Biology

25 pages, 2455 KiB

Open AccessArticle

Bioprospecting of a Novel Plant Growth-Promoting Bacterium Bacillus altitudinis KP-14 for Enhancing Miscanthus × giganteus Growth in Metals Contaminated Soil

by Kumar Pranaw, Valentina Pidlisnyuk, Josef Trögl and Hana Malinská

Biology 2020, 9(9), 305; https://doi.org/10.3390/biology9090305 - 22 Sep 2020

Cited by 19 | Viewed by 4665

Abstract

Use of plant growth-promoting bacteria (PGPB) for cultivation of the biofuel crop Miscanthus × giganteus (Mxg) in post-military and post-mining sites is a promising approach for the bioremediation of soils contaminated by metals. In the present study, PGPB were isolated from [...] Read more.

Use of plant growth-promoting bacteria (PGPB) for cultivation of the biofuel crop Miscanthus × giganteus (Mxg) in post-military and post-mining sites is a promising approach for the bioremediation of soils contaminated by metals. In the present study, PGPB were isolated from contaminated soil and screened for tolerance against abiotic stresses caused by salinity, pH, temperature, and lead (Pb). Selected strains were further assessed and screened for plant growth-promoting attributes. The isolate showing the most potential, Bacillus altitudinis KP-14, was tested for enhancement of Mxg growth in contaminated soil under greenhouse conditions. It was found to be highly tolerant to diverse abiotic stresses, exhibiting tolerance to salinity (0–15%), pH (4–8), temperature (4–50 °C), and Pb (up to 1200 ppm). The association of B. altitudinis KP-14 with Mxg resulted in a significant (p ≤ 0.001) impact on biomass enhancement: the total shoot and dry root weights were significantly enhanced by 77.7% and 55.5%, respectively. The significant enhancement of Mxg biomass parameters by application of B. altitudinis KP-14 strongly supports the use of this strain as a biofertilizer for the improvement of plant growth in metal-contaminated soils. Full article

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11 pages, 2109 KiB

Open AccessBrief Report

Complement in Reproductive White Adipose Tissue Characterizes the Obese Preeclamptic-Like BPH/5 Mouse Prior to and During Pregnancy

by Kelsey N. Olson, Dorien Reijnders, Viviane C. L. Gomes, R. Caitlin Hebert, Chin-Chi Liu, Jacqueline M. Stephens, Leanne M. Redman, Nataki C. Douglas and Jennifer L. Sones

Biology 2020, 9(9), 304; https://doi.org/10.3390/biology9090304 - 22 Sep 2020

Cited by 8 | Viewed by 3548

Abstract

Preeclampsia (PE) is a serious hypertensive disorder of pregnancy characterized by abnormal placental development with an unknown etiology. To better understand which women will develop PE, a number of maternal risk factors have been identified, including obesity. Visceral white adipose tissue (WAT) contains [...] Read more.

Preeclampsia (PE) is a serious hypertensive disorder of pregnancy characterized by abnormal placental development with an unknown etiology. To better understand which women will develop PE, a number of maternal risk factors have been identified, including obesity. Visceral white adipose tissue (WAT) contains inflammatory mediators that may contribute to PE. To explore this, we utilized the blood pressure high (BPH)/5 mouse model of superimposed PE that spontaneously recapitulates the maternal PE syndrome. We hypothesized that BPH/5 visceral WAT adjacent to the female reproductive tract (reproductive WAT) is a source of complement factors that contribute to the inflammatory milieu and angiogenic imbalance at the maternal–fetal interface in this model and in preeclamptic women. To test our hypothesis, we calorie-restricted BPH/5 females for two weeks prior to pregnancy and the first seven days of pregnancy, which attenuated complement component 3 (C3) but not complement factor B, nor complement factor D, (adipsin) in the reproductive WAT or the implantation site in BPH/5. Furthermore, calorie restriction during pregnancy restored vascular endothelial and placental growth factor mRNA levels in the BPH/5 implantation site. These data show maternal reproductive WAT may be a source of increased C3 during pregnancy, which is increased at the maternal–fetal interface in preeclamptic BPH/5 mice. It also suggests that calorie restriction could regulate inflammatory mediators thought to contribute to placental dysfunction in PE. Future studies are necessary to examine the effect of calorie restriction on C3 throughout pregnancy and the role of maternal obesity in PE. Full article

(This article belongs to the Section Physiology)

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21 pages, 4970 KiB

Open AccessArticle

Design and Characterization of a Minimally Invasive Bipolar Electrode for Electroporation

by Giulia Merola, Roberta Fusco, Elio Di Bernardo, Valeria D’Alessio, Francesco Izzo, Vincenza Granata, Deyanira Contartese, Matteo Cadossi, Alberto Audenino and Giacomo Perazzolo Gallo

Biology 2020, 9(9), 303; https://doi.org/10.3390/biology9090303 - 21 Sep 2020

Cited by 6 | Viewed by 3042

Abstract

Objective: To test a new bipolar electrode for electroporation consisting of a single minimally invasive needle. Methods: A theoretical study was performed by using Comsol Multiphysics^® software. The prototypes of electrode have been tested on potatoes and pigs, adopting an irreversible electroporation [...] Read more.

Objective: To test a new bipolar electrode for electroporation consisting of a single minimally invasive needle. Methods: A theoretical study was performed by using Comsol Multiphysics^® software. The prototypes of electrode have been tested on potatoes and pigs, adopting an irreversible electroporation protocol. Different applied voltages and different geometries of bipolar electrode prototype have been evaluated. Results: Simulations and pre-clinical tests have shown that the volume of ablated area is mainly influenced by applied voltage, while the diameter of the electrode had a lesser impact, making the goal of minimal-invasiveness possible. The conductive pole’s length determined an increase of electroporated volume, while the insulated pole length inversely affects the electroporated volume size and shape; when the insulated pole length decreases, a more regular shape of the electric field is obtained. Moreover, the geometry of the electrode determined a different shape of the electroporated volume. A parenchymal damage in the liver of pigs due to irreversible electroporation protocol was observed. Conclusion: The minimally invasive bipolar electrode is able to treat an electroporated volume of about 10 mm in diameter by using a single-needle electrode. Moreover, the geometry and the electric characteristics can be selected to produce ellipsoidal ablation volumes. Full article

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21 pages, 4403 KiB

Open AccessArticle

Piperine Regulates Nrf-2/Keap-1 Signalling and Exhibits Anticancer Effect in Experimental Colon Carcinogenesis in Wistar Rats

by Muneeb U. Rehman, Summya Rashid, Azher Arafah, Wajhul Qamar, Rana M. Alsaffar, Ajaz Ahmad, Nada M. Almatroudi, Saeed M. A. Alqahtani, Shahzada Mudasir Rashid and Sheikh Bilal Ahmad

Biology 2020, 9(9), 302; https://doi.org/10.3390/biology9090302 - 21 Sep 2020

Cited by 25 | Viewed by 3919

Abstract

Colon cancer is the most common cancer in men and women globally, killing millions of people annually. Though there widespread development has been made in the management of colorectal cancer, still there is an urgent need to find novel targets for its effective [...] Read more.

Colon cancer is the most common cancer in men and women globally, killing millions of people annually. Though there widespread development has been made in the management of colorectal cancer, still there is an urgent need to find novel targets for its effective treatment. Piperine is an alkaloid found in black pepper having anticancer, anti-inflammatory activities, safe and nutritive for human consumption. Nuclear factor-erythroid 2–kelch-like ECH-associated protein 1(Nrf-2/Keap-1)/Heme-oxygenase1 (HO-1) signaling pathway plays a vital part in shielding cells from intracellular oxidative stress and inflammation. A potential cross-talk between the Nrf-2 and NF-κB pathways is recognized during cancerous growth and expansion. We studied this pathway extensively in the present study to discover novel targets in the prevention of chemically induced colon cancer with piperine to simulate human colon cancer pathology. Animals were divided into four groups. Groups1 and 2 were used as a negative control and positive control where 1,2–Dimethylhydrazine, DMH was administered in group 2, while group 3 and 4 were prevention groups where piperine at two different doses was given two weeks prior to DMH and continued until end of experiment. We found that piperine inhibited NF-κB by the activation of Nrf-2, blocking downstream inflammatory mediators/cytokines (TNF-α, IL-6, IL-1β, Cox-2, PGE-2, iNOS, NO, MPO), triggering an antioxidant response machinery (HO-1, NQO-1, GSH, GR, GPx, CAT, SOD), scavenging ROS, and decreasing lipid peroxidation. Histological findings further validated our molecular findings. It also downregulates CEA, MDF and ACF, markers of precancerous lesions in colon, alleviates infiltration of mast cells and depletes the mucous layer. Our results indicate that piperine may be an effective molecule for the prophylactic treatment of colon carcinogenesis by targeting the NF-κB/Nrf-2/Keap-1/HO-1 pathway as a progressive strategy in the preclusion and effective treatment of colorectal cancer. Full article

(This article belongs to the Special Issue Bioactivity of Medicinal Plants and Extracts)

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8 pages, 1126 KiB

Open AccessArticle

Can Chitin and Chitosan Replace the Lichen Evernia prunastri for Environmental Biomonitoring of Cu and Zn Air Contamination?

by Stefano Loppi, Andrea Vannini, Fabrizio Monaci, Daniel Dagodzo, Felix Blind, Michael Erler and Stefan Fränzle

Biology 2020, 9(9), 301; https://doi.org/10.3390/biology9090301 - 19 Sep 2020

Cited by 4 | Viewed by 2975

Abstract

This study compared the ability of the lichen Evernia prunastri, chitin and chitosan to take up Cu²⁺ and Zn²⁺. It was hypothesized that chitin and chitosan have an accumulation capacity comparable to the lichen, so that these biopolymers could [...] Read more.

This study compared the ability of the lichen Evernia prunastri, chitin and chitosan to take up Cu²⁺ and Zn²⁺. It was hypothesized that chitin and chitosan have an accumulation capacity comparable to the lichen, so that these biopolymers could replace the use of E. prunastri for effective biomonitoring of Cu and Zn air pollution. Samples of the lichen E. prunastri, as well as chitin (from shrimps) and chitosan (from crabs), were incubated with Cu and Zn solutions at concentrations of 0 (control), 10, 25, 50, 75, and 100 µM and analyzed by Inductively Coupled Plasma Mass Spectrometry (ICP-MS). Metal concentrations accumulated by lichen, chitin and chitosan samples were strongly and linearly correlated with the concentrations in the treatment solutions. The lichen always showed significantly higher accumulation values compared to chitin and chitosan, which showed similar accumulation features. The outcomes of this study confirmed the great effectiveness of the lichen Evernia prunastri for environmental biomonitoring and showed that chitin and chitosan have a lower accumulation capacity, thus suggesting that although these biopolymers have the potential for replacing E. prunastri in polluted areas, their suitability may be limited in areas with intermediate or low pollution levels. Full article

(This article belongs to the Section Plant Science)

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13 pages, 797 KiB

Open AccessArticle

Effect of Sperm Concentration and Storage Temperature on Goat Spermatozoa during Liquid Storage

by Sara Sadeghi, Raquel Del Gallego, Balma García-Colomer, Ernesto A. Gómez, Jesús L. Yániz, Jaime Gosálvez, Carmen López-Fernández and Miguel A. Silvestre

Biology 2020, 9(9), 300; https://doi.org/10.3390/biology9090300 - 19 Sep 2020

Cited by 15 | Viewed by 4287

Abstract

The use of cooled semen is relatively common in goats. There are a number of advantages of cooled semen doses, including easier handling of artificial insemination (AI) doses, transport, more AI doses per ejaculate, and higher fertility rates in comparison with frozen AI [...] Read more.

The use of cooled semen is relatively common in goats. There are a number of advantages of cooled semen doses, including easier handling of artificial insemination (AI) doses, transport, more AI doses per ejaculate, and higher fertility rates in comparison with frozen AI doses. However, cooled semen has a short shelf life. The objective of this study was to examine the effect of temperature and sperm concentration on the in vitro sperm quality during liquid storage for 48 h, including sperm motility and kinetics, response to oxidation, mitochondrial membrane potential (MMP) and DNA fragmentation in goats. Three experiments were performed. In the first, the effects of liquid preservation of semen at different temperatures (5 °C or 17 °C), durations (0, 24 and 48 h) and sperm concentrations (250 × 10⁶ sperm/mL (1:2 dilution rate), 166.7 × 10⁶ sperm/mL (1:3 dilution rate) or 50 × 10⁶ sperm/mL (1:10 dilution rate)) on sperm motility and kinetics were studied. In the second experiment, the effect of temperature, sperm washing and concentration on sperm motility and DNA fragmentation was studied. Finally, the effect of sperm concentration and duration of storage at 5 °C on sperm motility, response to oxidative stress and MMP was examined. We found that refrigerated liquid storage of goat sperm impaired sperm quality, such as motility, MMP and response to oxidation, as storage time increased; however, sperm DNA fragmentation index was not significantly affected. Liquid storage at 5 °C preserved higher total motility than at 17 °C. Moreover, we observed that the reduction of sperm concentration below 500 × 10⁶ sperm/mL did not seem to improve the quality of spermatozoa conserved in milk-based extender in the conditions tested. Full article

(This article belongs to the Special Issue Factors Affecting In Vitro Assessment of Sperm Quality)

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19 pages, 2408 KiB

Open AccessArticle

Pandæsim: An Epidemic Spreading Stochastic Simulator

by Patrick Amar

Biology 2020, 9(9), 299; https://doi.org/10.3390/biology9090299 - 18 Sep 2020

Cited by 4 | Viewed by 2525

Abstract

Many methods have been used to model epidemic spreading. They include ordinary differential equation systems for globally homogeneous environments and partial differential equation systems to take into account spatial localisation and inhomogeneity. Stochastic differential equations systems have been used to model the inherent [...] Read more.

Many methods have been used to model epidemic spreading. They include ordinary differential equation systems for globally homogeneous environments and partial differential equation systems to take into account spatial localisation and inhomogeneity. Stochastic differential equations systems have been used to model the inherent stochasticity of epidemic spreading processes. In our case study, we wanted to model the numbers of individuals in different states of the disease, and their locations in the country. Among the many existing methods we used our own variant of the well known Gillespie stochastic algorithm, along with the sub-volumes method to take into account the spatial localisation. Our algorithm allows us to easily switch from stochastic discrete simulation to continuous deterministic resolution using mean values. We applied our approaches on the study of the Covid-19 epidemic in France. The stochastic discrete version of Pandæsim showed very good correlations between the simulation results and the statistics gathered from hospitals, both on day by day and on global numbers, including the effects of the lockdown. Moreover, we have highlighted interesting differences in behaviour between the continuous and discrete methods that may arise in some particular conditions. Full article

(This article belongs to the Special Issue Theories and Models on COVID-19 Epidemics)

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20 pages, 2223 KiB

Open AccessArticle

Antioxidant, Antimicrobial, and Bioactive Potential of Two New Haloarchaeal Strains Isolated from Odiel Salterns (Southwest Spain)

by Patricia Gómez-Villegas, Javier Vigara, Marta Vila, João Varela, Luísa Barreira and Rosa Léon

Biology 2020, 9(9), 298; https://doi.org/10.3390/biology9090298 - 18 Sep 2020

Cited by 24 | Viewed by 3736

Abstract

The need to survive in extreme environments has furnished haloarchaea with a series of components specially adapted to work in such conditions. The possible application of these molecules in the pharmaceutical and industrial fields has received increasing attention; however, many potential bioactivities of [...] Read more.

The need to survive in extreme environments has furnished haloarchaea with a series of components specially adapted to work in such conditions. The possible application of these molecules in the pharmaceutical and industrial fields has received increasing attention; however, many potential bioactivities of haloarchaea are still poorly explored. In this paper, we describe the isolation and identification of two new haloarchaeal strains from the saltern ponds located in the marshlands of the Odiel River, in the southwest of Spain, as well as the in vitro assessment of their antioxidant, antimicrobial, and bioactive properties. The acetone extract obtained from the new isolated Haloarcula strain exhibited the highest antioxidant activity, while the acetone extracts from both isolated strains demonstrated a strong antimicrobial activity, especially against other halophilic microorganisms. Moreover, these extracts showed a remarkable ability to inhibit the enzyme cyclooxygenase-2 and to activate the melanogenic enzyme tyrosinase, indicating their potential against chronic inflammation and skin pigmentation disorders. Finally, the aqueous protein-rich extracts obtained from both haloarchaea exhibited an important inhibitory effect on the activity of the acetylcholinesterase enzyme, involved in the hydrolysis of cholinergic neurotransmitters and related to several neurological diseases. Full article

(This article belongs to the Special Issue Extremophilic Archaea)

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17 pages, 5883 KiB

Open AccessArticle

Salt Stress-Induced Structural Changes Are Mitigated in Transgenic Tomato Plants Over-Expressing Superoxide Dismutase

by Liliya R. Bogoutdinova, Elena M. Lazareva, Inna A. Chaban, Neonila V. Kononenko, Tatyana Dilovarova, Marat R. Khaliluev, Ludmila V. Kurenina, Alexander A. Gulevich, Elena A. Smirnova and Ekaterina N. Baranova

Biology 2020, 9(9), 297; https://doi.org/10.3390/biology9090297 - 18 Sep 2020

Cited by 18 | Viewed by 3477

Abstract

Various abiotic stresses cause the appearance of reactive oxygen species (ROS) in plant cells, which seriously damage the cellular structures. The engineering of transgenic plants with higher production of ROS-scavenging enzyme in plant cells could protect the integrity of such a fine intracellular [...] Read more.

Various abiotic stresses cause the appearance of reactive oxygen species (ROS) in plant cells, which seriously damage the cellular structures. The engineering of transgenic plants with higher production of ROS-scavenging enzyme in plant cells could protect the integrity of such a fine intracellular structure as the cytoskeleton and each cellular compartment. We analyzed the morphological changes in root tip cells caused by the application of iso-osmotic NaCl and Na₂SO₄ solutions to tomato plants harboring an introduced superoxide dismutase gene. To study the roots of tomato plants cultivar Belyi Naliv (WT) and FeSOD-transgenic line, we examined the distribution of ROS and enzyme-linked immunosorbent detection of α-tubulin. In addition, longitudinal sections of the root apexes were compared. Transmission electronic microscopy of atypical cytoskeleton structures was also performed. The differences in the microtubules cortical network between WT and transgenic plants without salt stress were detected. The differences were found in the cortical network of microtubules between WT and transgenic plants in the absence of salt stress. While an ordered microtubule network was revealed in the root cells of WT tomato, no such degree of ordering was detected in transgenic line cells. The signs of microtubule disorganization in root cells of WT plants were manifested under the NaCl treatment. On the contrary, the cytoskeleton structural organization in the transgenic line cells was more ordered. Similar changes, including the cortical microtubules disorganization, possibly associated with the formation of atypical tubulin polymers as a response to salt stress caused by Na₂SO₄ treatment, were also observed. Changes in cell size, due to both vacuolization and impaired cell expansion in columella zone and cap initials, were responsible for the root tip tissue modification. Full article

(This article belongs to the Section Plant Science)

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28 pages, 2398 KiB

Open AccessArticle

A Putative Prophylactic Solution for COVID-19: Development of Novel Multiepitope Vaccine Candidate against SARS-COV-2 by Comprehensive Immunoinformatic and Molecular Modelling Approach

by Hafiz Muzzammel Rehman, Muhammad Usman Mirza, Mian Azhar Ahmad, Mahjabeen Saleem, Matheus Froeyen, Sarfraz Ahmad, Roquyya Gul, Huda Ahmed Alghamdi, Muhammad Shahbaz Aslam, Muhammad Sajjad and Munir Ahmad Bhinder

Biology 2020, 9(9), 296; https://doi.org/10.3390/biology9090296 - 18 Sep 2020

Cited by 16 | Viewed by 4905

Abstract

The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few [...] Read more.

The outbreak of 2019-novel coronavirus (SARS-CoV-2) that causes severe respiratory infection (COVID-19) has spread in China, and the World Health Organization has declared it a pandemic. However, no approved drug or vaccines are available, and treatment is mainly supportive and through a few repurposed drugs. The urgency of the situation requires the development of SARS-CoV-2-based vaccines. Immunoinformatic and molecular modelling are time-efficient methods that are generally used to accelerate the discovery and design of the candidate peptides for vaccine development. In recent years, the use of multiepitope vaccines has proved to be a promising immunization strategy against viruses and pathogens, thus inducing more comprehensive protective immunity. The current study demonstrated a comprehensive in silico strategy to design stable multiepitope vaccine construct (MVC) from B-cell and T-cell epitopes of essential SARS-CoV-2 proteins with the help of adjuvants and linkers. The integrated molecular dynamics simulations analysis revealed the stability of MVC and its interaction with human Toll-like receptors (TLRs), which trigger an innate and adaptive immune response. Later, the in silico cloning in a known pET28a vector system also estimated the possibility of MVC expression in Escherichia coli. Despite that this study lacks validation of this vaccine construct in terms of its efficacy, the current integrated strategy encompasses the initial multiple epitope vaccine design concepts. After validation, this MVC can be present as a better prophylactic solution against COVID-19. Full article

(This article belongs to the Special Issue Theories and Models on COVID-19 Epidemics)

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27 pages, 540 KiB

Open AccessReview

Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing

by Girum Fitihamlak Ejigu and Jaehee Jung

Biology 2020, 9(9), 295; https://doi.org/10.3390/biology9090295 - 18 Sep 2020

Cited by 38 | Viewed by 12642

Abstract

Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide [...] Read more.

Next-Generation Sequencing (NGS) has made it easier to obtain genome-wide sequence data and it has shifted the research focus into genome annotation. The challenging tasks involved in annotation rely on the currently available tools and techniques to decode the information contained in nucleotide sequences. This information will improve our understanding of general aspects of life and evolution and improve our ability to diagnose genetic disorders. Here, we present a summary of both structural and functional annotations, as well as the associated comparative annotation tools and pipelines. We highlight visualization tools that immensely aid the annotation process and the contributions of the scientific community to the annotation. Further, we discuss quality-control practices and the need for re-annotation, and highlight the future of annotation. Full article

(This article belongs to the Special Issue Computational Biology)

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20 pages, 4712 KiB

Open AccessArticle

A Poplar Rust Effector Protein Associates with Protein Disulfide Isomerase and Enhances Plant Susceptibility

by Mst Hur Madina, Md Saifur Rahman, Xiaoqiang Huang, Yang Zhang, Huanquan Zheng and Hugo Germain

Biology 2020, 9(9), 294; https://doi.org/10.3390/biology9090294 - 16 Sep 2020

Cited by 8 | Viewed by 3930

Abstract

Melampsora larici-populina (Mlp), the causal agent of Populus leaf rust, secretes an array of effectors into the host through the haustorium to gain nutrients and suppress immunity. The precise mechanisms by which these effectors promote virulence remain unclear. To address this question, [...] Read more.

Melampsora larici-populina (Mlp), the causal agent of Populus leaf rust, secretes an array of effectors into the host through the haustorium to gain nutrients and suppress immunity. The precise mechanisms by which these effectors promote virulence remain unclear. To address this question, we developed a transgenic Arabidopsis line expressing a candidate effector, Mlp124357. Constitutive expression of the effector increased plant susceptibility to pathogens. A GxxxG motif present in Mlp124357 is required for its subcellular localization at the vacuolar membrane of the plant cell, as replacement of the glycine residues with alanines led to the delocalization of Mlp124357 to the nucleus and cytoplasm. We used immunoprecipitation and mass spectrometry (MS) to identify Mlp124357 interaction partners. Only one of the putative interaction partners knock-out line caused delocalization of the effector, indicating that Arabidopsis protein disulfide isomerase-11 (AtPDI-11) is required for the effector localization. This interaction was further confirmed by a complementation test, a yeast-two hybrid assay and a molecular modeling experiment. Moreover, localization results and infection assays suggest that AtPDI-11 act as a helper for Mlp124357. In summary, our findings established that one of Mlp effectors resides at the vacuole surface and modulates plant susceptibility. Full article

(This article belongs to the Section Plant Science)

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9 pages, 254 KiB

Open AccessCommunication

Maternal Obesity Does Not Exacerbate the Effects of LPS Injection on Pregnancy Outcomes in Mice

by Natasha Virginkar and Julian K. Christians

Biology 2020, 9(9), 293; https://doi.org/10.3390/biology9090293 - 16 Sep 2020

Viewed by 2612

Abstract

Obesity increases the risk of a number of pregnancy complications, potentially due to chronic inflammation. We predicted that an obesogenic high-fat diet (HFD) in mice would create an inflammatory environment that would exacerbate the effects of lipopolysaccharide (LPS), an inflammatory insult, administered during [...] Read more.

Obesity increases the risk of a number of pregnancy complications, potentially due to chronic inflammation. We predicted that an obesogenic high-fat diet (HFD) in mice would create an inflammatory environment that would exacerbate the effects of lipopolysaccharide (LPS), an inflammatory insult, administered during pregnancy. Females were placed on a HFD or a low-fat diet (LFD) prior to mating, injected with 2 µg LPS or control on gestational day 7 and collected on day 14. Treatment with LPS increased the odds that a female thought to be pregnant at injection had no conceptuses at day 14 (p = 0.024), suggesting that injection with LPS was more likely to induce complete abortion. However, there was no effect of diet on the odds of having no conceptuses at day 14 and no interaction between diet and LPS injection. Diet and LPS injection had no effect on the number of viable fetuses in females still pregnant at day 14. For fetal weight, there was a significant interaction between diet and treatment (p = 0.017), whereby LPS reduced fetal weight in HFD females but not in LFD females. However, LPS treatment of HFD females reduced fetal weight to that observed in control-injected LFD females. Although LPS increased the odds of abortion, there was little evidence that a HFD exacerbated the effects of LPS. Full article

(This article belongs to the Section Physiology)

20 pages, 7538 KiB

Open AccessArticle

Cytotoxicity and Pro-Apoptotic, Antioxidant and Anti-Inflammatory Activities of Geopropolis Produced by the Stingless Bee Melipona fasciculata Smith

by Josianne Rocha Barboza, Francisco Assis Nascimento Pereira, Renan Amphilophio Fernandes, Cleydlenne Costa Vasconcelos, Maria do Socorro de Sousa Cartágenes, Alberto Jorge Oliveira Lopes, Andreia Cristina de Melo, Isabella dos Santos Guimarães, Cláudia Quintino da Rocha and Maria Nilce de Sousa Ribeiro

Biology 2020, 9(9), 292; https://doi.org/10.3390/biology9090292 - 15 Sep 2020

Cited by 7 | Viewed by 3213

Abstract

Geopropolis is produced by some stingless bee species, such as Melipona fasciculata Smith, a native species from Brazil. This study aims to investigate the antioxidant and anti-inflammatory activities and cytotoxicity effects of geopropolis hydroethanolic extracts against lung (H460 and A549) and ovarian (A2780 [...] Read more.

Geopropolis is produced by some stingless bee species, such as Melipona fasciculata Smith, a native species from Brazil. This study aims to investigate the antioxidant and anti-inflammatory activities and cytotoxicity effects of geopropolis hydroethanolic extracts against lung (H460 and A549) and ovarian (A2780 and ES2) cancer cell lines and non-tumor (HUVEC) cell lines using chemical identification by LC/MS/MS analysis and in silico assays to determine which compounds are associated with bioactivity. The antioxidant activity of extracts and inhibitory activity against COX enzymes were assessed by in vitro assays; cytotoxicity effect was evaluated by the MTT assay; cell cycle was assessed by flow cytometry and apoptosis by Western blotting. The geopropolis extracts showed great radical scavenging potential, preferential inhibition of COX-2, decreased cancer cell viability, non-cytotoxic effects against the non-tumoral cell line, besides modulating the cell cycle and inducing cancer cell apoptosis through the activation of caspase-3 and PARP protein cleavage. The in silico study suggests that corilagin, typhaneoside, taraxerone and marsformosanone, identified by LC/MS/MS, can be associated with anti-inflammatory activity and cytotoxic effects. Thus, the current study suggests the potential of geopropolis concerning the research field of new pharmacological alternatives regarding cancer therapy. Full article

(This article belongs to the Special Issue Bioactivity of Medicinal Plants and Extracts)

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8 pages, 2058 KiB

Open AccessArticle

The Efficacy of the Novel TSPO Ligands 2-Cl-MGV-1 and 2,4-Di-Cl-MGV-1 Compared to the Classical TSPO Ligand PK 11195 to Counteract the Release of Chemokines from LPS-Stimulated BV-2 Microglial Cells

by Sheelu Monga, Abraham Weizman and Moshe Gavish

Biology 2020, 9(9), 291; https://doi.org/10.3390/biology9090291 - 14 Sep 2020

Cited by 4 | Viewed by 2335

Abstract

The impact of ligands of the 18 kDa translocator protein (TSPO) on the release of chemokines is not vastly investigated. In the present study, we assessed the effect of our novel TSPO ligands 2-Cl-MGV-1 and 2,4-Di-Cl-MGV-1 compared to the classical TSPO ligand PK [...] Read more.

The impact of ligands of the 18 kDa translocator protein (TSPO) on the release of chemokines is not vastly investigated. In the present study, we assessed the effect of our novel TSPO ligands 2-Cl-MGV-1 and 2,4-Di-Cl-MGV-1 compared to the classical TSPO ligand PK 11195 on chemokine release in LPS-stimulated BV-2 microglial cells. As per the effect of 2-Cl-MGV-1, CCL2, CCL3, and CCL5 were inhibited by 90%, CCL8 by 97%, and IL-2 by 77% (p < 0.05 for all). 2,4-Di-Cl-MGV-1 inhibited CCL2 release by 92%, CCL3 by 91%, CCL5 by 90%, CCL8 by 89%, and IL-2 by 80% (p < 0.05 for all). PK 11195 exhibited weaker inhibitory effects: CCL2 by 22%, CCL3 by 83%, CCL5 by 34%, CCL8 by 41%, and the cytokine IL-2 by 14% (p < 0.05 for all). Thus, it appears that the novel TSPO ligands are potent suppressors of LPS-stimulated BV-2 microglial cells, and their inhibitory effect is larger than that of PK 11195. Such immunomodulatory effects on microglial cells may be relevant to the treatment of neurodegenerative and neuroinflammatory diseases. Full article

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31 pages, 4731 KiB

Open AccessReview

Transcription Factors in Cartilage Homeostasis and Osteoarthritis

by Margot Neefjes, Arjan P. M. van Caam and Peter M. van der Kraan

Biology 2020, 9(9), 290; https://doi.org/10.3390/biology9090290 - 14 Sep 2020

Cited by 20 | Viewed by 5268

Abstract

Osteoarthritis (OA) is the most common degenerative joint disease, and it is characterized by articular cartilage loss. In part, OA is caused by aberrant anabolic and catabolic activities of the chondrocyte, the only cell type present in cartilage. These chondrocyte activities depend on [...] Read more.

Osteoarthritis (OA) is the most common degenerative joint disease, and it is characterized by articular cartilage loss. In part, OA is caused by aberrant anabolic and catabolic activities of the chondrocyte, the only cell type present in cartilage. These chondrocyte activities depend on the intra- and extracellular signals that the cell receives and integrates into gene expression. The key proteins for this integration are transcription factors. A large number of transcription factors exist, and a better understanding of the transcription factors activated by the various signaling pathways active during OA can help us to better understand the complex etiology of OA. In addition, establishing such a profile can help to stratify patients in different subtypes, which can be a very useful approach towards personalized therapy. In this review, we discuss crucial transcription factors for extracellular matrix metabolism, chondrocyte hypertrophy, chondrocyte senescence, and autophagy in chondrocytes. In addition, we discuss how insight into these factors can be used for treatment purposes. Full article

(This article belongs to the Special Issue Biology of Osteoarthritis)

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18 pages, 3777 KiB

Open AccessArticle

Targeted Central Nervous System Irradiation of Caenorhabditis elegans Induces a Limited Effect on Motility

by Michiyo Suzuki, Zu Soh, Hiroki Yamashita, Toshio Tsuji and Tomoo Funayama

Biology 2020, 9(9), 289; https://doi.org/10.3390/biology9090289 - 14 Sep 2020

Cited by 6 | Viewed by 5752

Abstract

To clarify the tissue responsible for a biological function, that function can be experimentally perturbed by an external stimulus, such as radiation. Radiation can be precisely and finely administered and any subsequent change in function examined. To investigate the involvement of the central [...] Read more.

To clarify the tissue responsible for a biological function, that function can be experimentally perturbed by an external stimulus, such as radiation. Radiation can be precisely and finely administered and any subsequent change in function examined. To investigate the involvement of the central nervous system (CNS) in Caenorhabditis elegans’ locomotion, we irradiated a limited 20-µm-diameter area of the CNS with a single dose and evaluated the resulting effects on motility. However, whether irradiated area (beam size)-dependent or dose-dependent effects on motility occur via targeted irradiation remain unknown. In the present study, we examined the irradiated area- and dose-dependent effects of CNS-targeted irradiation on the motility of C. elegans using a collimating microbeam system and confirmed the involvement of the CNS and body-wall muscle cells around the CNS in motility. After CNS-targeted microbeam irradiation, C. elegans’ motility was assayed. The results demonstrated a dose-dependent effect of CNS-targeted irradiation on motility reflecting direct effects on the irradiated CNS. In addition, when irradiated with 1000-Gy irradiation, irradiated area (beam size)-dependent effects were observed. This method has two technical advantages: Performing a series of on-chip imaging analyses before and after irradiation and targeted irradiation using a distinct ion-beam size. Full article

(This article belongs to the Special Issue Brain Damage and Repair: From Molecular Effects to CNS Disorders)

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15 pages, 1188 KiB

Open AccessArticle

Functional Feeding Groups of Aquatic Insects Influence Trace Element Accumulation: Findings for Filterers, Scrapers and Predators from the Po Basin

by Paolo Pastorino, Annalisa Zaccaroni, Alberto Doretto, Elisa Falasco, Marina Silvi, Alessandro Dondo, Antonia Concetta Elia, Marino Prearo and Francesca Bona

Biology 2020, 9(9), 288; https://doi.org/10.3390/biology9090288 - 14 Sep 2020

Cited by 11 | Viewed by 4342

Abstract

For this study, we measured the concentrations of 23 trace elements (Al, As, Ba, Bi, Cd, Cr, Co, Cu, Fe, Ga, Hg, In, Li, Mn, Mo, Ni, Pb, Se, Sr, Ti, Tl, V, and Zn) in the whole bodies of three functional feeding [...] Read more.

For this study, we measured the concentrations of 23 trace elements (Al, As, Ba, Bi, Cd, Cr, Co, Cu, Fe, Ga, Hg, In, Li, Mn, Mo, Ni, Pb, Se, Sr, Ti, Tl, V, and Zn) in the whole bodies of three functional feeding groups (FFG) (filterers—Hydropsychidae, scrapers—Heptageniidae, and predators—Odonata) of aquatic insects collected from two sites in the Po basin (Po Settimo and Malone Front, Northwest Italy) to determine: (a) how FFG influence trace element accumulations, (b) if scrapers accumulate higher elements compared to the other FFG, since they graze on periphyton, which represents one of the major sinks of metals, and (c) the potential use of macroinvertebrates to assess the bioavailability of trace elements in freshwater. The hierarchical clustering analysis generated three main groups based on trace element concentrations: the most abundant elements were Fe and Al, followed by Sr, In, Zn, V, Mo, and Cu. Tl was below the limit of detection (LOD) in all FFG. Ga was detected only in scrapers from both sites and Hg only in predators from Po Settimo. The principal component analysis showed that concentrations of Al, As, Bi, Cd, Co, Cr, Ga, Fe, In, Mn, Pb, Ni, and Sr were highest in scrapers, suggesting that trace elements accumulate from the ingestion of epilithic periphyton (biofilm). Odonata (predators) accumulate certain elements (Ba, Hg, Li, Se, V, Ti, and Zn) in higher concentrations by food ingestion composed of different aquatic organisms. Differently, Cu and Mo concentrations were the highest in filterers due to their bioavailability in the water column. Non-metric multidimensional scaling clearly differentiated the FFG based on their ability to accumulate trace elements. The findings from this study represent an important step toward the definition of an innovative approach based on trace element accumulation by macroinvertebrates. Full article

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14 pages, 2581 KiB

Open AccessArticle

Metabolites Produced by Kaistia sp. 32K Promote Biofilm Formation in Coculture with Methylobacterium sp. ME121

by Yoshiaki Usui, Tetsu Shimizu, Akira Nakamura and Masahiro Ito

Biology 2020, 9(9), 287; https://doi.org/10.3390/biology9090287 - 13 Sep 2020

Cited by 1 | Viewed by 2996

Abstract

Previously, we reported that the coculture of motile Methylobacterium sp. ME121 and non-motile Kaistia sp. 32K, isolated from the same soil sample, displayed accelerated motility of strain ME121 due to an extracellular polysaccharide (EPS) produced by strain 32K. Since EPS is a major [...] Read more.

Previously, we reported that the coculture of motile Methylobacterium sp. ME121 and non-motile Kaistia sp. 32K, isolated from the same soil sample, displayed accelerated motility of strain ME121 due to an extracellular polysaccharide (EPS) produced by strain 32K. Since EPS is a major component of biofilms, we aimed to investigate the biofilm formation in cocultures of the two strains. The extent of biofilm formation was measured by a microtiter dish assay with the dye crystal violet. A significant increase in the amount of biofilm was observed in the coculture of the two strains, as compared to that of the monocultures, which could be due to a metabolite produced by strain 32K. However, in the coculture with strain 32K, using Escherichia coli or Pseudomonas aeruginosa, there was no difference in the amount of biofilm formation as compared with the monoculture. Elevated biofilm formation was also observed in the coculture of strain ME121 with Kaistia adipata, which was isolated from a different soil sample. Methylobacterium radiotolerans, isolated from another soil sample, showed a significant increase in biofilm formation when cocultured with K. adipata, but not with strain 32K. We also found that the culture supernatants of strains 32K and K. adipata accelerated the motility of strains ME121 and M. radiotolerans, wherein culture supernatant of K. adipata significantly increased the motility of M. radiotolerans, as compared to that by the culture supernatant of strain 32K. These results indicated that there was a positive relationship between accelerated motility and increased biofilm formation in Methylobacterium spp. This is the first study to report that the metabolites from Kaistia spp. could specifically modulate the biofilm-forming ability of Methylobacterium spp. Methylobacterium spp. biofilms are capable of inhibiting the biofilm formation of mycobacteria, which are opportunistic pathogens that cause problems in infectious diseases. Thus, the metabolites from the culture supernatant of Kaistia spp. have the potential to contribute to the environment in which increased biofilm production of Methylobacterium is desired. Full article

(This article belongs to the Section Microbiology)

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14 pages, 3002 KiB

Open AccessArticle

Antifungal Activity and Phytochemical Screening of Vernonia amygdalina Extract against Botrytis cinerea Causing Gray Mold Disease on Tomato Fruits

by Siti Fairuz Yusoff, Farah Farhanah Haron, Mahmud Tengku Muda Mohamed, Norhayu Asib, Siti Zaharah Sakimin, Faizah Abu Kassim and Siti Izera Ismail

Biology 2020, 9(9), 286; https://doi.org/10.3390/biology9090286 - 11 Sep 2020

Cited by 28 | Viewed by 4944

Abstract

Gray mold disease caused by Botrytis cinerea is a damaging postharvest disease in tomato plants, and it is known to be a limiting factor in tomato production. This study aimed to evaluate antifungal activities of Vernonia amygdalina leaf extracts against B. cinerea and [...] Read more.

Gray mold disease caused by Botrytis cinerea is a damaging postharvest disease in tomato plants, and it is known to be a limiting factor in tomato production. This study aimed to evaluate antifungal activities of Vernonia amygdalina leaf extracts against B. cinerea and to screen the phytochemical compound in the crude extract that had the highest antifungal activity. In this study, crude extracts of hexane, dichloromethane, methanol, and water extracts with concentration levels at 100, 200, 300, 400, and 500 mg/mL were shown to significantly affect the inhibition of B. cinerea. Among the crude extracts, dichloromethane extract was shown to be the most potent in terms of antifungal activities. The SEM observation proved that the treatment altered the fungal morphology, which leads to fungal growth inhibition. For the in vivo bioassay, the fruits treated with dichloromethane extract at 400 and 500 mg/mL showed the lowest disease incidence with mild severity of infection. There were 23 chemical compounds identified in V. amygdalina dichloromethane extract using GCMS analysis. The top five major compounds were dominated by squalene (16.92%), phytol (15.05%), triacontane (11.31%), heptacosane (7.14%), and neophytadiene (6.28%). Some of these significant compounds possess high antifungal activities. This study proved that V. amygdalina from dichloromethane extract could be useful for inhibiting gray mold disease on tomato fruit and has potential as a natural antifungal agent. Full article

(This article belongs to the Special Issue Bioactivity of Medicinal Plants and Extracts)

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13 pages, 598 KiB

Open AccessReview

A Glance of p53 Functions in Brain Development, Neural Stem Cells, and Brain Cancer

by Yuqing Xiong, Yun Zhang, Shunbin Xiong and Abie E. Williams-Villalobo

Biology 2020, 9(9), 285; https://doi.org/10.3390/biology9090285 - 11 Sep 2020

Cited by 22 | Viewed by 8473

Abstract

p53 is one of the most intensively studied tumor suppressors. It transcriptionally regulates a broad range of genes to modulate a series of cellular events, including DNA damage repair, cell cycle arrest, senescence, apoptosis, ferroptosis, autophagy, and metabolic remodeling, which are fundamental for [...] Read more.

p53 is one of the most intensively studied tumor suppressors. It transcriptionally regulates a broad range of genes to modulate a series of cellular events, including DNA damage repair, cell cycle arrest, senescence, apoptosis, ferroptosis, autophagy, and metabolic remodeling, which are fundamental for both development and cancer. This review discusses the role of p53 in brain development, neural stem cell regulation and the mechanisms of inactivating p53 in gliomas. p53 null or p53 mutant mice show female biased exencephaly, potentially due to X chromosome inactivation failure and/or hormone-related gene expression. Oxidative cellular status, increased PI3K/Akt signaling, elevated ID1, and metabolism are all implicated in p53-loss induced neurogenesis. However, p53 has also been shown to promote neuronal differentiation. In addition, p53 mutations are frequently identified in brain tumors, especially glioblastomas. Mechanisms underlying p53 inactivation in brain tumor cells include disruption of p53 protein stability, gene expression and transactivation potential as well as p53 gene loss or mutation. Loss of p53 function and gain-of-function of mutant p53 are both implicated in brain development and tumor genesis. Further understanding of the role of p53 in the brain may provide therapeutic insights for brain developmental syndromes and cancer. Full article

(This article belongs to the Special Issue Genetics of cancer)

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16 pages, 1645 KiB

Open AccessArticle

Short-Term Effects of Early Menopause on Adiposity, Fatty Acids Profile and Insulin Sensitivity of a Swine Model of Female Obesity

by Ana Heras-Molina, José Luis Pesantez-Pacheco, Marta Vazquez-Gomez, Consolacion Garcia-Contreras, Susana Astiz, Beatriz Isabel and Antonio Gonzalez-Bulnes

Biology 2020, 9(9), 284; https://doi.org/10.3390/biology9090284 - 11 Sep 2020

Cited by 2 | Viewed by 2170

Abstract

Menopause strongly increases incidence and consequences of obesity and non-communicable diseases in women, with recent research suggesting a very early onset of changes in lipid accumulation, dyslipidemia, and insulin resistance. However, there is a lack of adequate preclinical models for its study. The [...] Read more.

Menopause strongly increases incidence and consequences of obesity and non-communicable diseases in women, with recent research suggesting a very early onset of changes in lipid accumulation, dyslipidemia, and insulin resistance. However, there is a lack of adequate preclinical models for its study. The present trial evaluated the usefulness of an alternative method to surgical ovariectomy, the administration of two doses of a GnRH analogue-protein conjugate (Vacsincel^®), for inducing ovarian inactivity in sows used as preclinical models of obesity and menopause. All the sows treated with the compound developed ovarian stoppage after the second dose and, when exposed to obesogenic diets during the following three months, showed changes in the patterns of fat deposition, in the fatty acids profiles at the different tissues and in the plasma concentrations of fructosamine, urea, β-hydroxibutirate, and haptoglobin when compared to obese fed with the same diet but maintaining ovarian activity. Altogether, these results indicate that menopause early augments the deleterious effects induced by overfeeding and obesity on metabolic traits, paving the way for future research on physiopathology of these conditions and possible therapeutic targets using the swine model. Full article

(This article belongs to the Special Issue Mechanistic Insights into the Pathogenesis of Type 2 Diabetes)

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26 pages, 5277 KiB

Open AccessReview

Cnidarian Immunity and the Repertoire of Defense Mechanisms in Anthozoans

by Maria Giovanna Parisi, Daniela Parrinello, Loredana Stabili and Matteo Cammarata

Biology 2020, 9(9), 283; https://doi.org/10.3390/biology9090283 - 11 Sep 2020

Cited by 27 | Viewed by 5293

Abstract

Anthozoa is the most specious class of the phylum Cnidaria that is phylogenetically basal within the Metazoa. It is an interesting group for studying the evolution of mutualisms and immunity, for despite their morphological simplicity, Anthozoans are unexpectedly immunologically complex, with large genomes [...] Read more.

Anthozoa is the most specious class of the phylum Cnidaria that is phylogenetically basal within the Metazoa. It is an interesting group for studying the evolution of mutualisms and immunity, for despite their morphological simplicity, Anthozoans are unexpectedly immunologically complex, with large genomes and gene families similar to those of the Bilateria. Evidence indicates that the Anthozoan innate immune system is not only involved in the disruption of harmful microorganisms, but is also crucial in structuring tissue-associated microbial communities that are essential components of the cnidarian holobiont and useful to the animal’s health for several functions including metabolism, immune defense, development, and behavior. Here, we report on the current state of the art of Anthozoan immunity. Like other invertebrates, Anthozoans possess immune mechanisms based on self/non-self-recognition. Although lacking adaptive immunity, they use a diverse repertoire of immune receptor signaling pathways (PRRs) to recognize a broad array of conserved microorganism-associated molecular patterns (MAMP). The intracellular signaling cascades lead to gene transcription up to endpoints of release of molecules that kill the pathogens, defend the self by maintaining homeostasis, and modulate the wound repair process. The cells play a fundamental role in immunity, as they display phagocytic activities and secrete mucus, which acts as a physicochemical barrier preventing or slowing down the proliferation of potential invaders. Finally, we describe the current state of knowledge of some immune effectors in Anthozoan species, including the potential role of toxins and the inflammatory response in the Mediterranean Anthozoan Anemonia viridis following injection of various foreign particles differing in type and dimensions, including pathogenetic bacteria. Full article

(This article belongs to the Special Issue Ancient Immunity. Phylogenetic Emergence of Recognition-Defence Mechanisms)

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15 pages, 718 KiB

Open AccessReview

Oxidative Stress and Reproductive Function in the Aging Male

by Paulina Nguyen-Powanda and Bernard Robaire

Biology 2020, 9(9), 282; https://doi.org/10.3390/biology9090282 - 11 Sep 2020

Cited by 35 | Viewed by 4486

Abstract

With the delay of parenthood becoming more common, the age at which men father children is on the rise. While the effects of advanced maternal age have been well documented, only recently have studies started to focus on the impact of advanced paternal [...] Read more.

With the delay of parenthood becoming more common, the age at which men father children is on the rise. While the effects of advanced maternal age have been well documented, only recently have studies started to focus on the impact of advanced paternal age (APA) in the context of male reproduction. As men age, the antioxidant defense system gradually becomes less efficient and elevated levels of reactive oxygen species (ROS) accumulate in spermatozoa; this can impair their functional and structural integrity. In this review, we present an overview of how oxidative stress is implicated in male reproductive aging by providing a summary of the sources and roles of ROS, the theories of aging, and the current animal and human studies that demonstrate the impacts of APA on the male germ line, the health of progeny and fertility, and how treatment with antioxidants may reverse these effects. Full article

(This article belongs to the Special Issue Oxidative Stress in Gametes and Embryos)

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17 pages, 3429 KiB

Open AccessArticle

TIP_finder: An HPC Software to Detect Transposable Element Insertion Polymorphisms in Large Genomic Datasets

by Simon Orozco-Arias, Nicolas Tobon-Orozco, Johan S. Piña, Cristian Felipe Jiménez-Varón, Reinel Tabares-Soto and Romain Guyot

Biology 2020, 9(9), 281; https://doi.org/10.3390/biology9090281 - 09 Sep 2020

Cited by 4 | Viewed by 4196

Abstract

Transposable elements (TEs) are non-static genomic units capable of moving indistinctly from one chromosomal location to another. Their insertion polymorphisms may cause beneficial mutations, such as the creation of new gene function, or deleterious in eukaryotes, e.g., different types of cancer in humans. [...] Read more.

Transposable elements (TEs) are non-static genomic units capable of moving indistinctly from one chromosomal location to another. Their insertion polymorphisms may cause beneficial mutations, such as the creation of new gene function, or deleterious in eukaryotes, e.g., different types of cancer in humans. A particular type of TE called LTR-retrotransposons comprises almost 8% of the human genome. Among LTR retrotransposons, human endogenous retroviruses (HERVs) bear structural and functional similarities to retroviruses. Several tools allow the detection of transposon insertion polymorphisms (TIPs) but fail to efficiently analyze large genomes or large datasets. Here, we developed a computational tool, named TIP_finder, able to detect mobile element insertions in very large genomes, through high-performance computing (HPC) and parallel programming, using the inference of discordant read pair analysis. TIP_finder inputs are (i) short pair reads such as those obtained by Illumina, (ii) a chromosome-level reference genome sequence, and (iii) a database of consensus TE sequences. The HPC strategy we propose adds scalability and provides a useful tool to analyze huge genomic datasets in a decent running time. TIP_finder accelerates the detection of transposon insertion polymorphisms (TIPs) by up to 55 times in breast cancer datasets and 46 times in cancer-free datasets compared to the fastest available algorithms. TIP_finder applies a validated strategy to find TIPs, accelerates the process through HPC, and addresses the issues of runtime for large-scale analyses in the post-genomic era. Full article

(This article belongs to the Section Bioinformatics)

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24 pages, 1726 KiB

Open AccessReview

Factors Associated with Increased Morbidity and Mortality of Obese and Overweight COVID-19 Patients

by Amany Magdy Beshbishy, Helal F. Hetta, Diaa E. Hussein, Abdullah A. Saati, Christian C. Uba, Nallely Rivero-Perez, Adrian Zaragoza-Bastida, Muhammad Ajmal Shah, Tapan Behl and Gaber El-Saber Batiha

Biology 2020, 9(9), 280; https://doi.org/10.3390/biology9090280 - 09 Sep 2020

Cited by 26 | Viewed by 7167

Abstract

Overweight and obesity are defined as an unnecessary accumulation of fat, which poses a risk to health. It is a well-identified risk factor for increased mortality due to heightened rates of heart disease, certain cancers, musculoskeletal disorders, and bacterial, protozoan and viral infections. [...] Read more.

Overweight and obesity are defined as an unnecessary accumulation of fat, which poses a risk to health. It is a well-identified risk factor for increased mortality due to heightened rates of heart disease, certain cancers, musculoskeletal disorders, and bacterial, protozoan and viral infections. The increasing prevalence of obesity is of concern, as conventional pathogenesis may indeed be increased in obese hosts rather than healthy hosts, especially during this COVID-19 pandemic. COVID-19 is a new disease and we do not have the luxury of cumulative data. Obesity activates the development of gene induced hypoxia and adipogenesis in obese animals. Several factors can influence obesity, for example, stress can increase the body weight by allowing people to consume high amounts of food with a higher propensity to consume palatable food. Obesity is a risk factor for the development of immune-mediated and some inflammatory-mediated diseases, including atherosclerosis and psoriasis, leading to a dampened immune response to infectious agents, leading to weaker post-infection impacts. Moreover, the obese host creates a special microenvironment for disease pathogenesis, marked by persistent low-grade inflammation. Therefore, it is advisable to sustain healthy eating habits by increasing the consumption of various plant-based and low-fat foods to protect our bodies and decrease the risk of infectious diseases, especially COVID-19. Full article

(This article belongs to the Special Issue Coronavirus Disease 2019 (COVID-19))

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16 pages, 9566 KiB

Open AccessArticle

Pituitary Actions of EGF on Gonadotropins, Growth Hormone, Prolactin and Somatolactins in Grass Carp

by Qiongyao Hu, Qinbo Qin, Shaohua Xu, Lingling Zhou, Chuanhui Xia, Xuetao Shi, Huiying Zhang, Jingyi Jia, Cheng Ye, Zhan Yin and Guangfu Hu

Biology 2020, 9(9), 279; https://doi.org/10.3390/biology9090279 - 08 Sep 2020

Cited by 5 | Viewed by 2576

Abstract

In mammals, epidermal growth factor (EGF) plays a vital role in both pituitary physiology and pathology. However, the functional role of EGF in the regulation of pituitary hormones has rarely reported in teleost. In our study, using primary cultured grass carp pituitary cells [...] Read more.

In mammals, epidermal growth factor (EGF) plays a vital role in both pituitary physiology and pathology. However, the functional role of EGF in the regulation of pituitary hormones has rarely reported in teleost. In our study, using primary cultured grass carp pituitary cells as an in vitro model, we examined the effects of EGF on pituitary hormone secretion and gene expression as well as the post-receptor signaling mechanisms involved. Firstly, we found that EGF significantly reduced luteinizing hormone (LHβ) mRNA expression via ErbB1 coupled to ERK1/2 pathway, but had no effect on LH release in grass carp pituitary cells. Secondly, the results showed that EGF was effective in up-regulating mRNA expression of growth hormone (GH), somatolactin α (SLα) and somatolactin β (SLβ) via ErbB1 and ErbB2 and subsequently coupled to MEK1/2/ERK1/2 and PI3K/Akt/mTOR pathways, respectively. However, EGF was not effective in GH release in pituitary cells. Thirdly, we found that EGF strongly induced pituitary prolactin (PRL) release and mRNA expression, which was mediated by ErbB1 and subsequent stimulation of MEK1/2/ERK1/2 and PI3K/Akt/mTOR pathways. Interestingly, subsequent study further found that neurokinin B (NKB) significantly suppressed EGF-induced PRL mRNA expression, which was mediated by neurokinin receptor (NK2R) and coupled to AC/cAMP/PKA signal pathway. These results suggested that EGF could differently regulate the pituitary hormones expression in grass carp pituitary cells. Full article

(This article belongs to the Section Biochemistry and Molecular Biology)

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18 pages, 4394 KiB

Open AccessArticle

Essentiality and Transcriptome-Enriched Pathway Scores Predict Drug-Combination Synergy

by Jin Li, Yang Huo, Xue Wu, Enze Liu, Zhi Zeng, Zhen Tian, Kunjie Fan, Daniel Stover, Lijun Cheng and Lang Li

Biology 2020, 9(9), 278; https://doi.org/10.3390/biology9090278 - 07 Sep 2020

Cited by 8 | Viewed by 3848

Abstract

In the prediction of the synergy of drug combinations, systems pharmacology models expand the scope of experiment screening and overcome the limitations of current computational models posed by their lack of mechanical interpretation and integration of gene essentiality. We therefore investigated the synergy [...] Read more.

In the prediction of the synergy of drug combinations, systems pharmacology models expand the scope of experiment screening and overcome the limitations of current computational models posed by their lack of mechanical interpretation and integration of gene essentiality. We therefore investigated the synergy of drug combinations for cancer therapies utilizing records in NCI ALMANAC, and we employed logistic regression to test the statistical significance of gene and pathway features in that interaction. We trained our predictive models using 43 NCI-60 cell lines, 165 KEGG pathways, and 114 drug pairs. Scores of drug-combination synergies showed a stronger correlation with pathway than gene features in overall trend analysis and a significant association with both genes and pathways in genome-wide association analyses. However, we observed little overlap of significant gene expressions and essentialities and no significant evidence that associated target and non-target genes and their pathways. We were able to validate four drug-combination pathways between two drug combinations, Nelarabine-Exemestane and Docetaxel-Vermurafenib, and two signaling pathways, PI3K-AKT and AMPK, in 16 cell lines. In conclusion, pathways significantly outperformed genes in predicting drug-combination synergy, and because they have very different mechanisms, gene expression and essentiality should be considered in combination rather than individually to improve this prediction. Full article

(This article belongs to the Special Issue Using Omics Data and Systems Biology Approaches Based on Network Analysis to Understand Biological Systems)

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22 pages, 3951 KiB

Open AccessArticle

Skim-Sequencing Based Genotyping Reveals Genetic Divergence of the Wild and Domesticated Population of Black Tiger Shrimp (Penaeus monodon) in the Indo-Pacific Region

by Li Lian Wong, Zulaikha Mat Deris, Yoji Igarashi, Songqian Huang, Shuichi Asakawa, Qasim Ayub, Shu Yong Lim, Mhd Ikhwanuddin, Shumpei Iehata, Kazutoshi Okamoto, Mariom and Md Asaduzzaman

Biology 2020, 9(9), 277; https://doi.org/10.3390/biology9090277 - 07 Sep 2020

Cited by 5 | Viewed by 4523

Abstract

The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, [...] Read more.

The domestication of a wild-caught aquatic animal is an evolutionary process, which results in genetic discrimination at the genomic level in response to strong artificial selection. Although black tiger shrimp (Penaeus monodon) is one of the most commercially important aquaculture species, a systematic assessment of genetic divergence and structure of wild-caught and domesticated broodstock populations of the species is yet to be documented. Therefore, we used skim sequencing (SkimSeq) based genotyping approach to investigate the genetic structure of 50 broodstock individuals of P. monodon species, collected from five sampling sites (n = 10 in each site) across their distribution in Indo-Pacific regions. The wild-caught P. monodon broodstock population were collected from Malaysia (MS) and Japan (MJ), while domesticated broodstock populations were collected from Madagascar (MMD), Hawaii, HI, USA (MMO), and Thailand (MT). After various filtering process, a total of 194,259 single nucleotide polymorphism (SNP) loci were identified, in which 4983 SNP loci were identified as putatively adaptive by the pcadapt approach. In both datasets, pairwise F_ST estimates high genetic divergence between wild and domesticated broodstock populations. Consistently, different spatial clustering analyses in both datasets categorized divergent genetic structure into two clusters: (1) wild-caught populations (MS and MJ), and (2) domesticated populations (MMD, MMO and MT). Among 4983 putatively adaptive SNP loci, only 50 loci were observed to be in the coding region. The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that non-synonymous mutated genes might be associated with the energy production, metabolic functions, respiration regulation and developmental rates, which likely act to promote adaptation to the strong artificial selection during the domestication process. This study has demonstrated the applicability of SkimSeq in a highly duplicated genome of P. monodon specifically, across a range of genetic backgrounds and geographical distributions, and would be useful for future genetic improvement program of this species in aquaculture. Full article

(This article belongs to the Section Marine Biology)

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16 pages, 1035 KiB

Open AccessArticle

Measurable Cytokine Concentrations in Pig Seminal Plasma Are Modified by Semen Handling and Storage

by Lorena Padilla, Isabel Barranco, Inmaculada Parrilla, Xiomara Lucas, Heriberto Rodriguez-Martinez and Jordi Roca

Biology 2020, 9(9), 276; https://doi.org/10.3390/biology9090276 - 07 Sep 2020

Cited by 3 | Viewed by 2293

Abstract

Sample handling and storing are critical steps for the reliable measurement of circulating biomolecules in biological fluids. This study evaluates how cytokine measurements in pig seminal plasma (SP) vary depending on semen handling and SP storage. Thirteen cytokines (GM-CSF, IFNγ, IL-1α, IL-1β, IL-1ra, [...] Read more.

Sample handling and storing are critical steps for the reliable measurement of circulating biomolecules in biological fluids. This study evaluates how cytokine measurements in pig seminal plasma (SP) vary depending on semen handling and SP storage. Thirteen cytokines (GM-CSF, IFNγ, IL-1α, IL-1β, IL-1ra, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-18 and TNFα) were measured using Luminex xMAP^® technology in individual seminal plasma (SP) samples (n = 62) from healthy breeding boars. Three separate experiments explored the delay (2 h and 24 h) in SP collection after ejaculation (Experiment 1) and SP storage, either short-term (5 °C, −20 °C and −80 °C for 72 h, Experiment 2) or long-term (at −20 °C and −80 °C for two months, Experiment 3), before analysis. Levels in fresh SP-samples were used as baseline control values. Delays in SP harvesting of up to 24 h did not substantially impact SP cytokine measurements. Some cytokines showed instability in stored SP samples, mainly in long-term storage. Ideally, cytokines in pig SP should be measured in fresh samples harvested within 24 h after ejaculation. If storage of SP is imperative, storage conditions should be adjusted for each cytokine. Full article

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