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Biology
Volume 9
Issue 4
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Biology, Volume 9, Issue 4 (April 2020) – 26 articles

Cover Story (view full-size image): Before we can answer questions on the origins of morphological and ecological diversity, we need a solid understanding of the phylogenetic relationships of the species of interest. Ideally, this phylogeny is backed by sufficient amounts of data and represents the diversity of the group. In this Issue, authors investigated the phylogenetic relationships of Terebelliformia, a group of mostly marine segmented worms (Annelida) that includes spaghetti worms, Pompeii worms, ice cream cone worms, and their relatives. A dataset of thousands of genetic loci sequenced for the main lineages of the group formed a well-supported backbone, which guided the analysis of smaller but taxonomically more representative datasets for 121 species. This approach provided a robust understanding into the relationships among different lineages and into the evolution of their remarkable morphological diversity. View this paper.
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11 pages, 742 KiB  
Article
The Prevalence and Impact of Hepatic Steatosis on Response to Direct-Acting Antiviral Therapy in HIV–HCV Coinfection
by Leigh P. Johnson and Richard K. Sterling
Biology 2020, 9(4), 87; https://doi.org/10.3390/biology9040087 - 24 Apr 2020
Cited by 3 | Viewed by 2818
Abstract
(1) Background: Direct-acting antiviral therapy for chronic hepatitis C virus (HCV) infection is associated with high sustained virologic response (SVR) and overcomes negative predictive factors, including steatosis, in patients without human immunodeficiency virus (HIV) coinfection. The impact of steatosis on SVR in patients [...] Read more.
(1) Background: Direct-acting antiviral therapy for chronic hepatitis C virus (HCV) infection is associated with high sustained virologic response (SVR) and overcomes negative predictive factors, including steatosis, in patients without human immunodeficiency virus (HIV) coinfection. The impact of steatosis on SVR in patients with HIV–HCV coinfection is unknown. (2) Methods: A retrospective analysis of patients treated with direct-acting antivirals was performed. Demographic, laboratory and direct-acting antiviral regimen data were prospectively collected. Metabolic syndrome and its components—diabetes mellitus, hypertension, dyslipidemia and obesity—were assessed. Hepatic steatosis (≥5%) was defined by liver biopsy or controlled attenuation parameter (CAP) measurement during vibration-controlled transient elastography (VCTE). (3) Results: A total of 151 HIV–HCV-coinfected patients on combined antiretroviral therapy and direct-acting antiviral therapy were included in this analysis. Prevalence of steatosis by liver biopsy (n = 34) or CAP (≥263 db/m) during VCTE (n = 92) was 27% and was independently associated with obesity (OR 3.11; 95% CI 1.43–6.82; p = 0.004) and the metabolic syndrome (OR 1.08; 95% CI 1.01–0.15; p = 0.01). The overall SVR rate (n = 148) was 95% and was not impacted by the presence of steatosis (p = 0.42). (4) Conclusions: Hepatic steatosis is common in HIV–HCV coinfection, correlates with obesity and the metabolic syndrome and does not impact SVR. Full article
(This article belongs to the Special Issue Non-alcoholic Liver Injury)
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13 pages, 936 KiB  
Review
Lymphocyte-Activation Gene 3 (LAG3) Protein as a Possible Therapeutic Target for Parkinson’s Disease: Molecular Mechanisms Connecting Neuroinflammation to α-Synuclein Spreading Pathology
by Efthalia Angelopoulou, Yam Nath Paudel, Chiara Villa, Mohd. Farooq Shaikh and Christina Piperi
Biology 2020, 9(4), 86; https://doi.org/10.3390/biology9040086 - 23 Apr 2020
Cited by 23 | Viewed by 6977
Abstract
Parkinson’s disease (PD) is the most common neurodegenerative movement disorder without any objective biomarker available to date. Increasing evidence highlights the critical role of neuroinflammation, including T cell responses, and spreading of aggregated α-synuclein in PD progression. Lymphocyte-activation gene 3 (LAG3) belongs to [...] Read more.
Parkinson’s disease (PD) is the most common neurodegenerative movement disorder without any objective biomarker available to date. Increasing evidence highlights the critical role of neuroinflammation, including T cell responses, and spreading of aggregated α-synuclein in PD progression. Lymphocyte-activation gene 3 (LAG3) belongs to the immunoglobulin (Ig) superfamily expressed by peripheral immune cells, microglia and neurons and plays a key role in T cell regulation. The role of LAG3 has been extensively investigated in several human cancers, whereas until recently, the role of LAG3 in the central nervous system (CNS) has been largely unknown. Accumulating evidence highlights the potential role of LAG3 in PD pathogenesis, mainly by binding to α-synuclein fibrils and affecting its endocytosis and intercellular transmission, which sheds more light on the connection between immune dysregulation and α-synuclein spreading pathology. Serum and cerebrospinal fluid (CSF) soluble LAG3 (sLAG3) levels have been demonstrated to be potentially associated with PD development and clinical phenotype, suggesting that sLAG3 could represent an emerging PD biomarker. Specific single nucleotide polymorphisms (SNPs) of the LAG3 gene have been also related to PD occurrence especially in the female population, enlightening the pathophysiological background of gender-related PD clinical differences. Given also the ongoing clinical trials investigating various LAG3-targeting strategies in human diseases, new opportunities are being developed for PD treatment research. In this review, we discuss recent preclinical and clinical evidence on the role of LAG3 in PD pathogenesis and biomarker potential, aiming to elucidate its underlying molecular mechanisms. Full article
(This article belongs to the Special Issue Molecular Targets and Targeting in Biomedical Sciences)
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17 pages, 2929 KiB  
Article
Structural and Functional Peculiarities of α-Crystallin
by Olga M. Selivanova and Oxana V. Galzitskaya
Biology 2020, 9(4), 85; https://doi.org/10.3390/biology9040085 - 23 Apr 2020
Cited by 21 | Viewed by 3625
Abstract
α-Crystallin is the major protein of the eye lens and a member of the family of small heat-shock proteins. Its concentration in the human eye lens is extremely high (about 450 mg/mL). Three-dimensional structure of native α-crystallin is unknown. First of all, this [...] Read more.
α-Crystallin is the major protein of the eye lens and a member of the family of small heat-shock proteins. Its concentration in the human eye lens is extremely high (about 450 mg/mL). Three-dimensional structure of native α-crystallin is unknown. First of all, this is the result of the highly heterogeneous nature of α-crystallin, which hampers obtaining it in a crystalline form. The modeling based on the electron microscopy (EM) analysis of α-crystallin preparations shows that the main population of the α-crystallin polydisperse complex is represented by oligomeric particles of rounded, slightly ellipsoidal shape with the diameter of about 13.5 nm. These complexes have molecular mass of about 700 kDa. In our opinion, the heterogeneity of the α-crystallin complex makes it impossible to obtain a reliable 3D model. In the literature, there is evidence of an enhanced chaperone function of α-crystallin during its dissociation into smaller components. This may indirectly indicate that the formation of heterogeneous complexes is probably necessary to preserve α-crystallin in a state inactive before stressful conditions. Then, not only the heterogeneity of the α-crystallin complex is an evolutionary adaptation that protects α-crystallin from crystallization but also the enhancement of the function of α-crystallin during its dissociation is also an evolutionary acquisition. An analysis of the literature on the study of α-crystallin in vitro led us to the assumption that, of the two α-crystallin isoforms (αA- and αB-crystallins), it is αA-crystallin that plays the role of a special chaperone for αB-crystallin. In addition, our data on X-ray diffraction analysis of α-crystallin at the sample concentration of about 170–190 mg/mL allowed us to assume that, at a high concentration, the eye lens α-crystallin can be in a gel-like stage. Finally, we conclude that, since all the accumulated data on structural-functional studies of α-crystallin were carried out under conditions far from native, they cannot adequately reflect the features of the functioning of α-crystallin in vivo. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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9 pages, 738 KiB  
Article
The Impact of Insurance and Marital Status on Survival in Patients with Nasopharyngeal Carcinoma
by Chih-Chun Wang, Ching-Chieh Yang, Shyh-An Yeh, Chung-I Huang, Tzer-Zen Hwang, Chuan-Chien Yang and Yu-Chieh Su
Biology 2020, 9(4), 84; https://doi.org/10.3390/biology9040084 - 22 Apr 2020
Cited by 9 | Viewed by 2712
Abstract
Objective: This study aimed to explore the influence of social support on the survival outcomes of patients with nasopharyngeal carcinoma (NPC). We examined whether the combined proxy influenced whether patients were more likely to receive radiotherapy. Methodology: data were collected from the 18 [...] Read more.
Objective: This study aimed to explore the influence of social support on the survival outcomes of patients with nasopharyngeal carcinoma (NPC). We examined whether the combined proxy influenced whether patients were more likely to receive radiotherapy. Methodology: data were collected from the 18 registries of the National Cancer Institute’s Surveillance, Epidemiology, and End Results database. The association between both insurance status and marital status and disease-specific survival rates were evaluated with a multivariate Cox proportional-hazards regression model to calculate the hazard ratios and associated confidence intervals. Odds ratio (OR) computed by logistic regression was also used to examine the relationship between the receipt of radiotherapy and insurance and marital status. Results: insured and uninsured patients differed significantly in T-stage, N-stage, M-stage, radiotherapy use, race, and marital status. The uninsured-non-married patients showed the lowest 5-year disease-specific survival rates. We further found unmarried patients with either Medicaid (OR, 0.40), or no insurance (OR, 0.24) had lower odds of receiving radiotherapy than those with insurance at diagnosis. Conclusions: uninsured-unmarried NPC patients had a significantly higher risk of distant metastasis at diagnosis, poorer 5-year disease-specific survival, and were less likely to receive radiotherapy than insured-married patients. Full article
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8 pages, 929 KiB  
Article
Clinical Effectiveness of a Combination of Black Elder Berries, Violet Herb, and Calendula Flowers in Chronic Obstructive Pulmonary Disease: The Results of a Double-Blinded Placebo-Controlled Study
by Tatiana V. Kirichenko, Igor A. Sobenin, Yuliya V. Markina, Elena V. Gerasimova, Andrey V. Grechko, Dmitry A. Kashirskikh, Elena B. Romanenko, Wei-Kai Wu and Alexander N. Orekhov
Biology 2020, 9(4), 83; https://doi.org/10.3390/biology9040083 - 22 Apr 2020
Cited by 1 | Viewed by 3925
Abstract
Chronic obstructive pulmonary disease (COPD) is a multifactorial disease, in which systemic inflammation plays a key role. This 6-month randomized double-blinded placebo-controlled study evaluates the possible effect of natural preparation Inflaminat on clinical symptoms of COPD, indicators of respiratory function, and exacerbation frequency [...] Read more.
Chronic obstructive pulmonary disease (COPD) is a multifactorial disease, in which systemic inflammation plays a key role. This 6-month randomized double-blinded placebo-controlled study evaluates the possible effect of natural preparation Inflaminat on clinical symptoms of COPD, indicators of respiratory function, and exacerbation frequency in 60 patients with moderate severity of COPD. Inflaminat is a combination of natural ingredients black elder (Sambucus nigra L.) berries, violet (Viola tricolor L.) herb, and calendula (Calendula officinalis L.) flowers. The preparation has been previously demonstrated to possess anticytokine and anti-inflammatory effects in experimental studies. In present study, COPD dynamics were evaluated by means of BCSS (Breathlessness, Cough, and Sputum Scale) and spirometry tests. It was shown that 6-months Inflaminat administration led to significant decrease of BCSS points from 3.0 ± 0.6 to 1.9 ± 0.7, (p = 0.002) as well as significant increase of FEV1 from 66 ± 18% to 73 ± 17%, (p = 0.042); there were no beneficial dynamics in placebo group. Side effects associated with preparation administration were not identified. The results of the study suggest that Inflaminat may be employed in treatment of patients with moderate severity of COPD, since it has a positive effect on COPD symptoms according BCSS and indicators of respiratory function FEV1. Full article
(This article belongs to the Section Medical Biology)
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17 pages, 4528 KiB  
Article
Overexpression of T-bet, GATA-3 and TGF-ß Induces IFN-γ, IL-4/13A, and IL-17A Expression in Atlantic Salmon
by Tiril H. Slettjord, Hege J. Sekkenes, Heng Chi, Jarl Bøgwald, Trilochan Swain, Roy A. Dalmo and Jaya Kumari Swain
Biology 2020, 9(4), 82; https://doi.org/10.3390/biology9040082 - 20 Apr 2020
Cited by 6 | Viewed by 4004
Abstract
The overexpression of GATA-3, T-bet and TGF-ß may theoretically induce IL-4/A, IFN-γ and IL-17A expression, respectively. Whether this also applies to fish is not yet known. The plasmid vectors encoding reporter gene (RFP)-tagged T-bet, GATA-3 and TGF-ß were used as [...] Read more.
The overexpression of GATA-3, T-bet and TGF-ß may theoretically induce IL-4/A, IFN-γ and IL-17A expression, respectively. Whether this also applies to fish is not yet known. The plasmid vectors encoding reporter gene (RFP)-tagged T-bet, GATA-3 and TGF-ß were used as overexpression tools, transfected into cells or injected intramuscularly to monitor the expression of IFN-γ, IL-4/13A and IL-17A. In addition, the fish were either experimentally challenged with Vibrio anguillarum (VA group) or Piscirickettsia salmonis (PS group). The reporter gene (RFP) inserted upstream of the GATA-3, T-bet and TGF-ß genes, was observed in muscle cell nuclei and in inflammatory cells after intramuscular (i.m.) injection. PS group: following the injection of GATA-3 and T-bet-encoding plasmids, the expression of GATA-3 and T-bet was high at the injection site. The spleen expression of IFN-γ, following the injection of a T-bet-encoding plasmid, was significantly higher on day 2. VA group: The T-bet and GATA-3-overexpressing fish expressed high T-bet and GATA-3 mRNA levels in the muscles and on day 4 post-challenge. The expression of TGF-ß in the muscles of fish injected with TGF-ß-encoding plasmids was significantly higher on days 7 (8 days pre-challenge) and 19 (4 days after challenge). The protective effects of the overexpression of T-bet, GATA-3 and TGF-ß on both bacterial infections were negligible. Full article
(This article belongs to the Section Immunology)
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13 pages, 4010 KiB  
Review
Evaluation of Inflammation Caused by Cardiopulmonary Bypass in a Small Animal Model
by Yutaka Fujii
Biology 2020, 9(4), 81; https://doi.org/10.3390/biology9040081 - 20 Apr 2020
Cited by 8 | Viewed by 5217
Abstract
Extracorporeal circulation (ECC) methods are being increasingly used for mechanical support of respiratory and cardio-circulatory failure. Especially, cardiopulmonary bypass (CPB) during cardiovascular surgery, sustenance of the patient’s life by providing an appropriate blood flow and oxygen supply to principal organs. On the other [...] Read more.
Extracorporeal circulation (ECC) methods are being increasingly used for mechanical support of respiratory and cardio-circulatory failure. Especially, cardiopulmonary bypass (CPB) during cardiovascular surgery, sustenance of the patient’s life by providing an appropriate blood flow and oxygen supply to principal organs. On the other hand, systemic inflammatory responses in patients undergoing cardiovascular surgery supported by CPB contribute significantly to CPB-associated mortality and morbidity. Our previous research showed that CPB causes a systemic inflammatory response and organ damage in a small animal CPB model. We have been studying the effects of hyperoxia and blood plasma substitute on CPB. In this review, we present a study focusing on the systemic inflammatory response during CPB, along with our findings. Full article
(This article belongs to the Section Medical Biology)
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21 pages, 550 KiB  
Review
Matrix Metalloproteases in Pancreatic Ductal Adenocarcinoma: Key Drivers of Disease Progression?
by Etienne J. Slapak, JanWillem Duitman, Cansu Tekin, Maarten F. Bijlsma and C. Arnold Spek
Biology 2020, 9(4), 80; https://doi.org/10.3390/biology9040080 - 18 Apr 2020
Cited by 57 | Viewed by 4331
Abstract
Pancreatic cancer is a dismal disorder that is histologically characterized by a dense fibrotic stroma around the tumor cells. As the extracellular matrix comprises the bulk of the stroma, matrix degrading proteases may play an important role in pancreatic cancer. It has been [...] Read more.
Pancreatic cancer is a dismal disorder that is histologically characterized by a dense fibrotic stroma around the tumor cells. As the extracellular matrix comprises the bulk of the stroma, matrix degrading proteases may play an important role in pancreatic cancer. It has been suggested that matrix metalloproteases are key drivers of both tumor growth and metastasis during pancreatic cancer progression. Based upon this notion, changes in matrix metalloprotease expression levels are often considered surrogate markers for pancreatic cancer progression and/or treatment response. Indeed, reduced matrix metalloprotease levels upon treatment (either pharmacological or due to genetic ablation) are considered as proof of the anti-tumorigenic potential of the mediator under study. In the current review, we aim to establish whether matrix metalloproteases indeed drive pancreatic cancer progression and whether decreased matrix metalloprotease levels in experimental settings are therefore indicative of treatment response. After a systematic review of the studies focusing on matrix metalloproteases in pancreatic cancer, we conclude that the available literature is not as convincing as expected and that, although individual matrix metalloproteases may contribute to pancreatic cancer growth and metastasis, this does not support the generalized notion that matrix metalloproteases drive pancreatic ductal adenocarcinoma progression. Full article
(This article belongs to the Special Issue Proteases—From Basic Structure to Function to Drug Design as Targeted Therapy)
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11 pages, 326 KiB  
Concept Paper
Whole Organism Model to Study Molecular Mechanisms of Differentiation and Dedifferentiation
by Areeba Anwar, Ruqaiyyah Siddiqui and Naveed Ahmed Khan
Biology 2020, 9(4), 79; https://doi.org/10.3390/biology9040079 - 17 Apr 2020
Cited by 3 | Viewed by 3234
Abstract
Cancer recurrence has remained a significant challenge, despite advances in therapeutic approaches. In part, this is due to our incomplete understanding of the biology of cancer stem cells and the underlying molecular mechanisms. The phenomenon of differentiation and dedifferentiation (phenotypic switching) is not [...] Read more.
Cancer recurrence has remained a significant challenge, despite advances in therapeutic approaches. In part, this is due to our incomplete understanding of the biology of cancer stem cells and the underlying molecular mechanisms. The phenomenon of differentiation and dedifferentiation (phenotypic switching) is not only unique to stem cells but it is also observed in several other organisms, as well as evolutionary-related microbes. Here, we propose the use of a primitive eukaryotic unicellular organism, Acanthamoeba castellanii, as a model to study the molecular mechanisms of cellular differentiation and dedifferentiation. Full article
(This article belongs to the Special Issue Stemness and Differentiation: A Systemic View)
13 pages, 1216 KiB  
Article
Seminal Plasma Anti-Müllerian Hormone: A Potential AI-Boar Fertility Biomarker?
by Isabel Barranco, Beatriz Fernandez-Fuertes, Lorena Padilla, Ariadna Delgado-Bermúdez, Asta Tvarijonaviciute and Marc Yeste
Biology 2020, 9(4), 78; https://doi.org/10.3390/biology9040078 - 10 Apr 2020
Cited by 12 | Viewed by 3426
Abstract
The anti-Müllerian hormone (AMH), a Sertoli cell-secreted glycoprotein that is present in seminal plasma (SP), is considered as a marker of spermatogenesis in humans. This study aimed to evaluate the presence of this hormone in boar SP, together with its putative relationship with [...] Read more.
The anti-Müllerian hormone (AMH), a Sertoli cell-secreted glycoprotein that is present in seminal plasma (SP), is considered as a marker of spermatogenesis in humans. This study aimed to evaluate the presence of this hormone in boar SP, together with its putative relationship with sperm quality, function, and in vivo fertility parameters in liquid-stored semen samples. The concentration of SP-AMH was assessed in 126 ejaculates from artificial insemination (AI)-boars (n = 92) while using a commercial Enzyme-Linked ImmunoSorbent Assay (ELISA) kit with monoclonal antibodies specific for Sus scrofa AMH (CEA228Po, Cloud-clone). Sperm quality (concentration, motility, viability, and acrosome damage) and functionality (membrane lipid disorder and intracellular H2O2 generation) were assessed in semen samples at 0 and 72 h of liquid-storage. In addition, fertility parameters from 3113 sows inseminated with the AI-boars were recorded in terms of farrowing rate, litter size, number of stillbirths per litter, and the duration of pregnancy over a 12-month period. The results revealed that the SP-AMH concentration varied widely among boar ejaculates, with no differences among breeds. Moreover, the SP-AMH concentration proved to be a good predictive biomarker for sperm concentration (p ˂ 0.05), but poor for other sperm quality, functionality, and in vivo fertility parameters of liquid-stored semen samples from AI-boars. Full article
(This article belongs to the Section Cell Biology)
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16 pages, 1019 KiB  
Review
Oxidative Stress in Male Infertility: Causes, Effects in Assisted Reproductive Techniques, and Protective Support of Antioxidants
by Jordi Ribas-Maynou and Marc Yeste
Biology 2020, 9(4), 77; https://doi.org/10.3390/biology9040077 - 10 Apr 2020
Cited by 56 | Viewed by 8941
Abstract
The spermatozoon is a highly specialized cell, whose main function is the transport of the intact male genetic material into the oocyte. During its formation and transit throughout male and female reproductive tracts, sperm cells are internally and externally surrounded by reactive oxygen [...] Read more.
The spermatozoon is a highly specialized cell, whose main function is the transport of the intact male genetic material into the oocyte. During its formation and transit throughout male and female reproductive tracts, sperm cells are internally and externally surrounded by reactive oxygen species (ROS), which are produced from both endogenous and exogenous sources. While low amounts of ROS are known to be necessary for crucial physiological sperm processes, such as acrosome reaction and sperm–oocyte interaction, high levels of those species underlie misbalanced antioxidant-oxidant molecules, generating oxidative stress (OS), which is one of the most damaging factors that affect sperm function and lower male fertility potential. The present work starts by reviewing the different sources of oxidative stress that affect sperm cells, continues by summarizing the detrimental effects of OS on the male germline, and discusses previous studies addressing the consequences of these detrimental effects on natural pregnancy and assisted reproductive techniques effectiveness. The last section is focused on how antioxidants can counteract the effects of ROS and how sperm fertilizing ability may benefit from these agents. Full article
(This article belongs to the Special Issue Oxidative Stress in Gametes and Embryos)
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27 pages, 5189 KiB  
Article
Molecular Identification and Evaluation of the Genetic Diversity of Dendrobium Species Collected in Southern Vietnam
by Nhu-Hoa Nguyen, Huyen-Trang Vu, Ngoc-Diep Le, Thanh-Diem Nguyen, Hoa-Xo Duong and Hoang-Dung Tran
Biology 2020, 9(4), 76; https://doi.org/10.3390/biology9040076 - 10 Apr 2020
Cited by 10 | Viewed by 4637
Abstract
Dendrobium has been widely used not only as ornamental plants but also as food and medicines. The identification and evaluation of the genetic diversity of Dendrobium species support the conservation of genetic resources of endemic Dendrobium species. Uniquely identifying Dendrobium species used as [...] Read more.
Dendrobium has been widely used not only as ornamental plants but also as food and medicines. The identification and evaluation of the genetic diversity of Dendrobium species support the conservation of genetic resources of endemic Dendrobium species. Uniquely identifying Dendrobium species used as medicines helps avoid misuse of medicinal herbs. However, it is challenging to identify Dendrobium species morphologically during their immature stage. Based on the DNA barcoding method, it is now possible to efficiently identify species in a shorter time. In this study, the genetic diversity of 76 Dendrobium samples from Southern Vietnam was investigated based on the ITS (Internal transcribed spacer), ITS2, matK (Maturase_K), rbcL (ribulose-bisphosphate carboxylase large subunit) and trnH-psbA (the internal space of the gene coding histidine transfer RNA (trnH) and gene coding protein D1, a polypeptide of the photosystem I reaction center (psaB)) regions. The ITS region was found to have the best identification potential. Nineteen out of 24 Dendrobium species were identified based on phylogenetic tree and Indel information of this region. Among these, seven identified species were used as medicinal herbs. The results of this research contributed to the conservation, propagation, and hybridization of indigenous Dendrobium species in Southern Vietnam. Full article
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15 pages, 463 KiB  
Article
Polymorphisms in Interleukin 13 Signaling and Interacting Genes Predict Advanced Fibrosis and Hepatocellular Carcinoma Development in Non-Alcoholic Steatohepatitis
by Marwa O. El-Derany
Biology 2020, 9(4), 75; https://doi.org/10.3390/biology9040075 - 9 Apr 2020
Cited by 18 | Viewed by 3733
Abstract
Background: non-alcoholic steatohepatitis (NASH) recently headlined hepatocellular carcinoma (HCC) worldwide. This study aims to unveil the role of some unaddressed critical players that might aid in understanding, predicting, and targeting NASH and NASH-HCC. Methods: Serum interleukin 13 (IL-13) levels and single nucleotide polymorphisms [...] Read more.
Background: non-alcoholic steatohepatitis (NASH) recently headlined hepatocellular carcinoma (HCC) worldwide. This study aims to unveil the role of some unaddressed critical players that might aid in understanding, predicting, and targeting NASH and NASH-HCC. Methods: Serum interleukin 13 (IL-13) levels and single nucleotide polymorphisms (SNPs) within interleukin (IL)-13 rs20541, IL-13 receptors (IL-13R1) rs2248841, (IL-13R2) rs5946040, signal transducer activator of transcription 6 (STAT6) rs167769, yes-associated protein (YAP1) rs11225163, programmed death-ligand 1 (PD-L1) rs2282055, and programmed death-ligand 2 (PD-L2) rs7854413 genes were analyzed by qRT-PCR. Multiple stepwise regression analysis was performed on a cohort of 134 Egyptian male patients diagnosed with NASH and NASH-HCC. RESULTS: higher serum alpha-fetoprotein (AFP) and higher serum IL-13 levels were directly associated with HCC development in NASH (odds ratio (OR) 19.6 and 1.9 p < 0.01). Reversibly, the presence of the C/C genotype in STAT6 rs167769 and the C allele carrier YAP1 rs11225163 were inversely associated with HCC in NASH patients (OR 0.015 and 0.047 p < 0.01). A predictive model was formulated with 97.5% specificity, 90.9% sensitivity, and 94.8% accuracy. Moreover, higher serum IL-13 levels and the presence of PD-L2 rs7854413 C allele carriers were associated with advanced fibrosis progression in NASH patients (OR 1.432 and 3.797 p < 0.01). Serum levels of IL-13 and C/C genotype in STAT6 rs167769 significantly increased the predictive capacity of serum AFP to predict HCC in F1–F2 and in F3–F4 fibrosis grades NASH patients. Conclusion: association between serum IL-13 and PD-L2 rs7854413 polymorphism successfully predict advanced fibrosis in NASH. However, HCC development in NASH is associated with higher serum AFP, IL-13 levels, and STAT6 rs167769, YAP1 rs11225163 polymorphisms. Full article
(This article belongs to the Special Issue Non-alcoholic Liver Injury)
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21 pages, 9767 KiB  
Article
The Efficacy of Sunitinib Treatment of Renal Cancer Cells Is Associated with the Protein PHAX In Vitro
by Rafia S. Al-Lamki, Nicholas J. Hudson, John R. Bradley, Anne Y. Warren, Tim Eisen, Sarah J. Welsh, Antony C. P. Riddick, Fiach C. O’Mahony, Arran Turnbull, Thomas Powles, SCOTRRCC Collaborative, Antonio Reverter, David J. Harrison and Grant D. Stewart
Biology 2020, 9(4), 74; https://doi.org/10.3390/biology9040074 - 7 Apr 2020
Cited by 1 | Viewed by 3415
Abstract
Anti-angiogenic agents, such as the multi-tyrosine kinase inhibitor sunitinib, are key first line therapies for metastatic clear cell renal cell carcinoma (ccRCC), but their mechanism of action is not fully understood. Here, we take steps towards validating a computational prediction based on differential [...] Read more.
Anti-angiogenic agents, such as the multi-tyrosine kinase inhibitor sunitinib, are key first line therapies for metastatic clear cell renal cell carcinoma (ccRCC), but their mechanism of action is not fully understood. Here, we take steps towards validating a computational prediction based on differential transcriptome network analysis that phosphorylated adapter RNA export protein (PHAX) is associated with sunitinib drug treatment. The regulatory impact factor differential network algorithm run on patient tissue samples suggests PHAX is likely an important regulator through changes in genome-wide network connectivity. Immunofluorescence staining of patient tumours showed strong localisation of PHAX to the microvasculature consistent with the anti-angiogenic effect of sunitinib. In normal kidney tissue, PHAX protein abundance was low but increased with tumour grade (G1 vs. G3/4; p < 0.01), consistent with a possible role in cancer progression. In organ culture, ccRCC cells had higher levels of PHAX protein expression than normal kidney cells, and sunitinib increased PHAX protein expression in a dose dependent manner (untreated vs. 100 µM; p < 0.05). PHAX knockdown in a ccRCC organ culture model impacted the ability of sunitinib to cause cancer cell death (p < 0.0001 untreated vs. treated), suggesting a role for PHAX in mediating the efficacy of sunitinib. Full article
(This article belongs to the Section Medical Biology)
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28 pages, 15591 KiB  
Article
Spaghetti to a Tree: A Robust Phylogeny for Terebelliformia (Annelida) Based on Transcriptomes, Molecular and Morphological Data
by Josefin Stiller, Ekin Tilic, Vincent Rousset, Fredrik Pleijel and Greg W. Rouse
Biology 2020, 9(4), 73; https://doi.org/10.3390/biology9040073 - 6 Apr 2020
Cited by 44 | Viewed by 8336
Abstract
Terebelliformia—“spaghetti worms” and their allies—are speciose and ubiquitous marine annelids but our understanding of how their morphological and ecological diversity evolved is hampered by an uncertain delineation of lineages and their phylogenetic relationships. Here, we analyzed transcriptomes of 20 terebelliforms and an outgroup [...] Read more.
Terebelliformia—“spaghetti worms” and their allies—are speciose and ubiquitous marine annelids but our understanding of how their morphological and ecological diversity evolved is hampered by an uncertain delineation of lineages and their phylogenetic relationships. Here, we analyzed transcriptomes of 20 terebelliforms and an outgroup to build a robust phylogeny of the main lineages grounded on 12,674 orthologous genes. We then supplemented this backbone phylogeny with a denser sampling of 121 species using five genes and 90 morphological characters to elucidate fine-scale relationships. The monophyly of six major taxa was supported: Pectinariidae, Ampharetinae, Alvinellidae, Trichobranchidae, Terebellidae and Melinninae. The latter, traditionally a subfamily of Ampharetidae, was unexpectedly the sister to Terebellidae, and hence becomes Melinnidae, and Ampharetinae becomes Ampharetidae. We found no support for the recently proposed separation of Telothelepodidae, Polycirridae and Thelepodidae from Terebellidae. Telothelepodidae was nested within Thelepodinae and is accordingly made its junior synonym. Terebellidae contained the subfamily-ranked taxa Terebellinae and Thelepodinae. The placement of the simplified Polycirridae within Terebellinae differed from previous hypotheses, warranting the division of Terebellinae into Lanicini, Procleini, Terebellini and Polycirrini. Ampharetidae (excluding Melinnidae) were well-supported as the sister group to Alvinellidae and we recognize three clades: Ampharetinae, Amaginae and Amphicteinae. Our analysis found several paraphyletic genera and undescribed species. Morphological transformations on the phylogeny supported the hypothesis of an ancestor that possessed both branchiae and chaetae, which is at odds with proposals of a “naked” ancestor. Our study demonstrates how a robust backbone phylogeny can be combined with dense taxon coverage and morphological traits to give insights into the evolutionary history and transformation of traits. Full article
(This article belongs to the Section Zoology)
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14 pages, 325 KiB  
Review
The Role of Prenatal Melatonin in the Regulation of Childhood Obesity
by Dmitry O. Ivanov, Inna I. Evsyukova, Gianluigi Mazzoccoli, George Anderson, Victoria O. Polyakova, Igor M. Kvetnoy, Annalucia Carbone and Ruslan A. Nasyrov
Biology 2020, 9(4), 72; https://doi.org/10.3390/biology9040072 - 5 Apr 2020
Cited by 21 | Viewed by 5599
Abstract
There is a growing awareness that pregnancy can set the foundations for an array of diverse medical conditions in the offspring, including obesity. A wide assortment of factors, including genetic, epigenetic, lifestyle, and diet can influence foetal outcomes. This article reviews the role [...] Read more.
There is a growing awareness that pregnancy can set the foundations for an array of diverse medical conditions in the offspring, including obesity. A wide assortment of factors, including genetic, epigenetic, lifestyle, and diet can influence foetal outcomes. This article reviews the role of melatonin in the prenatal modulation of offspring obesity. A growing number of studies show that many prenatal risk factors for poor foetal metabolic outcomes, including gestational diabetes and night-shift work, are associated with a decrease in pineal gland-derived melatonin and associated alterations in the circadian rhythm. An important aspect of circadian melatonin’s effects is mediated via the circadian gene, BMAL1, including in the regulation of mitochondrial metabolism and the mitochondrial melatoninergic pathway. Alterations in the regulation of mitochondrial metabolic shifts between glycolysis and oxidative phosphorylation in immune and glia cells seem crucial to a host of human medical conditions, including in the development of obesity and the association of obesity with the risk of other medical conditions. The gut microbiome is another important hub in the pathoetiology and pathophysiology of many medical conditions, with negative consequences mediated by a decrease in the short-chain fatty acid, butyrate. The effects of butyrate are partly mediated via an increase in the melatoninergic pathway, indicating interactions of the gut microbiome with melatonin. Some of the effects of melatonin seem mediated via the alpha 7 nicotinic receptor, whilst both melatonin and butyrate may regulate obesity through the opioidergic system. Oxytocin, a recently recognized inhibitor of obesity, may also be acting via the opioidergic system. The early developmental regulation of these processes and factors by melatonin are crucial to the development of obesity and many diverse comorbidities. Full article
(This article belongs to the Section Medical Biology)
19 pages, 2834 KiB  
Article
Knockdown of N-Acetylglucosaminyltransferase-II Reduces Matrix Metalloproteinase 2 Activity and Suppresses Tumorigenicity in Neuroblastoma Cell Line
by M. Kristen Hall, Austin A. Whitman, Douglas A. Weidner and Ruth A. Schwalbe
Biology 2020, 9(4), 71; https://doi.org/10.3390/biology9040071 - 4 Apr 2020
Cited by 6 | Viewed by 2896
Abstract
Neuroblastoma (NB) development and progression are accompanied by changes in N-glycans attached to proteins. Here, we investigated the role of N-acetylglucosaminyltransferase-II (GnTII, MGAT2) protein substrates in neuroblastoma (NB) cells. MGAT2 was silenced in human BE(2)-C NB (HuNB) cells to generate a novel [...] Read more.
Neuroblastoma (NB) development and progression are accompanied by changes in N-glycans attached to proteins. Here, we investigated the role of N-acetylglucosaminyltransferase-II (GnTII, MGAT2) protein substrates in neuroblastoma (NB) cells. MGAT2 was silenced in human BE(2)-C NB (HuNB) cells to generate a novel cell line, HuNB(-MGAT2), lacking complex type N-glycans, as in rat B35 NB cells. Changes in N-glycan types were confirmed by lectin binding assays in both cell lines, and the rescued cell line, HuNB(-/+MGAT2). Western blotting of cells heterologously expressing a voltage-gated K+ channel (Kv3.1b) showed that some hybrid N-glycans of Kv3.1b could be processed to complex type in HuNB(-/+MGAT2) cells. In comparing HuNB and HuNB(-MGAT2) cells, decreased complex N-glycans reduced anchorage-independent cell growth, cell proliferation, and cell invasiveness, while they enhanced cell-cell interactions. Cell proliferation, invasiveness and adhesion of the HuNB(-/+MGAT2) cells were more like the HuNB than HuNB(-MGAT2). Western blotting revealed lower protein levels of MMP-2, EGFR and Gab2 in glycosylation mutant cells relative to parental cells. Gelatin zymography demonstrated that decreased MMP-2 protein activity was related to lowered MMP-2 protein levels. Thus, our results support that decreased complex type N-glycans suppress cell proliferation and cell invasiveness in both NB cell lines via remodeling ECM. Full article
(This article belongs to the Section Cell Biology)
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7 pages, 276 KiB  
Opinion
Is It Time to Rethink Our Weight Loss Paradigms?
by Paulo Gentil, Ricardo Borges Viana, João Pedro Naves, Fabrício Boscolo Del Vecchio, Victor Coswig, Jeremy Loenneke and Claudio André Barbosa de Lira
Biology 2020, 9(4), 70; https://doi.org/10.3390/biology9040070 - 2 Apr 2020
Cited by 8 | Viewed by 7647
Abstract
Strategies aiming to promote weight loss usually include anything that results in an increase in energy expenditure (exercise) or a decrease in energy intake (diet). However, the probability of losing weight is low and the probability of sustained weight loss is even lower. [...] Read more.
Strategies aiming to promote weight loss usually include anything that results in an increase in energy expenditure (exercise) or a decrease in energy intake (diet). However, the probability of losing weight is low and the probability of sustained weight loss is even lower. Herein, we bring some questions and suggestions about the topic, with a focus on exercise interventions. Based on the current evidence, we should look at how metabolism changes in response to interventions instead of counting calories, so we can choose more efficient models that can account for the complexity of human organisms. In this regard, high-intensity training might be particularly interesting as a strategy to promote fat loss since it seems to promote many physiological changes that might favor long-term weight loss. However, it is important to recognize the controversy of the results regarding interval training (IT), which might be explained by the large variations in its application. For this reason, we have to be more judicious about how exercise is planned and performed and some factors, like supervision, might be important for the results. The intensity of exercise seems to modulate not only how many calories are expended after exercise, but also where they came from. Instead of only estimating the number of calories ingested and expended, it seems that we have to act positively in order to create an adequate environment for promoting healthy and sustainable weight loss. Full article
(This article belongs to the Section Physiology)
19 pages, 5401 KiB  
Article
Isolation and Identification of Fusarium spp., the Causal Agents of Onion (Allium cepa) Basal Rot in Northeastern Israel
by Ben Kalman, Dekel Abraham, Shaul Graph, Rafael Perl-Treves, Yael Meller Harel and Ofir Degani
Biology 2020, 9(4), 69; https://doi.org/10.3390/biology9040069 - 2 Apr 2020
Cited by 46 | Viewed by 12227
Abstract
Over the past decade, there have been accumulating reports from farmers and field extension personnel on the increasing incidence and spread of onion (Allium cepa) bulb basal rot in northern Israel. The disease is caused mainly by Fusarium species. Rotting onion [...] Read more.
Over the past decade, there have been accumulating reports from farmers and field extension personnel on the increasing incidence and spread of onion (Allium cepa) bulb basal rot in northern Israel. The disease is caused mainly by Fusarium species. Rotting onion bulbs were sampled from fields in the Golan Heights in northeastern Israel during the summers of 2017 and 2018. Tissue from the sampled onion bulbs was used for the isolation and identification of the infecting fungal species using colony and microscopic morphology characterization. Final confirmation of the pathogens was performed with PCR amplification and sequencing using fungi-specific and Fusarium species-specific primers. Four Fusarium spp. isolates were identified in onion bulbs samples collected from the contaminated field: F. proliferatum, F. oxysporum f. sp. cepae, and two species less familiar as causative agents of this disease, F. acutatum and F. anthophilium. Phylogenetic analysis revealed that these species subdivided into two populations, a northern group isolated from white (Riverside cv.) onion bulbs, and a southern group isolated from red (565/505 cv.) bulbs. Pathogenicity tests conducted with seedlings and bulbs under moist conditions proved that all species could cause the disease symptoms, but with different degrees of virulence. Inoculating seeds with spore suspensions of the four species, in vitro, significantly reduced seedlings’ germination rate, hypocotyl elongation, and fresh biomass. Mature onion bulbs infected with the fungal isolates produced typical rot symptoms 14 days post-inoculation, and the fungus from each infected bulb was re-isolated and identified to satisfy Koch’s postulates. The onion bulb assay also reflected the degree of sensitivity of different onion cultivars to the disease. This work is the first confirmed report of the direct and primary cause of Fusarium onion basal rot disease in northeastern Israel. These findings are a necessary step towards uncovering the mycoflora of the diseased onion plants and developing a preventive program that would reduce the disease damage. Full article
(This article belongs to the Special Issue Plant-Pathogen Interaction)
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14 pages, 3050 KiB  
Article
Estrogen Signaling Induces Mitochondrial Dysfunction-Associated Autophagy and Senescence in Breast Cancer Cells
by Khuloud Bajbouj, Jasmin Shafarin, Jalal Taneera and Mawieh Hamad
Biology 2020, 9(4), 68; https://doi.org/10.3390/biology9040068 - 1 Apr 2020
Cited by 9 | Viewed by 4225
Abstract
Previous work has shown that although estrogen (E2) disrupts cellular iron metabolism and induces oxidative stress in breast and ovarian cancer cells, it fails to induce apoptosis. However, E2 treatment was reported to enhance the apoptotic effects of doxorubicin in cancer cells. This [...] Read more.
Previous work has shown that although estrogen (E2) disrupts cellular iron metabolism and induces oxidative stress in breast and ovarian cancer cells, it fails to induce apoptosis. However, E2 treatment was reported to enhance the apoptotic effects of doxorubicin in cancer cells. This suggests that E2 can precipitate anti-growth effects that render cancer cells more susceptible to chemotherapy. To investigate such anti-growth non-apoptotic, effects of E2 in cancer cells, MDA-MB-231 and MCF-7 cells were evaluated for the expression of key autophagy and senescence markers and for mitochondrial damage following E2 treatment. Treated cells experienced mitochondrial membrane depolarization along with increased expression of LC3-I/II, Pink1 and LAMP2, increased LC3-II accumulation and increased lysosomal and mitochondrial accumulation and flattening. E2-treated MCF-7 cells also showed reduced P53 and pRb780 expression and increased Rb and P21 expression. Increased expression of the autophagy markers ATG3 and Beclin1 along with increased levels of β-galactosidase activity and IL-6 production were evident in E2-treated MCF-7 cells. These findings suggest that E2 precipitates a form of mitochondrial damage that leads to cell senescence and autophagy in breast cancer cells. Full article
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12 pages, 1387 KiB  
Article
Tumor-infiltrating Leukocytes Suppress Local Inflammation Via Interleukin-1 Receptor Antagonist in a Syngeneic Prostate Cancer Model
by Yu-Ching Fan, Wei-Yu Chen, Kuan-Der Lee and Yuan-Chin Tsai
Biology 2020, 9(4), 67; https://doi.org/10.3390/biology9040067 - 31 Mar 2020
Cited by 6 | Viewed by 3539
Abstract
Background: Several lines of evidence have demonstrated the tumor-promoting function of inflammation. Since many chemokines are important in coordinating immune cells during inflammation, monitoring intratumoral chemokines provides a way to study the tumor microenvironment. Methods: To identify tumorigenic chemokines, we compared two syngeneic [...] Read more.
Background: Several lines of evidence have demonstrated the tumor-promoting function of inflammation. Since many chemokines are important in coordinating immune cells during inflammation, monitoring intratumoral chemokines provides a way to study the tumor microenvironment. Methods: To identify tumorigenic chemokines, we compared two syngeneic mouse prostate cancer cell lines by an antibody array and quantitative reverse-transcription polymerase chain reaction (RT-PCR). The tumor microenvironment was analyzed by monitoring gene expressions in mouse tumor tissues, primary cells, and tumor-infiltrating leukocytes (TILs). Result: We identified a group of pro-inflammatory chemokines associated with a tumorigenic transgenic adenocarcinoma mouse prostate (TRAMP)-C1 cell line. In the tumor microenvironment, the TILs secrete a natural anti-inflammatory factor, interleukin-1 receptor antagonist (IL1RN), which inhibits the functions of pro-inflammatory molecules and likely accounts for tumor type-specific anti-inflammation functions. Conclusion: Our results support that tumor cells recruit TILs by pro-inflammatory chemokines to establish an IL1RN-mediated anti-inflammatory environment in the syngeneic prostate cancer model. Full article
(This article belongs to the Section Immunology)
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12 pages, 2665 KiB  
Article
Role of PA2G4P4 pseudogene in bladder cancer tumorigenesis
by Laura Pisapia, Sara Terreri, Pasquale Barba, Marianna Mastroianni, Maria Donnini, Vincenzo Mercadante, Alessandro Palmieri, Paolo Verze, Vincenzo Mirone, Vincenzo Altieri, Gianluigi Califano, Giovanna Lucia Liguori, Maria Strazzullo, Amelia Cimmino and Giovanna Del Pozzo
Biology 2020, 9(4), 66; https://doi.org/10.3390/biology9040066 - 31 Mar 2020
Cited by 6 | Viewed by 3177
Abstract
Background: Many pseudogenes possess biological activities and play important roles in the pathogenesis of various types of cancer including bladder cancer (BlCa), which still lacks suitable molecular biomarkers. Recently, pseudogenes were found to be significantly enriched in a pan-cancer classification based on the [...] Read more.
Background: Many pseudogenes possess biological activities and play important roles in the pathogenesis of various types of cancer including bladder cancer (BlCa), which still lacks suitable molecular biomarkers. Recently, pseudogenes were found to be significantly enriched in a pan-cancer classification based on the Cancer Genome Atlas gene expression data. Among them, the top-ranking pseudogene was the proliferation-associated 2G4 pseudogene 4 (PA2G4P4). Methods: Genomic and transcript features of PA2G4P4 were determined by GeneBank database analysis followed by 5’ RACE experiments. Therefore, we conducted a retrospective molecular study on a cohort of 45 patients of BlCa. PA2G4P4 expression was measured by RT-qPCR, whereas PA2G4P4 transcript distribution was analyzed by in situ hybridization on both normal and cancerous histological sections and compared to the immunolocalization of its parental PA2G4/EBP1 protein. Finally, we tested the effects of PA2G4P4 depletion on proliferation, migration, and death of BlCa cells. Results: We showed for the first time PA2G4P4 overexpression in BlCa tissues and in cell lines. PA2G4P4 distribution strictly overlaps PA2G4/EBP1 protein localization. Moreover, we showed that PA2G4P4 knockdown affects both proliferation and migration of BlCa cells, highlighting its potential oncogenic role. Conclusions: PA2G4P4 may play a functional role as an oncogene in BlCa development, suggesting it as a good candidate for future investigation and new clinical applications. Full article
(This article belongs to the Section Cell Biology)
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15 pages, 1151 KiB  
Review
Osteoarthritis and Toll-Like Receptors: When Innate Immunity Meets Chondrocyte Apoptosis
by Goncalo Barreto, Mikko Manninen and Kari K. Eklund
Biology 2020, 9(4), 65; https://doi.org/10.3390/biology9040065 - 30 Mar 2020
Cited by 71 | Viewed by 8678
Abstract
Osteoarthritis (OA) has long been viewed as a degenerative disease of cartilage, but accumulating evidence indicates that inflammation has a critical role in its pathogenesis. In particular, chondrocyte-mediated inflammatory responses triggered by the activation of innate immune receptors by alarmins (also known as [...] Read more.
Osteoarthritis (OA) has long been viewed as a degenerative disease of cartilage, but accumulating evidence indicates that inflammation has a critical role in its pathogenesis. In particular, chondrocyte-mediated inflammatory responses triggered by the activation of innate immune receptors by alarmins (also known as danger signals) are thought to be involved. Thus, toll-like receptors (TLRs) and their signaling pathways are of particular interest. Recent reports suggest that among the TLR-induced innate immune responses, apoptosis is one of the critical events. Apoptosis is of particular importance, given that chondrocyte death is a dominant feature in OA. This review focuses on the role of TLR signaling in chondrocytes and the role of TLR activation in chondrocyte apoptosis. The functional relevance of TLR and TLR-triggered apoptosis in OA are discussed as well as their relevance as candidates for novel disease-modifying OA drugs (DMOADs). Full article
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32 pages, 1775 KiB  
Article
Phylogenetic Analyses of Sites in Different Protein Structural Environments Result in Distinct Placements of the Metazoan Root
by Akanksha Pandey and Edward L. Braun
Biology 2020, 9(4), 64; https://doi.org/10.3390/biology9040064 - 28 Mar 2020
Cited by 21 | Viewed by 5635
Abstract
Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the [...] Read more.
Phylogenomics, the use of large datasets to examine phylogeny, has revolutionized the study of evolutionary relationships. However, genome-scale data have not been able to resolve all relationships in the tree of life; this could reflect, at least in part, the poor-fit of the models used to analyze heterogeneous datasets. Some of the heterogeneity may reflect the different patterns of selection on proteins based on their structures. To test that hypothesis, we developed a pipeline to divide phylogenomic protein datasets into subsets based on secondary structure and relative solvent accessibility. We then tested whether amino acids in different structural environments had distinct signals for the topology of the deepest branches in the metazoan tree. We focused on a dataset that appeared to have a mixture of signals and we found that the most striking difference in phylogenetic signal reflected relative solvent accessibility. Analyses of exposed sites (residues located on the surface of proteins) yielded a tree that placed ctenophores sister to all other animals whereas sites buried inside proteins yielded a tree with a sponge+ctenophore clade. These differences in phylogenetic signal were not ameliorated when we conducted analyses using a set of maximum-likelihood profile mixture models. These models are very similar to the Bayesian CAT model, which has been used in many analyses of deep metazoan phylogeny. In contrast, analyses conducted after recoding amino acids to limit the impact of deviations from compositional stationarity increased the congruence in the estimates of phylogeny for exposed and buried sites; after recoding amino acid trees estimated using the exposed and buried site both supported placement of ctenophores sister to all other animals. Although the central conclusion of our analyses is that sites in different structural environments yield distinct trees when analyzed using models of protein evolution, our amino acid recoding analyses also have implications for metazoan evolution. Specifically, our results add to the evidence that ctenophores are the sister group of all other animals and they further suggest that the placozoa+cnidaria clade found in some other studies deserves more attention. Taken as a whole, these results provide striking evidence that it is necessary to achieve a better understanding of the constraints due to protein structure to improve phylogenetic estimation. Full article
(This article belongs to the Special Issue Feature Papers 2019)
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12 pages, 585 KiB  
Review
Contribution of Neurotrophins to the Immune System Regulation and Possible Connection to Alcohol Addiction
by Evgenii M. Kozlov, Andrey V. Grechko, Yegor S. Chegodaev, Wei-Kai Wu and Alexander N. Orekhov
Biology 2020, 9(4), 63; https://doi.org/10.3390/biology9040063 - 28 Mar 2020
Cited by 13 | Viewed by 4457
Abstract
The first references to neurotrophic factors date back to the middle of the 20th century when the nerve growth factor (NGF) was first discovered. Later studies delivered a large amount of data on neurotrophic factors. However, many questions regarding neurotrophin signaling still remain [...] Read more.
The first references to neurotrophic factors date back to the middle of the 20th century when the nerve growth factor (NGF) was first discovered. Later studies delivered a large amount of data on neurotrophic factors. However, many questions regarding neurotrophin signaling still remain unanswered. One of the principal topics in neurotrophin research is their role in the immune system regulation. Another important research question is the possible involvement of neurotrophin signaling in the pathological processes associated with alcoholism. Among known neurotrophins, NT-4 remains the least studied and appears to be involved in alcoholism and chronic stress pathogenesis. In this review we discuss known neurotrophin signaling cascades mediated by different neurotrophin receptors, as well as provide a generalization of the data regarding the influence of neurotrophins NGF, BDNF, and NT-4 on the immune system and their potential contribution to the pathogenesis of alcoholism. Full article
(This article belongs to the Section Cell Biology)
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19 pages, 3469 KiB  
Review
A Review of Candidate Genes and Pathways in Preeclampsia–An Integrated Bioinformatical Analysis
by Muhammad Aliff Mohamad, Nur Fariha Mohd Manzor, Noor Fadzilah Zulkifli, Nurzaireena Zainal, Abd Rahman Hayati and Asral Wirda Ahmad Asnawi
Biology 2020, 9(4), 62; https://doi.org/10.3390/biology9040062 - 27 Mar 2020
Cited by 16 | Viewed by 4772
Abstract
Preeclampsia is a pregnancy-specific disorder characterized by the presence of hypertension with the onset of either proteinuria, maternal organ or uteroplacental dysfunction. Preeclampsia is one of the leading causes of maternal and fetal mortality and morbidity worldwide. However, the etiopathologies of preeclampsia are [...] Read more.
Preeclampsia is a pregnancy-specific disorder characterized by the presence of hypertension with the onset of either proteinuria, maternal organ or uteroplacental dysfunction. Preeclampsia is one of the leading causes of maternal and fetal mortality and morbidity worldwide. However, the etiopathologies of preeclampsia are not fully understood. Many studies have indicated that genes are differentially expressed between normal and in the disease state. Hence, this study systematically searched the literature on human gene expression that was differentially expressed in preeclampsia. An electronic search was performed through 2019 through PubMed, Scopus, Ovid-Medline, and Gene Expression Omnibus where the following MeSH (Medical Subject Heading) terms were used and they had been specified as the primary focus of the articles: Gene, placenta, preeclampsia, and pregnancy in the title or abstract. We also found additional MeSH terms through Cochrane Library: Transcript, sequencing, and profiling. From 687 studies retrieved from the search, only original publications that had performed high throughput sequencing of human placental tissues that reported on differentially expressed genes in pregnancies with preeclampsia were included. Two reviewers independently scrutinized the titles and abstracts before examining the eligibility of studies that met the inclusion criteria. For each study, study design, sample size, sampling type, and method for gene analysis and gene were identified. The genes listed were further analyzed with the DAVID, STRING and Cytoscape MCODE. Three original research articles involving preeclampsia comprising the datasets in gene expression were included. By combining three studies together, 250 differentially expressed genes were produced at a significance setting of p < 0.05. We identified candidate genes: LEP, NRIP1, SASH1, and ZADHHC8P1. Through GO analysis, we found extracellular matrix organization as the highly significant enriched ontology in a group of upregulated genes and immune process in downregulated genes. Studies on a genetic level have the potential to provide new insights into the regulation and to widen the basis for identification of changes in the mechanism of preeclampsia. Integrated bioinformatics could identify differentially expressed genes which could be candidate genes and potential pathways in preeclampsia that may improve our understanding of the cause and underlying molecular mechanisms that could be used as potential biomarkers for risk stratification and treatment. Full article
(This article belongs to the Section Genetics and Genomics)
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