However, significant barriers to their adoption in SSA include a lack of field data and knowledge on the natural enemies of pests, safety, efficacy, the spectrum of activities, the availability and costs of biopesticides, the lack of sources of resistance for different cultivars, and spatial and temporal inconsistencies for cultural methods. Here, we critically review the control options for bean pests, particularly the black bean aphid (Aphis fabae) and pod borers (Maruca vitrata). We identified natural pest regulation as the option with the greatest potential for this farming system. We recommend that farmers adapt to using biological control due to its compatibility with other sustainable approaches, such as cultural tools, resistant varieties, and biopesticides for effective management, especially in SSA. Full article

(This article belongs to the Special Issue Biological Control in Agroecosystems)

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17 pages, 1671 KiB

Open AccessReview

Human Papillomavirus in Breast Carcinogenesis: A Passenger, a Cofactor, or a Causal Agent?

by Rancés Blanco, Diego Carrillo-Beltrán, Juan P. Muñoz, Alejandro H. Corvalán, Gloria M. Calaf and Francisco Aguayo

Biology 2021, 10(8), 804; https://doi.org/10.3390/biology10080804 - 20 Aug 2021

Cited by 9 | Viewed by 5215

Abstract

Breast cancer (BC) is the most commonly diagnosed malignancy in women worldwide as well as the leading cause of cancer-related death in this gender. Studies have identified that human papillomavirus (HPV) is a potential risk factor for BC development. While vaccines that protect [...] Read more.

Breast cancer (BC) is the most commonly diagnosed malignancy in women worldwide as well as the leading cause of cancer-related death in this gender. Studies have identified that human papillomavirus (HPV) is a potential risk factor for BC development. While vaccines that protect against oncogenic HPVs infection have been commercially available, global disparities persist due to their high cost. Interestingly, numerous authors have detected an increased high risk (HR)-HPV infection in BC specimens when compared with non-tumor tissues. Therefore, it was suggested that HR-HPV infection could play a role in breast carcinogenesis in a subset of cases. Additional epidemiological and experimental evidence is still needed regarding the role of HR-HPV infection in the development and progression of BC. Full article

(This article belongs to the Section Medical Biology)

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17 pages, 1878 KiB

Open AccessSystematic Review

The Significance of Utilizing A Corticotomy on Periodontal and Orthodontic Outcomes: A Systematic Review and Meta-Analysis

by Jonathan Gao, Trung Nguyen, Snehlata Oberoi, Heesoo Oh, Sunil Kapila, Richard T. Kao and Guo-Hao Lin

Biology 2021, 10(8), 803; https://doi.org/10.3390/biology10080803 - 19 Aug 2021

Cited by 10 | Viewed by 3563

Abstract

Purpose: This systematic review compares the clinical and radiographic outcomes for patients who received only a corticotomy or periodontal accelerated osteogenic orthodontics (PAOO) with those who received a conventional orthodontic treatment. Methods: An electronic search of four databases and a hand search of [...] Read more.

Purpose: This systematic review compares the clinical and radiographic outcomes for patients who received only a corticotomy or periodontal accelerated osteogenic orthodontics (PAOO) with those who received a conventional orthodontic treatment. Methods: An electronic search of four databases and a hand search of peer-reviewed journals for relevant articles published in English between January 1980 and June 2021 were performed. Human clinical trials of ≥10 patients treated with a corticotomy or PAOO with radiographic and/or clinical outcomes were included. Meta-analyses were performed to analyze the weighted mean difference (WMD) and confidence interval (CI) for the recorded variables. Results: Twelve articles were included in the quantitative analysis. The meta-analysis revealed a localized corticotomy distal to the canine can significantly increase canine distalization (WMD = 1.15 mm, 95% CI = 0.18–2.12 mm, p = 0.02) compared to a conventional orthodontic treatment. In addition, PAOO also showed a significant gain of buccal bone thickness (WMD = 0.43 mm, 95% CI = 0.09–0.78 mm, p = 0.01) and an improvement of bone density (WMD = 32.86, 95% CI = 11.83–53.89, p = 0.002) compared to the corticotomy group. Conclusion: Based on the findings of the meta-analyses, the localized use of a corticotomy can significantly increase the amount of canine distalization during orthodontic treatment. Additionally, the use of a corticotomy as a part of a PAOO procedure significantly increases the rate of orthodontic tooth movement and it is accompanied by an increased buccal bone thickness and bone density compared to patients undergoing a conventional orthodontic treatment. Full article

(This article belongs to the Section Medical Biology)

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17 pages, 19928 KiB

Open AccessArticle

Impact of the Epigenetically Regulated Hoxa-5 Gene in Neural Differentiation from Human Adipose-Derived Stem Cells

by Rosa Hernández, Cristina Jiménez-Luna, Raúl Ortiz, Fernando Setién, Miguel López, Gloria Perazzoli, Manel Esteller, María Berdasco, Jose Prados and Consolación Melguizo

Biology 2021, 10(8), 802; https://doi.org/10.3390/biology10080802 - 19 Aug 2021

Cited by 3 | Viewed by 2541

Abstract

Human adipose-derived mesenchymal stem cells (hASCs) may be used in some nervous system pathologies, although obtaining an adequate degree of neuronal differentiation is an important barrier to their applicability. This requires a deep understanding of the expression and epigenetic changes of the most [...] Read more.

Human adipose-derived mesenchymal stem cells (hASCs) may be used in some nervous system pathologies, although obtaining an adequate degree of neuronal differentiation is an important barrier to their applicability. This requires a deep understanding of the expression and epigenetic changes of the most important genes involved in their differentiation. We used hASCs from human lipoaspirates to induce neuronal-like cells through three protocols (Neu1, 2, and 3), determined the degree of neuronal differentiation using specific biomarkers in culture cells and neurospheres, and analyzed epigenetic changes of genes involved in this differentiation. Furthermore, we selected the Hoxa-5 gene to determine its potential to improve neuronal differentiation. Our results showed that an excellent hASC neuronal differentiation process using Neu1 which efficiently modulated NES, CHAT, SNAP25, or SCN9A neuronal marker expression. In addition, epigenetic studies showed relevant changes in Hoxa-5, GRM4, FGFR1, RTEL1, METRN, and PAX9 genes. Functional studies of the Hoxa-5 gene using CRISPR/dCas9 and lentiviral systems showed that its overexpression induced hASCs neuronal differentiation that was accelerated with the exposure to Neu1. These results suggest that Hoxa-5 is an essential gene in hASCs neuronal differentiation and therefore, a potential candidate for the development of cell therapy strategies in neurological disorders. Full article

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24 pages, 3057 KiB

Open AccessArticle

A Model of the Early Visual System Based on Parallel Spike-Sequence Detection, Showing Orientation Selectivity

by Alejandro Santos-Mayo, Stephan Moratti, Javier de Echegaray and Gianluca Susi

Biology 2021, 10(8), 801; https://doi.org/10.3390/biology10080801 - 19 Aug 2021

Cited by 2 | Viewed by 3229

Abstract

Since the first half of the twentieth century, numerous studies have been conducted on how the visual cortex encodes basic image features. One of the hallmarks of basic feature extraction is the phenomenon of orientation selectivity, of which the underlying neuronal-level computational mechanisms [...] Read more.

Since the first half of the twentieth century, numerous studies have been conducted on how the visual cortex encodes basic image features. One of the hallmarks of basic feature extraction is the phenomenon of orientation selectivity, of which the underlying neuronal-level computational mechanisms remain partially unclear despite being intensively investigated. In this work we present a reduced visual system model (RVSM) of the first level of scene analysis, involving the retina, the lateral geniculate nucleus and the primary visual cortex (V1), showing orientation selectivity. The detection core of the RVSM is the neuromorphic spike-decoding structure MNSD, which is able to learn and recognize parallel spike sequences and considerably resembles the neuronal microcircuits of V1 in both topology and operation. This structure is equipped with plasticity of intrinsic excitability to embed recent findings about V1 operation. The RVSM, which embeds 81 groups of MNSD arranged in 4 oriented columns, is tested using sets of rotated Gabor patches as input. Finally, synthetic visual evoked activity generated by the RVSM is compared with real neurophysiological signal from V1 area: (1) postsynaptic activity of human subjects obtained by magnetoencephalography and (2) spiking activity of macaques obtained by multi-tetrode arrays. The system is implemented using the NEST simulator. The results attest to a good level of resemblance between the model response and real neurophysiological recordings. As the RVSM is available online, and the model parameters can be customized by the user, we propose it as a tool to elucidate the computational mechanisms underlying orientation selectivity. Full article

(This article belongs to the Special Issue Information Processing in Neuronal Circuits and Systems)

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17 pages, 2798 KiB

Open AccessArticle

Neuroprotective Effects of Glochidion zeylanicum Leaf Extract against H₂O₂/Glutamate-Induced Toxicity in Cultured Neuronal Cells and Aβ-Induced Toxicity in Caenorhabditis elegans

by Chatrawee Duangjan, Panthakarn Rangsinth, Shaoxiong Zhang, Xiaojie Gu, Michael Wink and Tewin Tencomnao

Biology 2021, 10(8), 800; https://doi.org/10.3390/biology10080800 - 19 Aug 2021

Cited by 7 | Viewed by 3478

Abstract

Oxidative stress plays a crucial role in the development of age-related neurodegenerative diseases. Previously, Glochidion zeylanicum methanol (GZM) extract has been reported to have antioxidant and anti-aging properties. However, the effect of GZM on neuroprotection has not been reported yet; furthermore, the mechanism [...] Read more.

Oxidative stress plays a crucial role in the development of age-related neurodegenerative diseases. Previously, Glochidion zeylanicum methanol (GZM) extract has been reported to have antioxidant and anti-aging properties. However, the effect of GZM on neuroprotection has not been reported yet; furthermore, the mechanism involved in its antioxidant properties remains unresolved. The study is aimed to demonstrate the neuroprotective properties of GZM extract and their underlying mechanisms in cultured neuronal (HT-22 and Neuro-2a) cells and Caenorhabditis elegans models. GZM extract exhibited protective effects against glutamate/H₂O₂-induced toxicity in cultured neuronal cells by suppressing the intracellular reactive oxygen species (ROS) generation and enhancing the expression of endogenous antioxidant enzymes (SODs, GPx, and GSTs). GZM extract also triggered the expression of SIRT1/Nrf2 proteins and mRNA transcription of antioxidant genes (NQO1, GCLM, and EAAT3) which are the master regulators of cellular defense against oxidative stress. Additionally, GZM extract exhibited protective effects to counteract β-amyloid (Aβ)-induced toxicity in C. elegans and promoted neuritogenesis properties in Neuro-2a cells. Our observations suggest that GZM leaf extract has interesting neuritogenesis and neuroprotective potential and can possibly act as potential contender for the treatment of oxidative stress-induced Alzheimer’s disease (AD) and related neurodegenerative conditions; however, this needs to be studied further in other in vivo systems. Full article

(This article belongs to the Special Issue Neurodegenerative Diseases: Molecular Mechanisms and Therapeutic Applications)

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17 pages, 5650 KiB

Open AccessArticle

A Recommendation for a Pre-Standardized Marine Microalgal Dry Weight Determination Protocol for Laboratory Scale Culture Using Ammonium Formate as a Washing Agent

by Yam Sim Khaw, Hui Teng Tan, Arissara Sopawong, Noor Azmi Shaharuddin, Abdul Rahman Omar and Fatimah Md. Yusoff

Biology 2021, 10(8), 799; https://doi.org/10.3390/biology10080799 - 19 Aug 2021

Viewed by 2063

Abstract

Microalgal biomass is one of the crucial criteria in microalgal studies. Many reported methods, even the well-established protocol on microalgal dry weight (DW) determination, vary greatly, and reliable comparative assessment amongst published results could be problematic. This study aimed to determine the best [...] Read more.

Microalgal biomass is one of the crucial criteria in microalgal studies. Many reported methods, even the well-established protocol on microalgal dry weight (DW) determination, vary greatly, and reliable comparative assessment amongst published results could be problematic. This study aimed to determine the best condition of critical parameters in marine microalgal DW determination for laboratory-scale culture using four different marine microalgal species. These parameters included the washing process, grades of glass microfiber filter (GMF), GMF pretreatment conditions, washing agent (ammonium formate) concentrations, culture: washing agent ratios (v:v) and washing cycles. GMF grade GF/A with precombustion at 450 °C provided the most satisfactory DW and the highest ash-free dry weight (AFDW)/DW ratio. Furthermore, 0.05 M ammonium formate with 1:2 culture: washing agent ratio and a minimum of two washing cycles appeared to be the best settings of microalgal DW determination. The present treatment increased the AFDW/DW ratio of the four respective microalgae by a minimum of 19%. The findings of this study could serve as a pivotal reference in developing a standardized protocol of marine microalgal DW determination to obtain veracious and reliable marine microalgal DW. Full article

(This article belongs to the Section Biotechnology)

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9 pages, 1903 KiB

Open AccessArticle

Effect of Vibrio-Derived Extracellular Protease vEP-45 on the Blood Complement System

by So Hyun Kwon, Jung Eun Park, Yeong Hee Cho and Jung Sup Lee

Biology 2021, 10(8), 798; https://doi.org/10.3390/biology10080798 - 18 Aug 2021

Viewed by 1929

Abstract

Vibrio vulnificus is a pathogenic bacterium that can causes wound infections and fetal septicemia. We have reported that V. vulnificus ATCC29307 produces an extracellular zinc-metalloprotease (named vEP-45). Our previous results showed that vEP-45 can convert prothrombin to active thrombin and also activate the [...] Read more.

Vibrio vulnificus is a pathogenic bacterium that can causes wound infections and fetal septicemia. We have reported that V. vulnificus ATCC29307 produces an extracellular zinc-metalloprotease (named vEP-45). Our previous results showed that vEP-45 can convert prothrombin to active thrombin and also activate the plasma kallikrein/kinin system. In this study, the effect of vEP-45 on the activation of the complement system was examined. We found that vEP-45 could proteolytically convert the key complement precursor molecules, including C3, C4, and C5, to their corresponding active forms (e.g., C3a, C3b, C4a, C4b, and C5a) in vitro cleavage assays. C5b production from C5 cleavage mediated by vEP-45 was not observed, whereas the level of C5a was increased in a dose-dependent manner compared to that of the non-treated control. The cleavage of the complement proteins in human plasma by vEP-45 was also confirmed via Western blotting. Furthermore, vEP-45 could convert C3 and C5 to active C3a and C5a as a proinflammatory mediator, while no cleavage of C4 was observed. These results suggest that vEP-45 can activate the complement system involved in innate immunity through an alternative pathway. Full article

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24 pages, 29369 KiB

Open AccessArticle

Contrasting Host-Parasite Population Structure: Morphology and Mitogenomics of a Parasitic Flatworm on Pelagic Deepwater Cichlid Fishes from Lake Tanganyika

by Nikol Kmentová, Christoph Hahn, Stephan Koblmüller, Holger Zimmermann, Jiří Vorel, Tom Artois, Milan Gelnar and Maarten P. M. Vanhove

Biology 2021, 10(8), 797; https://doi.org/10.3390/biology10080797 - 18 Aug 2021

Cited by 8 | Viewed by 3570

Abstract

Little phylogeographic structure is presumed for highly mobile species in pelagic zones. Lake Tanganyika is a unique ecosystem with a speciose and largely endemic fauna famous for its remarkable evolutionary history. In bathybatine cichlid fishes, the pattern of lake-wide population differentiation differs among [...] Read more.

Little phylogeographic structure is presumed for highly mobile species in pelagic zones. Lake Tanganyika is a unique ecosystem with a speciose and largely endemic fauna famous for its remarkable evolutionary history. In bathybatine cichlid fishes, the pattern of lake-wide population differentiation differs among species. We assessed the congruence between the phylogeographic structure of bathybatine cichlids and their parasitic flatworm Cichlidogyrus casuarinus to test the magnifying glass hypothesis. Additionally, we evaluated the use of a PoolSeq approach to study intraspecific variation in dactylogyrid monogeneans. The lake-wide population structure of C. casuarinus ex Hemibates stenosoma was assessed based on a portion of the cox1 gene combined with morphological characterisation. Additionally, intraspecific mitogenomic variation among 80 parasite samples from one spatially constrained metapopulation was assessed using shotgun NGS. While no clear geographic genetic structure was detected in parasites, both geographic and host-related phenotypic variation was apparent. The incongruence with the genetic north-south gradient observed in H. stenosoma may be explained by the broad host range of this flatworm including eupelagic bathybatine host species that form panmictic populations across the lake. In addition, we present the first parasite mitogenome from Lake Tanganyika and propose a methodological framework for studying the intraspecific mitogenomic variation of dactylogyrid monogeneans. Full article

(This article belongs to the Special Issue Host-Parasite Interactions: Trends in Molecular Ecology)

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21 pages, 4147 KiB

Open AccessArticle

Possible Synergistic Antidiabetic Effects of Quantified Artemisia judaica Extract and Glyburide in Streptozotocin-Induced Diabetic Rats via Restoration of PPAR-α mRNA Expression

by Abdulaziz S. Saeedan, Gamal A. Soliman, Rehab F. Abdel-Rahman, Reham M. Abd-Elsalam, Hanan A. Ogaly, Khalid M. Alharthy and Maged S. Abdel-Kader

Biology 2021, 10(8), 796; https://doi.org/10.3390/biology10080796 - 18 Aug 2021

Cited by 6 | Viewed by 3096

Abstract

Several members of the genus Artemisia are used in both Western and African traditional medicine for the control of diabetes. A considerable number of diabetic patients switch to using oral antidiabetic drugs in combination with certain herbs instead of using oral antidiabetic drugs [...] Read more.

Several members of the genus Artemisia are used in both Western and African traditional medicine for the control of diabetes. A considerable number of diabetic patients switch to using oral antidiabetic drugs in combination with certain herbs instead of using oral antidiabetic drugs alone. This study examined the effect of Artemisia judaica extract (AJE) on the antidiabetic activity of glyburide (GLB) in streptozotocin (STZ)-induced diabetes. Forty-two male Wistar rats were divided into seven equal groups. Normal rats of the first group were treated with the vehicle. The diabetic rats in the second–fifth groups received vehicle, GLB (5 mg/kg), AJE low dose (250 mg/kg), and AJE high dose (500 mg/kg), respectively. Groups sixth–seventh were treated with combinations of GLB plus the lower dose of AJE and GLB plus the higher dose of AJE, respectively. All administrations were done orally for eight weeks. Fasting blood glucose (FBG) and insulin levels, glycated hemoglobin (HbA1c) percentage, serum lipid profile, and biomarkers of oxidative stress were estimated. The histopathological examination of the pancreas and the immunohistochemical analysis of anti-insulin, anti-glucagon, and anti-somatostatin protein expressions were also performed. The analysis of the hepatic mRNA expression of PPAR-α and Nrf2 genes were performed using quantitative RT-PCR. All treatments significantly lowered FBG levels when compared with the STZ-control group with the highest percentage reduction exhibited by the GLB plus AJE high dose combination. This combination highly improved insulin levels, HbA1c, and lipid profile in blood of diabetic rats compared to GLB monotherapy. In addition, all medicaments restored insulin content in the β-cells and diminished the levels of glucagon and somatostatin of the α- and δ-endocrine cells in the pancreatic islets. Furthermore, the GLB plus AJE high dose combination was the most successful in restoring PPAR-α and Nrf2 mRNA expression in the liver. In conclusion, these data indicate that the GLB plus AJE high dose combination gives greater glycemic improvement in male Wistar rats than GLB monotherapy. Full article

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16 pages, 3177 KiB

Open AccessArticle

Cloning and Functional Verification of CYP408A3 and CYP6CS3 Related to Chlorpyrifos Resistance in the Sogatella furcifera (Horváth) (Hemiptera: Delphacidae)

by Yanwei Ruan, Xinxian Liu, Changwei Gong, Yuming Zhang, Litao Shen, Hasnain Ali, Yanyan Huang and Xuegui Wang

Biology 2021, 10(8), 795; https://doi.org/10.3390/biology10080795 - 18 Aug 2021

Cited by 3 | Viewed by 1868

Abstract

The white-back planthopper (WBPH), Sogatella furcifera, mainly harms rice and occurs in most rice regions in China and Asia. With the use of chemical pesticides, S. furcifera has developed varying degrees of resistance to a variety of pesticides. In our study, a [...] Read more.

The white-back planthopper (WBPH), Sogatella furcifera, mainly harms rice and occurs in most rice regions in China and Asia. With the use of chemical pesticides, S. furcifera has developed varying degrees of resistance to a variety of pesticides. In our study, a chlorpyrifos-resistant population (44.25-fold) was built through six generations of screening with a sublethal dose of chlorpyrifos (LD₅₀) from a field population. The expression levels of ten selected resistance-related P450 genes were analyzed by RT-qPCR and found that CYP408A3 and CYP6CS3 were significantly more expressed in the third instar nymphs of the XY17-G5 and XY17-G6 populations, about 25-fold more than the Sus-Lab strain, respectively (p < 0.01). To elucidate their molecular function in the development of resistance towards chlorpyrifos, we cloned two P450 full lengths and predicted their tertiary protein structures. CYP408A3 and CYP6CS3 were also downregulated after injecting dsCYP408A3, dsCYP6CS3, or their mixture compared to the control group. Moreover, the mortality rates of the dsCYP6CS3 (91.7%) and the mixture injection treatment (93.3%) treated by the LC₅₀ concentration of chlorpyrifos were significantly higher than the blank control group (51.7%) and dsCYP408A3 injection treatment (69.3%) at 72 h (p < 0.01). Meanwhile, the P450 enzyme activities in the dsRNA treatments were lower than that in the control (XY17-G6) (p < 0.01). Therefore, the P450 gene CYP6CS3 may be one of the main genes in the development of chlorpyrifos resistance in S. furcifera. Full article

(This article belongs to the Section Toxicology)

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6 pages, 805 KiB

Open AccessBrief Report

The Distribution and Prevalence of High-Risk HPV Genotypes Other than HPV-16 and HPV-18 among Women Attending Gynecologists’ Offices in Kazakhstan

by Gulzhanat Aimagambetova, Aisha Babi, Alpamys Issanov, Sholpan Akhanova, Natalya Udalova, Svetlana Koktova, Askhat Balykov, Zhanna Sattarkyzy, Zhuldyz Abakasheva, Azliyati Azizan, Chee Kai Chan and Torgyn Issa

Biology 2021, 10(8), 794; https://doi.org/10.3390/biology10080794 - 18 Aug 2021

Cited by 9 | Viewed by 2763

Abstract

Cervical cancer represents a great burden to public health of women. This study aimed to obtain a nationwide genotyping survey and analysis of high risk-HPV including those that are caused by HPV types other than HPV-16 and HPV-18, among women in Kazakhstan. This [...] Read more.

Cervical cancer represents a great burden to public health of women. This study aimed to obtain a nationwide genotyping survey and analysis of high risk-HPV including those that are caused by HPV types other than HPV-16 and HPV-18, among women in Kazakhstan. This study was conducted based on the collection of survey and cervical swabs of 1645 women across the country. The samples were genotyped for high-risk HPV types based on real-time PCR methods. Collected data was analyzed with the focus on high-risk HPV types other than HPV-16 and -18. Infection was present in 22% of women who participated in the study. The most prevalent types were HPV-31 among single infections and HPV-68 among multiple infections. Conclusively, despite the lack of attention high-risk HPV types beyond HPV-16 and -18 get in attempts of cervical cancer prevention in Kazakhstan, their prevalence is high and plays a large role in cervical cancer epidemiological situation. Full article

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18 pages, 3782 KiB

Open AccessArticle

Cigarette Smoking Alters the Expression of Circulating microRNAs and Its Potential Diagnostic Value in Female Lung Cancer Patients

by Eric Gustavo Ramírez-Salazar, Luis Vicente Gayosso-Gómez, Renata Baez-Saldaña, Ramcés Falfán-Valencia, Rogelio Pérez-Padilla, Anjarath L. Higuera-Iglesias, María E. Vázquez-Manríquez and Blanca Ortiz-Quintero

Biology 2021, 10(8), 793; https://doi.org/10.3390/biology10080793 - 18 Aug 2021

Cited by 11 | Viewed by 2200

Abstract

Cigarette smoking is a known risk factor for the development of lung cancer. We investigated whether circulating microRNA expression levels and their potential diagnostic value are affected by cigarette smoking in adenocarcinoma (AD) patients and healthy (H) participants. In total, 71 female AD [...] Read more.

Cigarette smoking is a known risk factor for the development of lung cancer. We investigated whether circulating microRNA expression levels and their potential diagnostic value are affected by cigarette smoking in adenocarcinoma (AD) patients and healthy (H) participants. In total, 71 female AD patients and 91 H individuals were recruited, including 42 AD never-smokers (AD/CS−), 29 AD smokers (AD/CS+), 54 H never-smokers (H/CS−), and 37 H smokers (H/CS+). PCR array (754 microRNAs) and qPCR were performed on sera from the discovery and validation cohorts, respectively. The expression levels of miR-532-5p, miR-25-3p, and miR-133a-3p were significantly higher in adenocarcinoma patients than in healthy participants, independent of their smoking status. Multivariate analysis showed that levels of miR-133a-3p were independently associated with smoking. ROC analysis showed that only miR-532-5p discriminated AD patients from H controls (AUC: 0.745). However, when making comparisons according to cigarette smoking status, miR-532-5p discriminated AD/CS− patients from H/CS− controls with a higher AUC (AUC:0.762); miR-25-3p discriminated AD/CS+ patients from H/CS+ controls (AUC: 0.779), and miR-133a discriminated AD/CS+ patients from H/CS+ controls with the highest AUC of 0.935. Cancer and lung-cancer-enriched pathways were significantly associated with the three miRNAs; in addition, nicotinate/nicotinamide metabolism, inflammation, and pulmonary hypertension were associated with miR-133a-3p. Our findings highlight how cigarette smoking affects the reliable identification of circulating miRNAs as diagnostic biomarkers in lung cancer and suggest a smoking-dependent pathogenic role of miR-133a-3p in smokers. Full article

(This article belongs to the Section Medical Biology)

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21 pages, 9631 KiB

Open AccessArticle

Microbial Involvement in Carbon Transformation via CH₄ and CO₂ in Saline Sedimentary Pool

by Weronika Goraj, Anna Szafranek-Nakonieczna, Jarosław Grządziel, Cezary Polakowski, Mirosław Słowakiewicz, Yanhong Zheng, Anna Gałązka, Zofia Stępniewska and Anna Pytlak

Biology 2021, 10(8), 792; https://doi.org/10.3390/biology10080792 - 17 Aug 2021

Cited by 3 | Viewed by 2315

Abstract

Methane and carbon dioxide are one of the most important greenhouse gases and significant components of the carbon cycle. Biogeochemical methane transformation may occur even in the extreme conditions of deep subsurface ecosystems. This study presents methane-related biological processes in saline sediments of [...] Read more.

Methane and carbon dioxide are one of the most important greenhouse gases and significant components of the carbon cycle. Biogeochemical methane transformation may occur even in the extreme conditions of deep subsurface ecosystems. This study presents methane-related biological processes in saline sediments of the Miocene Wieliczka Formation, Poland. Rock samples (W2, W3, and W4) differed in lithology (clayey salt with veins of fibrous salt and lenses of gypsum and anhydrite; siltstone and sandstone; siltstone with veins of fibrous salt and lenses of anhydrite) and the accompanying salt type (spiza salts or green salt). Microbial communities present in the Miocene strata were studied using activity measurements and high throughput sequencing. Biological activity (i.e., carbon dioxide and methane production or methane oxidation) occurred in all of the studied clayey salt and siltstone samples but mainly under water-saturated conditions. Microcosm studies performed at elevated moisture created more convenient conditions for the activity of both methanogenic and methanotrophic microorganisms than the intact sediments. This points to the fact that water activity is an important factor regulating microbial activity in saline subsurface sediments. Generally, respiration was higher in anaerobic conditions and ranged from 36 ± 2 (W2_200%t.w.c) to 48 ± 4 (W3_200%t.w.c) nmol CO₂ gdw⁻¹ day⁻¹. Methanogenic activity was the highest in siltstone and sandstone (W3, 0.025 ± 0.018 nmol CH₄ gdw⁻¹ day⁻¹), while aerobic methanotrophic activity was the highest in siltstone with salt and anhydrite (W4, 220 ± 66 nmol CH₄ gdw⁻¹ day⁻¹). The relative abundance of CH₄-utilizing microorganisms (Methylomicrobium, Methylomonas, Methylocystis) constituted 0.7–3.6% of all taxa. Methanogens were represented by Methanobacterium (0.01–0.5%). The methane-related microbes were accompanied by a significant number of unclassified microorganisms (3–64%) and those of the Bacillus genus (4.5–91%). The stable isotope composition of the CO₂ and CH₄ trapped in the sediments suggests that methane oxidation could have influenced δ¹³C_CH4, especially in W3 and W4. Full article

(This article belongs to the Section Microbiology)

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20 pages, 2172 KiB

Open AccessReview

Effects of Silicon and Silicon-Based Nanoparticles on Rhizosphere Microbiome, Plant Stress and Growth

by Vishnu D. Rajput, Tatiana Minkina, Morteza Feizi, Arpna Kumari, Masudulla Khan, Saglara Mandzhieva, Svetlana Sushkova, Hassan El-Ramady, Krishan K. Verma, Abhishek Singh, Eric D. van Hullebusch, Rupesh Kumar Singh, Hanuman Singh Jatav and Ravish Choudhary

Biology 2021, 10(8), 791; https://doi.org/10.3390/biology10080791 - 17 Aug 2021

Cited by 95 | Viewed by 9623

Abstract

Silicon (Si) is considered a non-essential element similar to cadmium, arsenic, lead, etc., for plants, yet Si is beneficial to plant growth, so it is also referred to as a quasi-essential element (similar to aluminum, cobalt, sodium and selenium). An element is considered [...] Read more.

Silicon (Si) is considered a non-essential element similar to cadmium, arsenic, lead, etc., for plants, yet Si is beneficial to plant growth, so it is also referred to as a quasi-essential element (similar to aluminum, cobalt, sodium and selenium). An element is considered quasi-essential if it is not required by plants but its absence results in significant negative consequences or anomalies in plant growth, reproduction and development. Si is reported to reduce the negative impacts of different stresses in plants. The significant accumulation of Si on the plant tissue surface is primarily responsible for these positive influences in plants, such as increasing antioxidant activity while reducing soil pollutant absorption. Because of these advantageous properties, the application of Si-based nanoparticles (Si-NPs) in agricultural and food production has received a great deal of interest. Furthermore, conventional Si fertilizers are reported to have low bioavailability; therefore, the development and implementation of nano-Si fertilizers with high bioavailability could be crucial for viable agricultural production. Thus, in this context, the objectives of this review are to summarize the effects of both Si and Si-NPs on soil microbes, soil properties, plant growth and various plant pathogens and diseases. Si-NPs and Si are reported to change the microbial colonies and biomass, could influence rhizospheric microbes and biomass content and are able to improve soil fertility. Full article

(This article belongs to the Special Issue Insights into the Role of Nanomaterials on Anatomical and Physiological and Molecular Indices of Plants under Stress Conditions)

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18 pages, 2396 KiB

Open AccessArticle

agReg-SNPdb: A Database of Regulatory SNPs for Agricultural Animal Species

by Selina Klees, Felix Heinrich, Armin Otto Schmitt and Mehmet Gültas

Biology 2021, 10(8), 790; https://doi.org/10.3390/biology10080790 - 17 Aug 2021

Cited by 7 | Viewed by 3975

Abstract

Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the [...] Read more.

Transcription factors (TFs) govern transcriptional gene regulation by specifically binding to short DNA motifs, known as transcription factor binding sites (TFBSs), in regulatory regions, such as promoters. Today, it is well known that single nucleotide polymorphisms (SNPs) in TFBSs can dramatically affect the level of gene expression, since they can cause a change in the binding affinity of TFs. Such SNPs, referred to as regulatory SNPs (rSNPs), have gained attention in the life sciences due to their causality for specific traits or diseases. In this study, we present agReg-SNPdb, a database comprising rSNP data of seven agricultural and domestic animal species: cattle, pig, chicken, sheep, horse, goat, and dog. To identify the rSNPs, we constructed a bioinformatics pipeline and identified a total of 10,623,512 rSNPs, which are located within TFBSs and affect the binding affinity of putative TFs. Altogether, we implemented the first systematic analysis of SNPs in promoter regions and their impact on the binding affinity of TFs for livestock and made it usable via a web interface. Full article

(This article belongs to the Section Bioinformatics)

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