Biology

18 pages, 2745 KiB

Open AccessArticle

A New IL6 Isoform in Chinese Soft-Shelled Turtle (Pelodiscus sinesis) Discovered: Its Regulation during Cold Stress and Infection

by Zuobing Zhang, Miao Tian, Ruxin Song, Xiao Xing, Yong Fan, Lan Wang, Cuijuan Niu and Roy A. Dalmo

Biology 2020, 9(5), 111; https://doi.org/10.3390/biology9050111 - 25 May 2020

Cited by 6 | Viewed by 3011

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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Figure 1

Figure 1
Nucleotide and deduced amino acid sequences of psIL6 and psIL6ns. Additional nucleotides of psIL6ns are in italic and shaded. Translation starting sites for psIL6 and psIL6ns are in uppercases. Signal peptide of psIL6 is boxed. The IL6-superfamily domain has a single strikethrough. The IL6/G-CSF/MGF family signature characteristic (C-X(9)-C-X(6)-G-L-X(2)-Y/F-X(3)-L) is shaded. Instability motifs (attta) are underlined and polyadenylation signal (aataaa) is above the dashed line. Full article ">Figure 2
Multiple sequence alignment of the deduced IL6 in the Chinese soft-shelled turtle and other selected animals. The consensus residues are shaded. In the consensus line, asterisks (*) resemble completely identical residues in all selected species, and dots (.), and colons (:) represent similarity. MUSCLE program was used for the alignment. Accession numbers of genes are supplied in <a href="#app1-biology-09-00111" class="html-app">Supplementary Table S4</a> and the first two letters of the sequence name represent the initial letters of species’ Latin name. Signal peptide, Helix A-E, and AB loop of human IL6 are clearly denoted. Conserved cysteines are indicated with triangles and putative disulfide bonds are linked with single lines. Critical amino acid residues in the IL6/G-CSF/MGF family signature characteristics were labeled with solid arrows. Full article ">Figure 3
Phylogenetic tree showing the relationship between the turtle IL6 gene and genes of IL6 families in other selected vertebrate species. The phylogram was constructed on MUSCLE and MEGA X. The neighbor-joining method was used. Johns–Taylor–Thornton model with Gamma value of 1.676610112 and bootstrap values of 1000 replications were adopted. Accession numbers are supplied in <a href="#app1-biology-09-00111" class="html-app">Supplementary Figure S4</a>. psIL6 and psIL6ns are labeled with a filled square. Full article ">Figure 4
The constitutive expression of psIL6 and IL6ns mRNA was determined by real-time PCR in seven tissues from eight turtles. The results were calculated in a relative expression method, and presented as mean + SD. ef1α was chosen as the reference gene. If there is not any same letter (uppercased vs. uppercased, lowercased vs. lowercased) in any two different groups, it represents that there is a statistical significance (p < 0.05); ** p < 0.01; *** p < 0.001. One-way ANOVA analysis was performed to analyze the data in different tissues and Tukey’s method was applied as a post hoc test. Unpaired T test was used to compare psIL6 and IL6ns transcript levels in the same tissues. Full article ">Figure 5
Transcript levels of psIL6 and psIL6ns in primary spleen cells upon stimulation. The relative expression method was used in the calculation with ef1α as the reference gene. In the X-axis, stimulation times (h) are listed. (a) psIL6 and (b) psIL6ns expression after poly I: C (5 μg mL−1) stimulation, (c) psIL6 and (d) psIL6ns expression after ConA (25 μg mL−1) stimulation. The data are presented as mean + SD (n = 6). Different letters above the bars represent statistical significance between the time-points (p < 0.05); ** p < 0.01; *** p < 0.001. Two-way ANOVA analysis was carried out followed by Bonferroni’s multiple comparison test for the multiple comparison. When a non-parametric method was found applicable, Kruskal–Wallis analysis was first used and when there was a significance, the Mann–Whitney U test was used as a post hoc test. Full article ">Figure 6
Semi-quantitative RT-PCR results of psIL6 and psIL6ns expression in the brain, spleen, distal ileum, and large intestine after oral administration of A. hydrophila. ef1α was chosen as the reference gene. C-RT: PBS-treated turtle; T-RT: A. hydrophila treated turtle. + represents the addition of reverse-transcriptase when running the reverse-transcription; —represents the replacement of reverse-transcriptase with H2O when running the reverse-transcription. H2O means the template was H2O. Full article ">Figure 7
Expression of psiIL6 (a) and psIL6ns (b) in the spleen after S. aureus and A. hydrophila in vivo challenge within 7 days after cold stress. The relative expression method was applied in the calculation with ef1α as the reference gene. The data are presented as mean + SD (n = 6). Capitalized and small letters: Statistical comparison between time points within a treatment group. Different letter denotes statistically significant difference (p < 0.05, capitalized vs. capitalized, small letters vs. small letters). (a) psIL6 and (b) psIL6ns expression. * p < 0.05; ** p < 0.01; *** p < 0.001. ns: No statistically significant difference between the treatment groups. Two-way ANOVA analysis was carried out followed by Bonferroni’s multiple comparison test for multiple comparison. When a non-parametric method was found applicable, Kruskal–Wallis analysis was first used and when there was a significance, the Mann–Whitney U test was used as a post hoc test. Full article ">Figure 8
Expression of the psIL6 and psIL6ns gene in the intestine (distal ileum) after S. aureus and A. hydrophila in vivo infection within 7 days after acute cold stress. Capitalized and small letters: Statistical comparison between time points within a treatment group. Different letter denotes statistically significant difference (p < 0.05, capitalized vs. capitalized, small letters vs. small letters). (a) psIL6 and (b) psIL6ns expression. The data are presented as mean + SD (n = 6). * p < 0.05; ** p < 0.01; *** p < 0.001. ns: No statistically significant difference between the treatment groups. Two-way ANOVA analysis was carried out, followed by Bonferroni’s multiple comparison test in the multiple comparison. When a non-parametric method was found applicable, Kruskal–Wallis analysis was first used and when there was a significance, the Mann–Whitney U test was used as a post hoc test. Full article ">

15 pages, 1884 KiB

Open AccessArticle

In Silico Identification of Type III PKS Chalcone and Stilbene Synthase Homologs in Marine Photosynthetic Organisms

by Daniele De Luca and Chiara Lauritano

Biology 2020, 9(5), 110; https://doi.org/10.3390/biology9050110 - 22 May 2020

Cited by 10 | Viewed by 4577

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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14 pages, 4367 KiB

Open AccessReview

Brain Control Reproduction by the Endocrine System of Female Blue Gourami (Trichogaster trichopterus)

by Gad Degani

Biology 2020, 9(5), 109; https://doi.org/10.3390/biology9050109 - 21 May 2020

Cited by 6 | Viewed by 4058

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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17 pages, 2144 KiB

Open AccessReview

Clinical Genetics of Prolidase Deficiency: An Updated Review

by Marta Spodenkiewicz, Michel Spodenkiewicz, Maureen Cleary, Marie Massier, Giorgos Fitsialos, Vincent Cottin, Guillaume Jouret, Céline Poirsier, Martine Doco-Fenzy and Anne-Sophie Lèbre

Biology 2020, 9(5), 108; https://doi.org/10.3390/biology9050108 - 21 May 2020

Cited by 34 | Viewed by 5661

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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14 pages, 834 KiB

Open AccessArticle

Novel Dynamic Structures of 2019-nCoV with Nonlocal Operator via Powerful Computational Technique

by Wei Gao, P. Veeresha, D. G. Prakasha and Haci Mehmet Baskonus

Biology 2020, 9(5), 107; https://doi.org/10.3390/biology9050107 - 21 May 2020

Cited by 138 | Viewed by 4556

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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10 pages, 1321 KiB

Open AccessArticle

Evolution of Hemoglobin Genes in a Subterranean Rodent Species (Lasiopodomys mandarinus)

by Hong Sun, Kaihong Ye, Denghui Liu, Dan Pan, Shiming Gu and Zhenlong Wang

Biology 2020, 9(5), 106; https://doi.org/10.3390/biology9050106 - 20 May 2020

Cited by 5 | Viewed by 3482

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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12 pages, 2574 KiB

Open AccessEditor’s ChoiceArticle

Period of Boar Ejaculate Collection Contributes to the Yearly Intra-Male Variability of Seminal Plasma Cytokines

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

Biology 2020, 9(5), 105; https://doi.org/10.3390/biology9050105 - 20 May 2020

Cited by 4 | Viewed by 2831

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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Graphical abstract

Graphical abstract
Full article ">Figure 1
Violin plots representing the concentrations of granulocyte macrophage colony-stimulating factor (GM-CSF), interferon-gamma (IFNγ), interleukin (IL)-1α, IL-1β, IL-1ra, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-18, and tumor necrosis factor-α (TNFα) in seminal plasma of nine boars (20 ejaculates per boar). The dashed line represents the median and the dotted lines the 25% and 75% quartiles. All cytokines showed differences among boars (p < 0.001). Full article ">Figure 2
Intraclass correlation coefficient (ICC 3,1) values in terms of single measures (dot) and 95% confidence intervals (bars) of cytokine concentrations in 180 boar seminal plasma samples. Cytokines: granulocyte-macrophage colony-stimulating factor (GM-CSF), interferon-gamma (IFNγ), interleukin (IL)-1α, IL-1β, IL-1ra, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-18, and tumor necrosis factor-α (TNFα). Full article ">Figure 3
Variation pattern of cytokine concentrations in seminal plasma from ejaculates collected from nine boars (20 ejaculates per boar) during the times of year when increasing (I, January to June) or decreasing daylight/temperature (D, July to December) dominated. Grey box indicates no differences between periods, while red and green boxes indicate a relationship between dominating seasonal parameters with high and low cytokine concentrations (p < 0.05), respectively. Cytokines: Granulocyte macrophage colony-stimulating factor (GM-CSF), interferon-gamma (IFNγ), interleukin (IL)-1α, IL-1β, IL-1ra, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-18, and tumor necrosis factor-α (TNFα). Full article ">Figure 4
Variation pattern in the total amount of seminal plasma cytokines in ejaculates collected from nine boars (20 ejaculates per boar) during the periods of increasing (I, January to June) or decreasing daylight/temperature (D, July to December). Grey box indicates no differences between periods, while red and green boxes indicate a relationship between dominating seasonal parameters with high and low total cytokine amounts (p < 0.05), respectively. Cytokines: Granulocyte macrophage colony-stimulating factor (GM-CSF), interferon-gamma (IFNγ), interleukin (IL)-1α, IL-1β, IL-1ra, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-18, and tumor necrosis factor-α (TNFα). Full article ">

14 pages, 1374 KiB

Open AccessArticle

The Utility of Genomic and Transcriptomic Data in the Construction of Proxy Protein Sequence Databases for Unsequenced Tree Nuts

by Cary Pirone-Davies, Melinda A. McFarland, Christine H. Parker, Yoko Adachi and Timothy R. Croley

Biology 2020, 9(5), 104; https://doi.org/10.3390/biology9050104 - 19 May 2020

Cited by 3 | Viewed by 3307

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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13 pages, 995 KiB

Open AccessReview

Clinical Features of Parkinson’s Disease: The Evolution of Critical Symptoms

by Csaba Váradi

Biology 2020, 9(5), 103; https://doi.org/10.3390/biology9050103 - 19 May 2020

Cited by 99 | Viewed by 22704

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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21 pages, 2194 KiB

Open AccessReview

Magnetotactic Bacteria and Magnetosomes as Smart Drug Delivery Systems: A New Weapon on the Battlefield with Cancer?

by Danuta Kuzajewska, Agata Wszołek, Wojciech Żwierełło, Lucyna Kirczuk and Agnieszka Maruszewska

Biology 2020, 9(5), 102; https://doi.org/10.3390/biology9050102 - 19 May 2020

Cited by 38 | Viewed by 7199

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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15 pages, 2720 KiB

Open AccessArticle

Comparative Analysis of Porcine Follicular Fluid Proteomes of Small and Large Ovarian Follicles

by Victor M. Paes, José R. de Figueiredo, Peter L. Ryan, Scott T. Willard and Jean M. Feugang

Biology 2020, 9(5), 101; https://doi.org/10.3390/biology9050101 - 17 May 2020

Cited by 12 | Viewed by 3722

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

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14 pages, 3967 KiB

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

by Biao Tang, Francesca Scarabel, Nicola Luigi Bragazzi, Zachary McCarthy, Michael Glazer, Yanyu Xiao, Jane M. Heffernan, Ali Asgary, Nicholas Hume Ogden and Jianhong Wu

Biology 2020, 9(5), 100; https://doi.org/10.3390/biology9050100 - 16 May 2020

Cited by 33 | Viewed by 12317

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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10 pages, 3281 KiB

Open AccessArticle

Rigosertib-Activated JNK1/2 Eliminate Tumor Cells through p66Shc Activation

by Julia K. Günther, Aleksandar Nikolajevic, Susanne Ebner, Jakob Troppmair and Sana Khalid

Biology 2020, 9(5), 99; https://doi.org/10.3390/biology9050099 - 15 May 2020

Cited by 5 | Viewed by 3386

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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Figure 1
Effect of Rigosertib on MAPK signaling. Representative Western blots show an increase in cJun N-terminal kinases 1/2 (JNK1/2) (A) and a decrease in ERK1/2 activity (B) in MCF7, PC3, and DU-145 cells stimulated with 50 μM Rigosertib for 18 h. Numbers on top of the blot indicate the fold change in protein phosphorylation upon Rigosertib treatment (normalized to loading control) relative to DMSO (solvent)-treated control samples. All experiments have been repeated at least three times with consistent results. A representative blot is shown. Full article ">Figure 2
Rigosertib increases p66Shc activity and cell death in tumor cell lines. Representative Western blots show an increase in p66Shc activity (A), γH2AX phosphorylation (B), and PARP cleavage (C) in MCF-7, PC3, and DU-145 cells stimulated with 50 μM Rigosertib for 18 h. Numbers on top of the blot indicate the fold change in protein phosphorylation upon Rigosertib treatment (normalized to loading control) relative to DMSO (solvent)-treated control samples. For PARP, the ratio of cleaved and intact protein is shown. MCF-7, PC3, and DU-145 were imaged in phase contrast to detect cellular morphology (D) and analyzed for cell death by Annexin/PI after treating cells with either Rigosertib (50 μM) or DMSO for 96 h. Results are presented as % of Annexin V-positive and PI-positive cells (E) and scattered plots (F). The drug-containing medium was refreshed after 48 h during 96 h incubation time. All experiments have been repeated at least three times with consistent results, except the Annexin/PI analysis for DU-145, which has been repeated twice. Values shown are mean ± S.D. A representative blot is shown. Scale bar size: 100 µm. Full article ">Figure 2 Cont.
Rigosertib increases p66Shc activity and cell death in tumor cell lines. Representative Western blots show an increase in p66Shc activity (A), γH2AX phosphorylation (B), and PARP cleavage (C) in MCF-7, PC3, and DU-145 cells stimulated with 50 μM Rigosertib for 18 h. Numbers on top of the blot indicate the fold change in protein phosphorylation upon Rigosertib treatment (normalized to loading control) relative to DMSO (solvent)-treated control samples. For PARP, the ratio of cleaved and intact protein is shown. MCF-7, PC3, and DU-145 were imaged in phase contrast to detect cellular morphology (D) and analyzed for cell death by Annexin/PI after treating cells with either Rigosertib (50 μM) or DMSO for 96 h. Results are presented as % of Annexin V-positive and PI-positive cells (E) and scattered plots (F). The drug-containing medium was refreshed after 48 h during 96 h incubation time. All experiments have been repeated at least three times with consistent results, except the Annexin/PI analysis for DU-145, which has been repeated twice. Values shown are mean ± S.D. A representative blot is shown. Scale bar size: 100 µm. Full article ">Figure 3
JNK1/2 regulation of p66Shc activity in tumor cell lines upon Rigosertib treatment. Representative Western blots demonstrating the effects of SP600125 (20 μM, JNK inhibitor) treatment before Rigosertib application (50 μM for 18 h) on cJun (A), ERK1/2 (B), and p66ShcS36 phosphorylation (C) in MCF7, PC3, and DU-145 cells. Numbers on top of the blot indicate the fold change in protein phosphorylation upon Rigosertib treatment (normalized to loading control) relative to DMSO (solvent)-treated control samples. All experiments have been repeated at least three times with consistent results. A representative blot is shown. Full article ">Figure 4
Rigosertib-mediated tumor cell killing is reduced by JNK1/2 inhibition. Representative Western blots documenting the effect of SP600125 treatment (20 μM, added one h before Rigosertib) on γH2AX phosphorylation (A) and PARP cleavage (B) in MCF7, PC3 and DU-145 cells. Rigosertib was applied for 18 h at a concentration of 50 µM). Numbers on top of the blot indicate the fold change in protein phosphorylation upon Rigosertib treatment (normalized to loading control) relative to DMSO (solvent) treated control samples. All experiments have been repeated at least three times with consistent results. A representative blot is shown. Full article ">Figure 5
During the submission of the revised manuscrip an incorrect version of this Figure has been submitted, The figure inserted now is as requested by the reviewers. p66Shc is necessary for Rigosertib-mediated tumor cell killing. Representative Western blots demonstrate γH2AX phosphorylation and PARP cleavage in p66Shc-HA-His transiently transfected MCF7 cells treated with Rigosertib (50 μM) or DMSO for 18 h. All experiments have been repeated at least three times with consistent results. A representative blot is shown. Full article ">Figure 6
Rigosertib-mediated cell death pathways (modified from Ritt et al. [<a href="#B7-biology-09-00099" class="html-bibr">7</a>]). Work by Ritt et al. identified the effect of Rigosertib-induced JNK activation on the suppression of the RAS signaling pathway and consequent blunting survival and growth signals. Our data point to an additional mechanism, which may be even more common, linking activated JNK1/2 to the activation of p66Shc, which has been implicated in ROS-mediated cell death under various conditions [<a href="#B12-biology-09-00099" class="html-bibr">12</a>]. Full article ">

19 pages, 1934 KiB

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

by Matthieu Dallons, Manon Delcourt, Corentin Schepkens, Manuel Podrecca and Jean-Marie Colet

Biology 2020, 9(5), 98; https://doi.org/10.3390/biology9050098 - 13 May 2020

Cited by 1 | Viewed by 4288

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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10 pages, 783 KiB

Open AccessArticle

Using Early Data to Estimate the Actual Infection Fatality Ratio from COVID-19 in France

by Lionel Roques, Etienne K Klein, Julien Papaïx, Antoine Sar and Samuel Soubeyrand

Biology 2020, 9(5), 97; https://doi.org/10.3390/biology9050097 - 8 May 2020

Cited by 60 | Viewed by 17967

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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24 pages, 3477 KiB

Open AccessArticle

A High-Resolution Mass Spectrometry-Based Quantitative Metabolomic Workflow Highlights Defects in 5-Fluorouracil Metabolism in Cancer Cells with Acquired Chemoresistance

by Sanjay Shahi, Ching-Seng Ang and Suresh Mathivanan

Biology 2020, 9(5), 96; https://doi.org/10.3390/biology9050096 - 6 May 2020

Cited by 4 | Viewed by 4928

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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Figure 1
Colorectal cancer (CRC) cells gain resistance to 5-fluorouracil (5-FU) with long term exposure to 5-FU. (A) For developing 5-FU resistance in LIM1215 cells, parental cells were cultured continuously until they got fully confluent with increasing concentrations of 5-FU (1, 5, 10, 25 to 50 µm). (B) FACS apoptosis assay performed with LIM1215 parental and resistant cells following treatment with 50 µm 5-FU for 72 h showed that resistant cells are protected from 5-FU mediated cell death. ns; not significant. Data is presented as mean ± s.e.m.; significance determined by Student’s t-test (n = 3). Full article ">Figure 2
Generation of 5-FU and FdUMP calibration curve. Lowest limit of detection and quantification are two key factors for the accurate results. To determine the limits of detection and for the relative comparison of the results, the calibration curve was generated using the peak area obtained from serially diluted 5-FU (A) and FdUMP (B) spiked into conditioned media from the parental cell culture. The green dot from the curve represents the peak area of the 0.780 ng/µL concentration of FdUMP, which was selected for the relative comparison of the detected compounds. Full article ">Figure 3
Development of quantitative metabolomics workflow to analyze 5-FU metabolism in CRC cells. (A) 5-Fluorouracil (5-FU) is an uracil analogue and within the cells it is rapidly converted into different metabolites. The active metabolites of 5-FU directly or indirectly affect replication and transcription leading the cells to undergo apoptosis. Following entry into the cells, 5-FU gets converted into fluorouridine (FURD), fluorouridine monophosphtate (FUMP) and fluorodeoxyuridine (FdURD). FURD gets converted into FUMP then to fluorouridine diphosphate (FUDP), which either subsequently forms fluorouridine triphosphate (FUTP) or gets converted into fluorodeoxyuridine diphosphate (FdUDP) and gets converted into FdUTP. FdUDP and the FdUDR gets converted into fluorodeoxyuridine monophosphate (FdUMP). FdUMP is a thymidylate synthase (TS) inhibitor that inhibits the synthesis of deoxythymidine triphosphate (dTTP) from deoxyuridine monophosphate (dUMP); hence, dUMP, in turn, can get converted into deoxyuridine triphosphate (dUTP). The FUTP, FdUTP and dUTP so formed gets incorporated into newly synthesizing DNA and RNA, leading to DNA and RNA damage. (B) Determination of changes in 5-FU and its metabolites in parental and 5-FU resistant LIM1215 cells was performed by quantitative metabolomic analysis. Parental and resistant cells were cultured until 70% confluency was reached and were treated with 50 µm 5-FU for 72 h. A comparative analysis needed the development of a protocol to effectively and efficiently extract 5-FU and its metabolites from within the cells as well as from the conditioned media with strategy for normalization of the results. The protocol shown was used to culture and treat the cells with equal volume of media with equal concentration of 5-FU. Cells were trypsinized, counted and extraction of compounds was performed following which the samples were freeze dried (C). (D) MS was coupled with F5 phase ultra high performance liquid chromatography (UHPLC) and data analysis was done using bioinformatics tools. Full article ">Figure 4
Relative quantitation of 5-FU and its metabolites. Full article ">Figure 5
Isotope pattern analysis and fragmentation tree analysis using SIRIUS. To further validate the results, the experimental prediction was compared with theoretical prediction and database searches using Sirius software. The m/z for both precursor and the product ions were subjected to analysis using SIRIUS, which compared the data to the PubChem as well as all the molecular formula of similar masses to provide an identification score. Example shown here was using FdUMP standard and FURD, whose standard was not available. The chromatograms depicting precursors and fragment ions peaks for FdUMP standard and FURD from test sample (A). (B) Result obtained from SIRIUS software following the comparison of the MS1 and MS2 spectrum derived from Skyline with PubChem only for FdUMP and PubChem and all possible molecular formula for FURD (MS2). Both comparisons from MS1 and MS2 gave positive score predicting correct identification for all compounds and all the results were within the acceptable mass deviation of 5 ppm. (C) The tool also predicts the fragment ions that could have been generated from the predicted molecular formula and represented as a fragmentation tree that explains the molecular formula for the selected fragment ions. ‘*’ represents the ion fragments that were used for the identification of the compounds that were successfully predicted with SIRIUS 4.0.1 as the fragment ion generated from dissociation of the precursor compound. Full article ">Figure 6
5-FU metabolism is dysregulated in resistant cells. To analyze the metabolism pathway of 5-FU in parental and resistant cells, LIM1215 cells were cultured in media with and without 50 µM 5-FU for 72 h. Media and cells were collected, and the metabolites were extracted. Trypan blue cell counting was used to determine the cell concentration and an equal number of cells were resuspended in methanol and mechanically lysed to extract the metabolites. Samples were subjected to tandem mass spectrometry coupled to F5 phased UHPLC. Raw data were processed and analyzed using bioinformatics tools, particularly, Skyline. Quantitation was based on the peak area obtained from Skyline and the comparison was normalized relative to the peak area of 0.780 ng/µL FdUMP standard. The graphs represent levels based on the peak area ratio of 5-FU and reduced levels of metabolites in resistant cells compared to parental cell lysates (A) and media (B), revealing that the 5-FU metabolism pathway is impaired in resistant cells. ns; not significant. Data is presented as mean ± s.e.m. determined by Student’s t-test (n = 10). Full article ">Figure 7
Resistant cells are sensitive to active metabolite FdUMP. Full article ">

16 pages, 3201 KiB

Open AccessArticle

3-Iodothyronamine Affects Thermogenic Substrates’ Mobilization in Brown Adipocytes

by Manuela Gencarelli, Annunziatina Laurino, Elisa Landucci, Daniela Buonvicino, Costanza Mazzantini, Grazia Chiellini and Laura Raimondi

Biology 2020, 9(5), 95; https://doi.org/10.3390/biology9050095 - 4 May 2020

Cited by 5 | Viewed by 3400

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

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The lipid content of cells with medium (M) and M+T1AM cells. M and M+T1AM cells were obtained as described in the Materials and Methods, and their lipid droplets were visualized (Panel a) and quantified (Panel c) by Oil-red O staining. A representative picture of a cell stained directly in culture wells taken with an inverted microscope is shown in Panel (b). The absorbance at 510 nm of the dye extracted from M and M+T1AM cells with isopropyl alcohol is reported in Panel (c). The results on the histogram represented the mean ± standard error of the mean (SEM) of the absorbance measured from three different cell preparations (* p < 0.05, vs. M cells). (a) The image magnification is 40×; scale bar 100 µm. Full article ">Figure 2
Differentiation marker levels in M and M+T1AM cells. M and M+T1AM cells, obtained as described in the Material and Methods, were analyzed for the expression levels of UCP-1, type 2 deiodinase (DIO2), GLUT4, adiponectin, and type 1 and type 3 beta adrenergic receptors β1- and β3-AR by Western-blot analysis or semi-quantitative PCR, as described in the “Materials and Methods”. In Panels (a,c,e,g,i,m), representative experiments are shown. Each gel was loaded with the cDNA or with proteins obtained from two different cell preparations. (b,d,f,h,l,n). Densitometric analysis is reported as the mean ± standard error of the mean (SEM; n = 4 cell preparations) of arbitrary units (AU; see the Methods; * p< 0.05; ** p < 0.01; *** p < 0.001 vs. M cells). Full article ">Figure 3
The basal and adrenergic mediated lipolysis in M and M+T1AM cells. The glycerol accumulated in M and M+T1AM cell medium in the absence (basal) or in the presence a not selective beta adrenergic agonist, 1 µM Isoproterenol (ISO), a selective β3AR agonist, a selective β3AR antagonist 0.1 µM BRL37344 (BRL), 0.1 µM SR 59230A (SR), or 0.1 µM BRL and 1 µM SR was measured fluorometrically as described in the Materials and Methods. Results on the histogram are presented as arbitrary units of fluorescence (AU)/105 cells and represented as the mean ± standard error mean (SEM) values from three different cell preparations with each point run in triplicate (*** p < 0.001 vs. basal release of M cells; §§ p < 0.01 vs. BRL treatment of M cells; ### p < 0.001 vs. basal release of M+T1AM cells). Full article ">Figure 4
M+T1AM cells show activation of PKA, CREB, and P38: the effect of adrenergic agonists on PKA activation. p-PKA/PKA was measured in M and M+T1AM cells not exposed (basal) or exposed for 15 min to 100 nM insulin (Ins) or 0.1 µM BRL37344 (BRL) as described in the Materials and Methods. A representative experiment is shown in Panel (a). Each gel was loaded with proteins prepared from two different cell preparations. Results on the histogram in Panel (b) are presented as arbitrary units (AU) and represent the mean ± standard error mean (SEM) values from two different cell preparations (*** p<0.001 vs. basal M cells; * p < 0.05 and ** p < 0.01 vs. basal M cells). The expression levels of p-CREB/CREB and p-P38 in M and M+T1AM cells were also examined. Representative experiments are shown in Panels (c,e). Results on the histograms in Panels (d,f) report the mean ± standard error of the SEM (n = 4 cell preparations) of AU (* p < 0.05; ** p < 0.01 vs. M cells). Full article ">Figure 5
The insulin-stimulated glucose uptake in M+T1AM and M cells: the effect at the AKT activation. The radiochemical determination of basal and insulin-stimulated glucose uptake in M and M+T1AM was carried out as described in the Materials and Methods. (a) Results on the histogram represent the mean ± standard error of the mean (SEM) of the radioactivity, expressed as DPM/105 cells, recovered in cells from three different preparations with each point run in triplicate (* p < 0.05 and *** p < 0.01 vs. basal release of M cells; §§§ p < 0.001 vs. insulin effect in M cells). M and M+T1AM cells were also analyzed to determine the p-AKT/AKT at basal and after insulin exposure conditions, as described in the Materials and Methods. (b) A representative experiment is shown. The gel was loaded with proteins derived from two different cell preparations (c). The densitometric analysis of p-AKT/AKT in M and M+T1AM cells is reported as arbitrary units (AU, see the Methods). Results on the histogram represent the mean ± standard error of the mean (SEM; n = 4 cell preparations) of AU (see Methods; * p < 0.05, ** p < 0.01, *** p < 0.001 vs. basal M cells; § p < 0.05 vs. basal M+T1AM cells). Full article ">Figure 6
ATP and p-AMPK cell levels in M and M+T1AM cells. M and M+T1AM cells were analyzed for ATP content and p-AKT/AKT expression as described in the Materials and Methods. Panel (a) shows ATP cellular content in M and M+T1AM cells at basal conditions and after 3 h incubation with 0.1 µM BRL37344 (BRL; * p < 0.05, §§ p < 0.001 vs. basal). Western blot analysis of p-AKT/AKT in M and M+T1AM cells is reported as arbitrary units (AU); see the Methods. A representative experiment is shown The gel was loaded with proteins derived from two different cell preparations (b) The histogram in Panel (c) represents the mean ± standard error of the mean (SEM; n = 4 cell preparations) of AU (see the Methods; * p < 0.05, ** p < 0.01, §§ p < 0.001 vs. basal). Full article ">

10 pages, 1545 KiB

Open AccessArticle

Temperature Decreases Spread Parameters of the New Covid-19 Case Dynamics

by Jacques Demongeot, Yannis Flet-Berliac and Hervé Seligmann

Biology 2020, 9(5), 94; https://doi.org/10.3390/biology9050094 - 3 May 2020

Cited by 104 | Viewed by 11088

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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Left: Start of covid-19 epidemic in countries with various climates. Right: Daily number of new cases from 25 January until 14 March 2020 in France. Full article ">Figure 2
(a) Virulence of covid-19 in liquids and secretions (from [<a href="#B27-biology-09-00094" class="html-bibr">27</a>]); (b) Linear regression of negative initial autocorrelation slope on mean weather temperature of six countries, France, UK, Spain, Italy, China and Chile (Pearson correlation coefficient R = 0.97, one-tailed p = 0.001). (c) Autocorrelation function A for three countries, France, Spain and Chile showing during February until 14 March 2020 a decrease in the positive correlation duration and the negative initial slope of the auto-correlation curve when the mean temperature of the country increases. Full article ">Figure 3
Daily increase in confirmed COVID-19 cases for administrative regions of France on 6 March 2020 (filled symbols, dotted line, log regression model) and on 15 March 2020 (circles, interrupted line, exponential regression model). Full article ">Figure 4
Slope of exponential model fitted to data in <a href="#biology-09-00094-t003" class="html-table">Table 3</a> as a function of mean annual temperature in that country. The Pearson correlation coefficient is R = −0.568, one-tailed p = 0.0036. Full article ">

11 pages, 1846 KiB

Open AccessCommunication

The Role of the Histone Methyltransferase EZH2 in Liver Inflammation and Fibrosis in STAM NASH Mice

by Seul Lee, Dong-Cheol Woo, Jeeheon Kang, Moonjin Ra, Ki Hyun Kim, Seoung Rak Lee, Dong Kyu Choi, Heejin Lee, Ki Bum Hong, Sang-Hyun Min, Yongjun Lee and Ji Hoon Yu

Biology 2020, 9(5), 93; https://doi.org/10.3390/biology9050093 - 2 May 2020

Cited by 22 | Viewed by 5312

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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Figure 1
Treatment with Enhancer of Zeste Homolog 2 (EZH2) inhibitors reduces liver steatosis in STAM NASH mice. (A) NASH STAM mice experimental design. STAM-Vehicle (Control) were injected with streptozotocin (STZ) on day 2 to induce a diabetic state. Mice were fed a high-fat diet from four weeks. Mice were dosed with either vehicle, Obeticholic acid, UNC1999, or EPZ6438 once a day from 6–9 weeks for the study. (B) Representative hematoxylin and eosin (H&E) stained (200x) liver sections from healthy (Normal), STAM-Vehicle (Control), STAM-Obeticholic acid (Obeticholic acid), STAM-UNC1999 (UNC1999), and STAM-EZH2 (EPZ6438) groups in the NASH mice. (C) Representative Oil Red O stained (200x) liver sections from healthy (Normal), STAM-Vehicle (Control), STAM-Obeticholic acid (Obeticholic acid), STAM-UNC1999 (UNC1999), and STAM-EZH2 (EPZ6438) groups in the NASH mice. Healthy (Normal), n = 5; Vehicle (Control), n = 5; STAM-Obeticholic acid (Obeticholic acid), n = 5; STAM-UNC1999 (UNC1999) n = 5; STAM-EZH2 (EPZ6438), n = 5. Full article ">Figure 2
Treatment with EZH2 inhibitors has no effect on body weight in STAM NASH mice. (A) Effect of EZH2 inhibitors (UNC1999, EPZ-6438) and obeticholic acid on body weight. (B) Effect of EZH2 inhibitors on the liver, kidney, and white adipose tissue relative weight. Relative organ weight was measured as the weight of the organ divided by the body weight. Data are shown as mean ± standard deviation (n = 5). Abbreviations: WAT, white adipose tissue. Full article ">Figure 3
Treatment with EZH2 inhibitors attenuates liver inflammation in STAM NASH mice. (A) Effect of EZH2 inhibitors (UNC1999, EPZ-6438) treatment on the serum levels of tumor necrosis factor-α (TNF-α). (B) Effects of EZH2 inhibitors and obeticholic acid treatment on the serum levels of alanine aminotransferase (ALT) and glucose. Statistically significant differences versus NASH group and EZH2 inhibitors treatment group are marked as * p < 0.05, respectively. Full article ">Figure 4
Treatment with EZH2 inhibitors inhibits ezh2 target Runx3 gene and liver inflammation-related IFN-γ gene in STAM NASH mice. Gene expression of EZH2 target and inflammatory marker from Real-Time PCR. Expression of genes in healthy (Normal), STAM-Vehicle (Control), STAM-UNC1999 (UNC1999), and STAM-EZH2 (EPZ6438) groups in the NASH mice. The final concentration of UNC1999 and EPZ6438 is 10 mg/kg. Statistically significant differences versus the STAM-Vehicle group and EZH2 inhibitors treatment group are marked as * p < 0.05 and ** p < 0.01, respectively. Full article ">Figure 5
Treatment with EZH2 inhibitors inhibits liver inflammation and fibrosis-related genes in STAM NASH mice. Gene expression of inflammatory and fibrosis markers from Real-Time PCR. Expression of marker genes in healthy (Normal), STAM-Vehicle (Control), STAM-Obeticholic acid (Obeticholic acid), STAM-UNC1999 (UNC1999) and STAM-EZH2 (EPZ6438) groups in the NASH mice. The final concentration of Obeticholic acid, UNC1999 and EPZ6438 is 10 mg/kg. Statistically significant differences versus the STAM-Vehicle group and EZH2 inhibitors treatment group are marked as * p < 0.05, respectively. Full article ">

25 pages, 8194 KiB

Open AccessArticle

Curcumin Sensitizes Kidney Cancer Cells to TRAIL-Induced Apoptosis via ROS Mediated Activation of JNK-CHOP Pathway and Upregulation of DR4

by Ismael Obaidi, Hilary Cassidy, Verónica Ibáñez Gaspar, Jasmin McCaul, Michael Higgins, Melinda Halász, Alison L. Reynolds, Breandan N. Kennedy and Tara McMorrow

Biology 2020, 9(5), 92; https://doi.org/10.3390/biology9050092 - 1 May 2020

Cited by 20 | Viewed by 6073

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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13 pages, 1527 KiB

Open AccessArticle

Epigenetic Changes in Host Ribosomal DNA Promoter Induced by an Asymptomatic Plant Virus Infection

by Miryam Pérez-Cañamás, Elizabeth Hevia and Carmen Hernández

Biology 2020, 9(5), 91; https://doi.org/10.3390/biology9050091 - 28 Apr 2020

Cited by 7 | Viewed by 4596

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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PLPV infection induces changes in the methylation pattern of rDNA promoter in N. benthamiana. (A) Diagram of the 45S rRNA transcriptional unit with the transcription start site indicated by an arrow. Stretch selected for analysis by bisulfite sequencing is detailed at the bottom, with the potential methylated cytosines labelled in pink (CG), purple (CHG), and orange (CHH). (B) Differential DNA methylation levels between mock-inoculated (green) and PLPV-infected plants (red) in the CG, CHG, and CHH sequence contexts. Error bars depict the standard deviations from two independent biological replicates and the statistical significance was tested using a paired t-test (* p < 0.05). (C) Position-specific methylation levels in the analyzed samples of rDNA. Full article ">Figure 2
Expression levels of DNA methylation/demethylation genes during a PLPV infection. RT-qPCR analysis of mRNA levels of the selected genes in systemic leaves from mock-inoculated (green) and PLPV-infected plants (red) harvested at 34 d.p.i. Bars depict standard deviations from three independent biological replicates and the statistical significance was tested using a paired t-test (* p < 0.05; ** p < 0.01). Full article ">Figure 3
Relative accumulation of pre-rRNA. (A) Fragment of the rRNA unit. Blue arrows below depict the position of the primers used in the analysis. (B) RT-qPCR analysis of systemic leaves from mock-inoculated (green) and PLPV-infected (red) plants harvested at 34 d.p.i. Bars depict standard deviations from three independent biological replicates and the statistical significance was tested using a paired t-test (** p < 0.01). Full article ">Figure 4
Analysis of the potential implication of the VSR p37 in rDNA promoter hypomethylation in N. benthamiana plants. (A) Differential DNA methylation levels between mock (green) and p37 (red) agroinfiltrated plants in the CG, CHG, and CHH sequence contexts. Error bars depict the standard deviations from two independent biological replicates. (B) RT-qPCR to estimate the relative expression levels of the genes involved in methylation/demethylation with imbalances in PLPV-infected plants. Data are representative of three biological replicates. The statistical significance was tested using a paired t-test (* p < 0.05; ** p < 0.01). Full article ">

10 pages, 896 KiB

Open AccessArticle

The Water Content Drives the Susceptibility of the Lichen Evernia prunastri and the Moss Brachythecium sp. to High Ozone Concentrations

by Andrea Vannini, Giulia Canali, Mario Pica, Cristina Nali and Stefano Loppi

Biology 2020, 9(5), 90; https://doi.org/10.3390/biology9050090 - 27 Apr 2020

Cited by 9 | Viewed by 3014

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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17 pages, 2154 KiB

Open AccessArticle

Next-Generation Sequencing and MALDI Mass Spectrometry in the Study of Multiresistant Processed Meat Vancomycin-Resistant Enterococci (VRE)

by Carolina Sabença, Telma de Sousa, Soraia Oliveira, Didier Viala, Laetitia Théron, Christophe Chambon, Michel Hébraud, Racha Beyrouthy, Richard Bonnet, Manuela Caniça, Patrícia Poeta and Gilberto Igrejas

Biology 2020, 9(5), 89; https://doi.org/10.3390/biology9050089 - 27 Apr 2020

Cited by 16 | Viewed by 4414

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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Figure 1
Representative spectrum of Enterococcus spp. without antibiotic. Full article ">Figure 2
Enterococcus faecium spectrum showing the peak m/z 6048 ± 1 (p-value is 0.00001) characteristic of these strains. Full article ">Figure 3
Peaks obtained for tetracycline. From the analysis of the ClinProTools software, the control spectrum without antibiotics (red) and the spectrum with the action of tetracycline (green) were obtained. The results show statistically significant peaks, with a p-value of 0.0000001, such as masses m/z 4424.01 and m/z 4526.45 noted by arrows. Full article ">Figure 4
The red spectrum represents the control and the green spectrum was obtained by the action of teicoplanin. The arrow shows a peak at m/z 4652.66 with greater intensity in the presence of the antibiotic. Full article ">Figure 5
The red spectrum represents the control, and the green spectrum was obtained by the action of ciprofloxacin. The arrow shows the peak at m/z 4652.66 with greater intensity in the presence of the antibiotic. Among the 27 specific peaks detected in the isolates resistant to ampicillin, only the peak with mass m/z 6338 was identified by the three classification algorithms, with an area under the curve (AUC) value of 0.89. This peak was also identified in erythromycin-resistant isolates. In contrast, three other peaks, m/z 2361.38, m/z 3304.92, and m/z 7240.29, proved to be exclusive to these isolates, which means they are potential biomarkers of ampicillin resistance. Full article ">Figure 6
The red spectrum represents the control, and the green spectrum was obtained by the action of ampicillin. The arrow shows the peak at m/z 3304.92 that was only detected in the presence of the antibiotic. Full article ">Figure 7
AUC value for the peak at m/z 4898.64. The value of the area under the ROC curve is 0.99, indicating a high-test pass for detecting the peak at m/z 4898.64. Full article ">

19 pages, 2733 KiB

Open AccessArticle

Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life

by Jacques Demongeot and Alexandra Henrion-Caude

Biology 2020, 9(5), 88; https://doi.org/10.3390/biology9050088 - 25 Apr 2020

Cited by 5 | Viewed by 5340

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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