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Biology, Volume 9, Issue 5 (May 2020) – 24 articles

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Cover Story (view full-size image) 5-FU-based chemotherapy remains the mainstay for colorectal cancer (CRC) treatment. However, cancer [...] Read more.
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Open AccessArticle
A New IL6 Isoform in Chinese Soft-Shelled Turtle (Pelodiscus sinesis) Discovered: Its Regulation during Cold Stress and Infection
Biology 2020, 9(5), 111; https://doi.org/10.3390/biology9050111 - 25 May 2020
Viewed by 413
Abstract
The Chinese soft-shelled turtle (Pelodiscus sinesis) is a widely cultured commercial species in East and Southeast Asian countries. The turtles frequently suffer from acute cold stress during farming in China. Stress-induced factor such as Interleukin-6 (IL6) is a multifunctional molecule that [...] Read more.
The Chinese soft-shelled turtle (Pelodiscus sinesis) is a widely cultured commercial species in East and Southeast Asian countries. The turtles frequently suffer from acute cold stress during farming in China. Stress-induced factor such as Interleukin-6 (IL6) is a multifunctional molecule that plays important roles in innate and adaptive immune response. In the present study, we found that the turtle possessed two IL6 transcripts, where one IL6 transcript contained a signal peptide sequence (psIL6), while the other IL6 transcript (psIL6ns) possessed no such signal peptide gene. To test any differential expression of the two isoforms during temperature and microbial stress, turtles were adapted to optimal environmental water temperature (25 °C), stressed by acute cooling for 24 h, followed with the challenge of Aeromonas hydrophila (1.8 × 108 CFU) or Staphylococcus aureus (5.8 × 108 CFU). Gene characterization revealed that psIL6ns, a splicer without codons encoding a signal peptide and identical to the one predicted from genomic sequence, and psIL6, a splicer with codons encoding a signal peptide, were both present. Inducible expression was documented in primary spleen cells stimulated with ConA and poly I: C. The splenic and intestinal expression of psIL6ns and psIL6 was increased in response to temperature stress and bacterial infection. Full article
(This article belongs to the Section Evolutionary Biology)
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Open AccessArticle
In Silico Identification of Type III PKS Chalcone and Stilbene Synthase Homologs in Marine Photosynthetic Organisms
Biology 2020, 9(5), 110; https://doi.org/10.3390/biology9050110 - 22 May 2020
Viewed by 432
Abstract
Marine microalgae are photosynthetic microorganisms at the base of the marine food webs. They are characterized by huge taxonomic and metabolic diversity and several species have been shown to have bioactivities useful for the treatment of human pathologies. However, the compounds and the [...] Read more.
Marine microalgae are photosynthetic microorganisms at the base of the marine food webs. They are characterized by huge taxonomic and metabolic diversity and several species have been shown to have bioactivities useful for the treatment of human pathologies. However, the compounds and the metabolic pathways responsible for bioactive compound synthesis are often still unknown. In this study, we aimed at analysing the microalgal transcriptomes available in the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) database for an in silico search of polyketide synthase type III homologs and, in particular, chalcone synthase (CHS) and stilbene synthase (STS), which are often referred to as the CHS/STS family. These enzymes were selected because they are known to produce compounds with biological properties useful for human health, such as cancer chemopreventive, anti-inflammatory, antioxidant, anti-angiogenic, anti-viral and anti-diabetic. In addition, we also searched for 4-Coumarate: CoA ligase, an upstream enzyme in the synthesis of chalcones and stilbenes. This study reports for the first time the occurrence of these enzymes in specific microalgal taxa, confirming the importance for microalgae of these pathways and giving new insights into microalgal physiology and possible biotechnological applications for the production of bioactive compounds. Full article
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Open AccessReview
Brain Control Reproduction by the Endocrine System of Female Blue Gourami (Trichogaster trichopterus)
Biology 2020, 9(5), 109; https://doi.org/10.3390/biology9050109 - 21 May 2020
Viewed by 360
Abstract
Blue gourami belongs to the Labyrinithici fish and the Anabantiform order. It is characterized by a specific organ located above its gills for the respiration of atmospheric oxygen. This specific adaptation to low oxygen levels affects reproduction that is controlled by the brain, [...] Read more.
Blue gourami belongs to the Labyrinithici fish and the Anabantiform order. It is characterized by a specific organ located above its gills for the respiration of atmospheric oxygen. This specific adaptation to low oxygen levels affects reproduction that is controlled by the brain, which integrates different effects on reproduction mainly through two axes—the gonadotropic brain pituitary gonad axis (BPG) and the hypothalamic-pituitary-somatotropic axis (HPS axis), including the interactions between them. This brain control reproduction of the Anabantoidei suborder summarizes information that has been published on the hormones involved in controlling the reproduction system of a model female blue gourami fish (Trichogaster trichopterus), including unpublished data. In the whole-brain transcriptome of blue gourami, 17 transcription genes change during vitellogenesis in the brain. The hormones involved in reproduction in blue gourami described in the present paper include: Kisspeptin 2 (Kiss 2) and its receptors 1 and 2 (KissR 1 and 2); gonadotropin-releasing hormone 1, 2 and 3 (GnRH1, 2 and 3); GnRH receptor; pituitary adenylate cyclase-activating polypeptide (PACAP) and its related peptide (PRP); somatolactin (SL); follicle-stimulating hormone (FSH); luteinizing hormone (LH); growth hormone (GH); prolactin (PRL), 17β-estradiol (E2); testosterone (T); vitellogenesis (VTL); and 17α,20β- dihydroxy-4-pregnen-3-one (17,20P). A proposed quality model is presented regarding the brain control oogenesis in blue gourami that has a Labyrinth organ about which relatively little information has been published. This paper summarizes the complex various factors involved in the interactions between external and internal elements affecting the brain of fish reproduction in the Anabantiform order. It is suggested to study in the future the involvement of receptors of hormones, pheromones, and genome changes in various organs belonging to the reproduction system during the reproduction cycles about which little is known. Full article
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Open AccessReview
Clinical Genetics of Prolidase Deficiency: An Updated Review
Biology 2020, 9(5), 108; https://doi.org/10.3390/biology9050108 - 21 May 2020
Viewed by 399
Abstract
Prolidase is a ubiquitous enzyme that plays a major role in the metabolism of proline-rich proteins. Prolidase deficiency is a rare autosomal recessive inborn metabolic and multisystemic disease, characterized by a protean association of symptoms, namely intellectual disability, recurrent infections, splenomegaly, skin lesions, [...] Read more.
Prolidase is a ubiquitous enzyme that plays a major role in the metabolism of proline-rich proteins. Prolidase deficiency is a rare autosomal recessive inborn metabolic and multisystemic disease, characterized by a protean association of symptoms, namely intellectual disability, recurrent infections, splenomegaly, skin lesions, auto-immune disorders and cytopenia. To our knowledge, no published review has assembled the different clinical data and research studies over prolidase deficiency. The aim of this study is to summarize the actual state of the art from the descriptions of all the patients with a molecular diagnosis of prolidase deficiency reported to date regarding the clinical, biological, histopathological features, therapeutic options and functional studies. Full article
(This article belongs to the Section Genetics and Genomics)
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Open AccessArticle
Novel Dynamic Structures of 2019-nCoV with Nonlocal Operator via Powerful Computational Technique
Biology 2020, 9(5), 107; https://doi.org/10.3390/biology9050107 - 21 May 2020
Cited by 3 | Viewed by 612
Abstract
In this study, we investigate the infection system of the novel coronavirus (2019-nCoV) with a nonlocal operator defined in the Caputo sense. With the help of the fractional natural decomposition method (FNDM), which is based on the Adomian decomposition and natural transform methods, [...] Read more.
In this study, we investigate the infection system of the novel coronavirus (2019-nCoV) with a nonlocal operator defined in the Caputo sense. With the help of the fractional natural decomposition method (FNDM), which is based on the Adomian decomposition and natural transform methods, numerical results were obtained to better understand the dynamical structures of the physical behavior of 2019-nCoV. Such behaviors observe the general properties of the mathematical model of 2019-nCoV. This mathematical model is composed of data reported from the city of Wuhan, China. Full article
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Open AccessArticle
Evolution of Hemoglobin Genes in a Subterranean Rodent Species (Lasiopodomys mandarinus)
Biology 2020, 9(5), 106; https://doi.org/10.3390/biology9050106 - 20 May 2020
Viewed by 365
Abstract
The Mandarin vole (Lasiopodomys mandarinus), a typical subterranean rodent, has undergone hematological adaptations to tolerate the hypoxic/hypercapnic underground environment. Hemoglobin (Hb) genes encode respiratory proteins functioning principally in oxygen binding and transport to various tissues and organs. To investigate the evolution [...] Read more.
The Mandarin vole (Lasiopodomys mandarinus), a typical subterranean rodent, has undergone hematological adaptations to tolerate the hypoxic/hypercapnic underground environment. Hemoglobin (Hb) genes encode respiratory proteins functioning principally in oxygen binding and transport to various tissues and organs. To investigate the evolution of α- and β-hemoglobin (Hb) in subterranean rodent species, we sequenced Hb genes of the Mandarin vole and the related aboveground Brandt’s vole (L. brandtii). Sequencing showed that in both voles, α-globin was encoded by a cluster of five functional genes in the following linkage order: HBZ, HBA-T1, HBQ-T1, HBA-T2, and HBQ-T2; among these, HBQ-T2 is a pseudogene in both voles. The β-globin gene cluster in both voles also included five functional genes in the following linkage order: HBE, HBE/HBG, HBG, HBB-T1, and HBB-T2. Phylogenetic analysis revealed that the Mandarin vole underwent convergent evolution with its related aboveground species (Brandt’s vole) but not with other subterranean rodent species. Selection pressure analyses revealed that α- and β-globin genes are under strong purifying selection (ω < 1), and branch-site analyses identified positive selection sites on HBAT-T1 and HBB-T1 in different subterranean rodent species. This suggests that the adaptive evolution of these genes enhanced the ability of Hb to store and transport oxygen in subterranean rodent species. Our findings highlight the critical roles of Hb genes in the evolution of hypoxia tolerance in subterranean rodent species. Full article
(This article belongs to the Section Evolutionary Biology)
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Open AccessArticle
Period of Boar Ejaculate Collection Contributes to the Yearly Intra-Male Variability of Seminal Plasma Cytokines
Biology 2020, 9(5), 105; https://doi.org/10.3390/biology9050105 - 20 May 2020
Viewed by 309
Abstract
The concentrations of cytokines in seminal plasma (SP) fluctuate over time in healthy males, weakening their practical usefulness as diagnostic tools. This study evaluated the relevance of intra-male variability in SP cytokines and to what extent the period of the year when ejaculate [...] Read more.
The concentrations of cytokines in seminal plasma (SP) fluctuate over time in healthy males, weakening their practical usefulness as diagnostic tools. This study evaluated the relevance of intra-male variability in SP cytokines and to what extent the period of the year when ejaculate is collected contributes to such variability. 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 the Luminex xMAP® technology for 180 SP samples of ejaculate collected over a year from nine healthy and fertile boars. The SP samples were grouped into two annual periods according to decreasing or increasing daylight and ambient temperature. Intra-male variability was higher than inter-male variability for all cytokines. All SP cytokines showed concentration differences between the two periods of the year, showing the highest concentration during the increasing daylength/temperature period, irrespective of the male. Similarly, some cytokines showed differences between daylength/temperature periods when focusing on their total amount in the ejaculate. No strong relationship (explaining more than 50% of the total variance) was found between annual fluctuations in SP-cytokine levels and semen parameters. In conclusion, the period of the year during which ejaculates were collected helps explain the intra-male variability of SP-cytokine levels in breeding boars. Full article
(This article belongs to the Section Immunology)
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Open AccessArticle
The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts
Biology 2020, 9(5), 104; https://doi.org/10.3390/biology9050104 - 19 May 2020
Viewed by 311
Abstract
As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic [...] Read more.
As the apparent incidence of tree nut allergies rises, the development of MS methods that accurately identify tree nuts in food is critical. However, analyses are limited by few available tree nut protein sequences. We assess the utility of translated genomic and transcriptomic data for library construction with Juglans regia, walnut, as a model. Extracted walnuts were subjected to nano-liquid chromatography–mass spectrometry (n-LC-MS/MS), and spectra were searched against databases made from a six-frame translation of the genome (6FT), a transcriptome, and three proteomes. Searches against proteomic databases yielded a variable number of peptides (1156–1275), and only ten additional unique peptides were identified in the 6FT database. Searches against a transcriptomic database yielded results similar to those of the National Center for Biotechnology Information (NCBI) proteome (1200 and 1275 peptides, respectively). Performance of the transcriptomic database was improved via the adjustment of RNA-Seq read processing methods, which increased the number of identified peptides which align to seed allergen proteins by ~20%. Together, these findings establish a path towards the construction of robust proxy protein databases for tree nut species and other non-model organisms. Full article
(This article belongs to the Special Issue Foodomics: Food Authentication, Processing and Nutrition)
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Open AccessReview
Clinical Features of Parkinson’s Disease: The Evolution of Critical Symptoms
Biology 2020, 9(5), 103; https://doi.org/10.3390/biology9050103 - 19 May 2020
Viewed by 545
Abstract
Parkinson’s disease (PD) is a multi-attribute neurodegenerative disorder combining motor and nonmotor symptoms without well-defined diagnostic clinical markers. The presence of primary motor features (bradykinesia, rest tremor, rigidity and loss of postural reflexes) are the most characteristic signs of PD that are also [...] Read more.
Parkinson’s disease (PD) is a multi-attribute neurodegenerative disorder combining motor and nonmotor symptoms without well-defined diagnostic clinical markers. The presence of primary motor features (bradykinesia, rest tremor, rigidity and loss of postural reflexes) are the most characteristic signs of PD that are also utilized to identify patients in current clinical practice. The successful implementation of levodopa treatment revealed that nonmotor features are the main contributors of patient disability in PD, and their occurrence might be earlier than motor symptoms during disease progression. Targeted detection of prodromal PD symptoms can open up new possibilities in the identification of PD patients and provide potential patient populations for developing novel neuroprotective therapies. In this review, the evolution of critical features in PD diagnosis is described with special attention to nonmotor symptoms and their possible detection. Full article
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Open AccessReview
Magnetotactic Bacteria and Magnetosomes as Smart Drug Delivery Systems: A New Weapon on the Battlefield with Cancer?
Biology 2020, 9(5), 102; https://doi.org/10.3390/biology9050102 - 19 May 2020
Viewed by 402
Abstract
An important direction of research in increasing the effectiveness of cancer therapies is the design of effective drug distribution systems in the body. The development of the new strategies is primarily aimed at improving the stability of the drug after administration and increasing [...] Read more.
An important direction of research in increasing the effectiveness of cancer therapies is the design of effective drug distribution systems in the body. The development of the new strategies is primarily aimed at improving the stability of the drug after administration and increasing the precision of drug delivery to the destination. Due to the characteristic features of cancer cells, distributing chemotherapeutics exactly to the microenvironment of the tumor while sparing the healthy tissues is an important issue here. One of the promising solutions that would meet the above requirements is the use of Magnetotactic bacteria (MTBs) and their organelles, called magnetosomes (BMs). MTBs are commonly found in water reservoirs, and BMs that contain ferromagnetic crystals condition the magnetotaxis of these microorganisms. The presented work is a review of the current state of knowledge on the potential use of MTBs and BMs as nanocarriers in the therapy of cancer. The growing amount of literature data indicates that MTBs and BMs may be used as natural nanocarriers for chemotherapeutics, such as classic anti-cancer drugs, antibodies, vaccine DNA, and siRNA. Their use as transporters increases the stability of chemotherapeutics and allows the transfer of individual ligands or their combinations precisely to cancerous tumors, which, in turn, enables the drugs to reach molecular targets more effectively. Full article
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Open AccessArticle
Comparative Analysis of Porcine Follicular Fluid Proteomes of Small and Large Ovarian Follicles
Biology 2020, 9(5), 101; https://doi.org/10.3390/biology9050101 - 17 May 2020
Viewed by 462
Abstract
Ovarian follicular fluid is widely used for in vitro oocyte maturation, but its in-depth characterization to extract full beneficial effects remains unclear. Here, we performed both shotgun (nanoscale liquid chromatography coupled to tandem mass spectrometry or nanoLC-MS/MS) and gel-based (two dimension-differential in-gel electrophoresis [...] Read more.
Ovarian follicular fluid is widely used for in vitro oocyte maturation, but its in-depth characterization to extract full beneficial effects remains unclear. Here, we performed both shotgun (nanoscale liquid chromatography coupled to tandem mass spectrometry or nanoLC-MS/MS) and gel-based (two dimension-differential in-gel electrophoresis or 2D-DIGE) proteomics, followed by functional bioinformatics to compare the proteomes of follicular fluids collected from small (<4 mm) and large (>6–12 mm) follicles of pig ovaries. A total of 2321 unique spots were detected with the 2D-DIGE across small and large follicles, while 2876 proteins with 88% successful annotations were detected with the shotgun approach. The shotgun and 2D-DIGE approaches revealed about 426 and 300 proteins that were respectively common across samples. Six proteins detected with both technical approaches were significantly differently expressed between small and large follicles. Pathways such as estrogen and PI3K-Akt signaling were significantly enriched in small follicles while the complement and coagulation cascades pathways were significantly represented in large follicles. Up-regulated proteins in small follicles were in favor of oocyte maturation, while those in large follicles were involved in the ovulatory process preparation. Few proteins with potential roles during sperm–oocyte interactions were especially detected in FF of large follicles and supporting the potential role of the ovarian FF on the intrafallopian sperm migration and interaction with the oocyte. Full article
(This article belongs to the Section Proteomics)
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Open AccessArticle
De-Escalation by Reversing the Escalation with a Stronger Synergistic Package of Contact Tracing, Quarantine, Isolation and Personal Protection: Feasibility of Preventing a COVID-19 Rebound in Ontario, Canada, as a Case Study
Biology 2020, 9(5), 100; https://doi.org/10.3390/biology9050100 - 16 May 2020
Viewed by 1227
Abstract
Since the beginning of the COVID-19 pandemic, most Canadian provinces have gone through four distinct phases of social distancing and enhanced testing. A transmission dynamics model fitted to the cumulative case time series data permits us to estimate the effectiveness of interventions implemented [...] Read more.
Since the beginning of the COVID-19 pandemic, most Canadian provinces have gone through four distinct phases of social distancing and enhanced testing. A transmission dynamics model fitted to the cumulative case time series data permits us to estimate the effectiveness of interventions implemented in terms of the contact rate, probability of transmission per contact, proportion of isolated contacts, and detection rate. This allows us to calculate the control reproduction number during different phases (which gradually decreased to less than one). From this, we derive the necessary conditions in terms of enhanced social distancing, personal protection, contact tracing, quarantine/isolation strength at each escalation phase for the disease control to avoid a rebound. From this, we quantify the conditions needed to prevent epidemic rebound during de-escalation by simply reversing the escalation process. Full article
(This article belongs to the Special Issue Theories and Models on COVID-19 Epidemics)
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Open AccessArticle
Rigosertib-Activated JNK1/2 Eliminate Tumor Cells through p66Shc Activation
Biology 2020, 9(5), 99; https://doi.org/10.3390/biology9050099 - 15 May 2020
Viewed by 435
Abstract
Rigosertib, via reactive oxygen species (ROS), stimulates cJun N-terminal kinases 1/2 (JNK1/2), which inactivate RAS/RAF signaling and thereby inhibit growth and survival of tumor cells. JNK1/2 are not only regulated by ROS—they in turn can also control ROS production. The prooxidant and cell [...] Read more.
Rigosertib, via reactive oxygen species (ROS), stimulates cJun N-terminal kinases 1/2 (JNK1/2), which inactivate RAS/RAF signaling and thereby inhibit growth and survival of tumor cells. JNK1/2 are not only regulated by ROS—they in turn can also control ROS production. The prooxidant and cell death function of p66Shc requires phosphorylation by JNK1/2. Here, we provide evidence that establishes p66Shc, an oxidoreductase, as a JNK1/2 effector downstream of Rigosertib-induced ROS production, DNA damage, and cell death. This may provide a common pathway for suppression of tumor cell growth by Rigosertib. Full article
(This article belongs to the Section Cell Biology)
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Open AccessArticle
A Comparative Study of Rat Urine 1H-NMR Metabolome Changes Presumably Arising from Isoproterenol-Induced Heart Necrosis Versus Clarithromycin-Induced QT Interval Prolongation
Biology 2020, 9(5), 98; https://doi.org/10.3390/biology9050098 - 13 May 2020
Viewed by 527
Abstract
Cardiotoxicity remains a challenging concern both in drug development and in the management of various clinical situations. There are a lot of examples of drugs withdrawn from the market or stopped during clinical trials due to unpredicted cardiac adverse events. Obviously, current conventional [...] Read more.
Cardiotoxicity remains a challenging concern both in drug development and in the management of various clinical situations. There are a lot of examples of drugs withdrawn from the market or stopped during clinical trials due to unpredicted cardiac adverse events. Obviously, current conventional methods for cardiotoxicity assessment suffer from a lack of predictivity and sensitivity. Therefore, there is a need for developing new tools to better identify and characterize any cardiotoxicity that can occur during the pre-clinical and clinical phases of drug development as well as after marketing in exposed patients. In this study, isoproterenol and clarithromycin were used as prototypical cardiotoxic agents in rats in order to evaluate potential biomarkers of heart toxicity at very early stages using 1H-NMR-based metabonomics. While isoproterenol is known to cause heart necrosis, clarithromycin may induce QT interval prolongation. Heart necrosis and QT prolongation were validated by histological analysis, serum measurement of lactate dehydrogenase/creatine phosphate kinase and QTc measurement by electrocardiogram (ECG). Urine samples were collected before and repeatedly during daily exposure to the drugs for 1H-NMR based-metabonomics investigations. Specific metabolic signatures, characteristic of each tested drug, were obtained from which potential predictive biomarkers for drug-induced heart necrosis and drug-induced QT prolongation were retrieved. Isoproterenol-induced heart necrosis was characterized by higher levels of taurine, creatine, glucose and by lower levels of Krebs cycle intermediates, creatinine, betaine/trimethylamine N-oxide (TMAO), dimethylamine (DMA)/sarcosine. Clarithromycin-induced QT prolongation was characterized by higher levels of creatinine, taurine, betaine/TMAO and DMA/sarcosine and by lower levels of Krebs cycle intermediates, glucose and hippurate. Full article
(This article belongs to the Special Issue Molecular Targets and Targeting in Biomedical Sciences)
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Open AccessArticle
Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France
Biology 2020, 9(5), 97; https://doi.org/10.3390/biology9050097 - 08 May 2020
Cited by 5 | Viewed by 6405
Abstract
The number of screening tests carried out in France and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the infection fatality ratio (IFR). The main objective of this work [...] Read more.
The number of screening tests carried out in France and the methodology used to target the patients tested do not allow for a direct computation of the actual number of cases and the infection fatality ratio (IFR). The main objective of this work is to estimate the actual number of people infected with COVID-19 and to deduce the IFR during the observation window in France. We develop a ‘mechanistic-statistical’ approach coupling a SIR epidemiological model describing the unobserved epidemiological dynamics, a probabilistic model describing the data acquisition process and a statistical inference method. The actual number of infected cases in France is probably higher than the observations: we find here a factor ×8 (95%-CI: 5–12) which leads to an IFR in France of 0.5% (95%-CI: 0.3–0.8) based on hospital death counting data. Adjusting for the number of deaths in nursing homes, we obtain an IFR of 0.8% (95%-CI: 0.45–1.25). This IFR is consistent with previous findings in China (0.66%) and in the UK (0.9%) and lower than the value previously computed on the Diamond Princess cruse ship data (1.3%). Full article
(This article belongs to the Special Issue Theories and Models on COVID-19 Epidemics)
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Open AccessArticle
A High-Resolution Mass Spectrometry-Based Quantitative Metabolomic Workflow Highlights Defects in 5-Fluorouracil Metabolism in Cancer Cells with Acquired Chemoresistance
Biology 2020, 9(5), 96; https://doi.org/10.3390/biology9050096 - 06 May 2020
Viewed by 838
Abstract
Currently, 5-fluorouracil (5-FU)-based combination chemotherapy is the mainstay in the treatment of metastatic colorectal cancer (CRC), which benefits approximately 50% of the patients. However, these tumors inevitably acquire chemoresistance resulting in treatment failure. The molecular mechanisms driving acquired chemotherapeutic drug resistance in CRC [...] Read more.
Currently, 5-fluorouracil (5-FU)-based combination chemotherapy is the mainstay in the treatment of metastatic colorectal cancer (CRC), which benefits approximately 50% of the patients. However, these tumors inevitably acquire chemoresistance resulting in treatment failure. The molecular mechanisms driving acquired chemotherapeutic drug resistance in CRC is fundamental for the development of novel strategies for circumventing resistance. However, the specific phenomenon that drives the cancer cells to acquire resistance is poorly understood. Understanding the molecular mechanisms that regulate chemoresistance will uncover new avenues for the treatment of CRC. Among the various mechanisms of acquired chemoresistance, defects in the drug metabolism pathways could play a major role. In the case of 5-FU, it gets converted into various active metabolites, which, directly or indirectly, interferes with the replication and transcription of dividing cells causing DNA and RNA damage. In this project, we developed a high-resolution mass spectrometry-based method to effectively extract and quantify levels of the 5-FU metabolites in cell lysates and media of parental and 5-FU resistant LIM1215 CRC cells. The analysis highlighted that the levels of 5-FU metabolites are significantly reduced in 5-FU resistant cells. Specifically, the level of the nucleotide fluorodeoxyuridine monophosphate (FdUMP) is reduced with treatment of 5-FU clarifying the compromised 5-FU metabolism in resistant cells. Corroborating the metabolomic analysis, treatment of the resistant cells with FdUMP, an active metabolite of 5-FU, resulted in effective killing of the resistant cells. Overall, in this study, an effective protocol was developed for comparative quantitation of polar metabolites and nucleotide analogues from the adherent cells efficiently. Furthermore, the utility of FdUMP as an alternative for CRC therapy is highlighted. Full article
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Open AccessArticle
3-Iodothyronamine Affects Thermogenic Substrates’ Mobilization in Brown Adipocytes
Biology 2020, 9(5), 95; https://doi.org/10.3390/biology9050095 - 04 May 2020
Viewed by 473
Abstract
We investigated the effect of 3-iodothyronamine (T1AM) on thermogenic substrates in brown adipocytes (BAs). BAs isolated from the stromal fraction of rat brown adipose tissue were exposed to an adipogenic medium containing insulin in the absence (M) or in the presence of 20 [...] Read more.
We investigated the effect of 3-iodothyronamine (T1AM) on thermogenic substrates in brown adipocytes (BAs). BAs isolated from the stromal fraction of rat brown adipose tissue were exposed to an adipogenic medium containing insulin in the absence (M) or in the presence of 20 nM T1AM (M+T1AM) for 6 days. At the end of the treatment, the expression of p-PKA/PKA, p-AKT/AKT, p-AMPK/AMPK, p-CREB/CREB, p-P38/P38, type 1 and 3 beta adrenergic receptors (β1–β3AR), GLUT4, type 2 deiodinase (DIO2), and uncoupling protein 1 (UCP-1) were evaluated. The effects of cell conditioning with T1AM on fatty acid mobilization (basal and adrenergic-mediated), glucose uptake (basal and insulin-mediated), and ATP cell content were also analyzed in both cell populations. When compared to cells not exposed, M+T1AM cells showed increased p-PKA/PKA, p-AKT/AKT, p-CREB/CREB, p-P38/P38, and p-AMPK/AMPK, downregulation of DIO2 and β1AR, and upregulation of glycosylated β3AR, GLUT4, and adiponectin. At basal conditions, glycerol release was higher for M+T1AM cells than M cells, without any significant differences in basal glucose uptake. Notably, in M+T1AM cells, adrenergic agonists failed to activate PKA and lipolysis and to increase ATP level, but the glucose uptake in response to insulin exposure was more pronounced than in M cells. In conclusion, our results suggest that BAs conditioning with T1AM promote a catabolic condition promising to fight obesity and insulin resistance. Full article
(This article belongs to the Section Pharmacology)
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Open AccessArticle
Temperature Decreases Spread Parameters of the New Covid-19 Case Dynamics
Biology 2020, 9(5), 94; https://doi.org/10.3390/biology9050094 - 03 May 2020
Cited by 2 | Viewed by 2064
Abstract
(1) Background: The virulence of coronavirus diseases due to viruses like SARS-CoV or MERS-CoV decreases in humid and hot weather. The putative temperature dependence of infectivity by the new coronavirus SARS-CoV-2 or covid-19 has a high predictive medical interest. (2) Methods: External temperature [...] Read more.
(1) Background: The virulence of coronavirus diseases due to viruses like SARS-CoV or MERS-CoV decreases in humid and hot weather. The putative temperature dependence of infectivity by the new coronavirus SARS-CoV-2 or covid-19 has a high predictive medical interest. (2) Methods: External temperature and new covid-19 cases in 21 countries and in the French administrative regions were collected from public data. Associations between epidemiological parameters of the new case dynamics and temperature were examined using an ARIMA model. (3) Results: We show that, in the first stages of the epidemic, the velocity of contagion decreases with country- or region-wise temperature. (4) Conclusions: Results indicate that high temperatures diminish initial contagion rates, but seasonal temperature effects at later stages of the epidemy remain questionable. Confinement policies and other eviction rules should account for climatological heterogeneities, in order to adapt the public health decisions to possible geographic or seasonal gradients. Full article
(This article belongs to the Special Issue Theories and Models on COVID-19 Epidemics)
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Open AccessCommunication
The Role of the Histone Methyltransferase EZH2 in Liver Inflammation and Fibrosis in STAM NASH Mice
Biology 2020, 9(5), 93; https://doi.org/10.3390/biology9050093 - 02 May 2020
Viewed by 559
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a leading form of chronic liver disease, with few biomarkers and treatment options currently available. Non-alcoholic steatohepatitis (NASH), a progressive disease of NAFLD, may lead to fibrosis, cirrhosis, and hepatocellular carcinoma. Epigenetic modification can contribute to the [...] Read more.
Non-alcoholic fatty liver disease (NAFLD) is a leading form of chronic liver disease, with few biomarkers and treatment options currently available. Non-alcoholic steatohepatitis (NASH), a progressive disease of NAFLD, may lead to fibrosis, cirrhosis, and hepatocellular carcinoma. Epigenetic modification can contribute to the progression of NAFLD causing non-alcoholic steatohepatitis (NASH), in which the exact role of epigenetics remains poorly understood. To identify potential therapeutics for NASH, we tested small-molecule inhibitors of the epigenetic target histone methyltransferase EZH2, Tazemetostat (EPZ-6438), and UNC1999 in STAM NASH mice. The results demonstrate that treatment with EZH2 inhibitors decreased serum TNF-alpha in NASH. In this study, we investigated that inhibition of EZH2 reduced mRNA expression of inflammatory cytokines and fibrosis markers in NASH mice. In conclusion, these results suggest that EZH2 may present a promising therapeutic target in the treatment of NASH. Full article
(This article belongs to the Section Cell Biology)
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Open AccessArticle
Curcumin Sensitizes Kidney Cancer Cells to TRAIL-Induced Apoptosis via ROS Mediated Activation of JNK-CHOP Pathway and Upregulation of DR4
Biology 2020, 9(5), 92; https://doi.org/10.3390/biology9050092 - 01 May 2020
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Abstract
Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL), is a selective anticancer cytokine capable of exerting a targeted therapy approach. Disappointingly, recent research has highlighted the development of TRAIL resistance in cancer cells, thus minimising its usefulness in clinical settings. However, several recent studies have [...] Read more.
Tumour necrosis factor-related apoptosis-inducing ligand (TRAIL), is a selective anticancer cytokine capable of exerting a targeted therapy approach. Disappointingly, recent research has highlighted the development of TRAIL resistance in cancer cells, thus minimising its usefulness in clinical settings. However, several recent studies have demonstrated that cancer cells can be sensitised to TRAIL through the employment of a combinatorial approach, utilizing TRAIL in conjunction with other natural or synthetic anticancer agents. In the present study, the chemo-sensitising effect of curcumin on TRAIL-induced apoptosis in renal carcinoma cells (RCC) was investigated. The results indicate that exposure of kidney cancer ACHN cells to curcumin sensitised the cells to TRAIL, with the combination treatment of TRAIL and curcumin synergistically targeting the cancer cells without affecting the normal renal proximal tubular epithelial cells (RPTEC/TERT1) cells. Furthermore, this combination treatment was shown to induce caspase-dependent apoptosis, inhibition of the proteasome, induction of ROS, upregulation of death receptor 4 (DR4), alterations in mitogen-activated protein kinase (MAPK) signalling and induction of endoplasmic reticulum stress. An in vivo zebrafish embryo study demonstrated the effectiveness of the combinatorial regime to inhibit tumour formation without affecting zebrafish embryo viability or development. Overall, the results arising from this study demonstrate that curcumin has the ability to sensitise TRAIL-resistant ACHN cells to TRAIL-induced apoptosis. Full article
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Open AccessArticle
Epigenetic Changes in Host Ribosomal DNA Promoter Induced by an Asymptomatic Plant Virus Infection
Biology 2020, 9(5), 91; https://doi.org/10.3390/biology9050091 - 28 Apr 2020
Viewed by 744
Abstract
DNA cytosine methylation is one of the main epigenetic mechanisms in higher eukaryotes and is considered to play a key role in transcriptional gene silencing. In plants, cytosine methylation can occur in all sequence contexts (CG, CHG, and CHH), and its levels are [...] Read more.
DNA cytosine methylation is one of the main epigenetic mechanisms in higher eukaryotes and is considered to play a key role in transcriptional gene silencing. In plants, cytosine methylation can occur in all sequence contexts (CG, CHG, and CHH), and its levels are controlled by multiple pathways, including de novo methylation, maintenance methylation, and demethylation. Modulation of DNA methylation represents a potentially robust mechanism to adjust gene expression following exposure to different stresses. However, the potential involvement of epigenetics in plant-virus interactions has been scarcely explored, especially with regard to RNA viruses. Here, we studied the impact of a symptomless viral infection on the epigenetic status of the host genome. We focused our attention on the interaction between Nicotiana benthamiana and Pelargonium line pattern virus (PLPV, family Tombusviridae), and analyzed cytosine methylation in the repetitive genomic element corresponding to ribosomal DNA (rDNA). Through a combination of bisulfite sequencing and RT-qPCR, we obtained data showing that PLPV infection gives rise to a reduction in methylation at CG sites of the rDNA promoter. Such a reduction correlated with an increase and decrease, respectively, in the expression levels of some key demethylases and of MET1, the DNA methyltransferase responsible for the maintenance of CG methylation. Hypomethylation of rDNA promoter was associated with a five-fold augmentation of rRNA precursor levels. The PLPV protein p37, reported as a suppressor of post-transcriptional gene silencing, did not lead to the same effects when expressed alone and, thus, it is unlikely to act as suppressor of transcriptional gene silencing. Collectively, the results suggest that PLPV infection as a whole is able to modulate host transcriptional activity through changes in the cytosine methylation pattern arising from misregulation of methyltransferases/demethylases balance. Full article
(This article belongs to the Special Issue Plant-Pathogen Interaction)
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Open AccessArticle
The Water Content Drives the Susceptibility of the Lichen Evernia prunastri and the Moss Brachythecium sp. to High Ozone Concentrations
Biology 2020, 9(5), 90; https://doi.org/10.3390/biology9050090 - 27 Apr 2020
Viewed by 576
Abstract
The aim of this study was to evaluate the tolerance of lichens (Evernia prunastri) and mosses (Brachythecium sp.) to short-term (1 h), acute (1 ppm) O3 fumigation under different hydration states (dry, <10% water content, metabolism almost inactive; wet, [...] Read more.
The aim of this study was to evaluate the tolerance of lichens (Evernia prunastri) and mosses (Brachythecium sp.) to short-term (1 h), acute (1 ppm) O3 fumigation under different hydration states (dry, <10% water content, metabolism almost inactive; wet, >200% water content, metabolism fully active). We hypothesized that stronger damage would occur following exposure under wet conditions. In addition, we checked for the effect of recovery (1 week) after the exposure. Ozone fumigation negatively affected the content of chlorophyll only in wet samples, but in the moss, such a difference was no longer evident after one week of recovery. Photosynthetic efficiency was always impaired by O3 exposure, irrespective of the dry or wet state, and also after one week of recovery, but the effect was much stronger in wet samples. The antioxidant power was increased in wet moss and in dry lichen, while a decrease was found for wet lichens after 1 week. Our results confirm that the tolerance to O3 of lichens and mosses may be determined by their low water content, which is the case during the peaks of O3 occurring during the Mediterranean summer. The role of antioxidant power as a mechanism of resistance to high O3 concentrations needs to be further investigated. Full article
(This article belongs to the Section Plant Science)
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Open AccessArticle
Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)
Biology 2020, 9(5), 89; https://doi.org/10.3390/biology9050089 - 27 Apr 2020
Viewed by 447
Abstract
Vancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of Enterococcus spp. that originated from [...] Read more.
Vancomycin-resistant enterococci (VRE), due to their intrinsic resistance to various commonly used antibiotics and their malleable genome, make the treatment of infections caused by these bacteria less effective. The aims of this work were to characterize isolates of Enterococcus spp. that originated from processed meat, through phenotypic and genotypic techniques, as well as to detect putative antibiotic resistance biomarkers. The 19 VRE identified had high resistance to teicoplanin (89%), tetracycline (94%), and erythromycin (84%) and a low resistance to kanamycin (11%), gentamicin (11%), and streptomycin (5%). Based on a Next-Generation Sequencing NGS technique, most isolates were vanA-positive. The most prevalent resistance genes detected were erm(B) and aac(6’)-Ii, conferring resistance to the classes of macrolides and aminoglycosides, respectively. MALDI-TOF mass spectrometry (MS) analysis detected an exclusive peak of the Enterococcus genus at m/z (mass-to-charge-ratio) 4428 ± 3, and a peak at m/z 6048 ± 1 allowed us to distinguish Enterococcus faecium from the other species. Several statistically significant protein masses associated with resistance were detected, such as peaks at m/z 6358.27 and m/z 13237.3 in ciprofloxacin resistance isolates. These results reinforce the relevance of the combined and complementary NGS and MALDI-TOF MS techniques for bacterial characterization. Full article
(This article belongs to the Section Microbiology)
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Open AccessArticle
Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life
Biology 2020, 9(5), 88; https://doi.org/10.3390/biology9050088 - 25 Apr 2020
Viewed by 630
Abstract
(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at [...] Read more.
(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singular docosameric RNA molecule, we call the ALPHA sequence. Then, we searched for any relics of the peptides made from ALPHA in sequences deposited in the different public databases. (3) Results: Sequence matching between ALPHA and sequences from organisms among the earliest forms of life on Earth were found at high statistical relevance. We hypothesize that the frequency of appearance of relics from ALPHA sequence in present genomes has a functional necessity. (4) Conclusions: Given the fitness of ALPHA as a supportive sequence of the framework of all existing theories, and the evolution of Archaea and giant viruses, it is anticipated that the unique properties of this singular archetypal ALPHA sequence should prove useful as a model matrix for future applications, ranging from synthetic biology to DNA computing. Full article
(This article belongs to the Special Issue Perspectives of Theoretical Medicine)
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