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Biomolecules, Volume 9, Issue 1 (January 2019)

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Cover Story (view full-size image) The alignment of chromosomes to the spindle equator during mitosis, which is a prerequisite for [...] Read more.
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Open AccessEditorial Acknowledgement to Reviewers of Biomolecules in 2018
Biomolecules 2019, 9(1), 36; https://doi.org/10.3390/biom9010036
Published: 21 January 2019
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Abstract
Rigorous peer-review is the cornerstone of high-quality academic publishing [...] Full article
Open AccessReview The Many Faces of FKBP51
Biomolecules 2019, 9(1), 35; https://doi.org/10.3390/biom9010035
Received: 7 December 2018 / Revised: 14 January 2019 / Accepted: 14 January 2019 / Published: 21 January 2019
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Abstract
The FK506-binding protein 51 (FKBP51) has emerged as a key regulator of endocrine stress responses in mammals and as a potential therapeutic target for stress-related disorders (depression, post-traumatic stress disorder), metabolic disorders (obesity and diabetes) and chronic pain. Recently, FKBP51 has been implicated [...] Read more.
The FK506-binding protein 51 (FKBP51) has emerged as a key regulator of endocrine stress responses in mammals and as a potential therapeutic target for stress-related disorders (depression, post-traumatic stress disorder), metabolic disorders (obesity and diabetes) and chronic pain. Recently, FKBP51 has been implicated in several cellular pathways and numerous interacting protein partners have been reported. However, no consensus on the underlying molecular mechanisms has yet emerged. Here, we review the protein interaction partners reported for FKBP51, the proposed pathways involved, their relevance to FKBP51’s physiological function(s), the interplay with other FKBPs, and implications for the development of FKBP51-directed drugs. Full article
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Open AccessReview Nicotinamide Mononucleotide: Exploration of Diverse Therapeutic Applications of a Potential Molecule
Biomolecules 2019, 9(1), 34; https://doi.org/10.3390/biom9010034
Received: 4 January 2019 / Revised: 15 January 2019 / Accepted: 15 January 2019 / Published: 21 January 2019
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Abstract
Nicotinamide mononucleotide (NMN) is a nucleotide that is most recognized for its role as an intermediate of nicotinamide adenine dinucleotide (NAD+) biosynthesis. Although the biosynthetic pathway of NMN varies between eukaryote and prokaryote, two pathways are mainly followed in case of eukaryotic human—one [...] Read more.
Nicotinamide mononucleotide (NMN) is a nucleotide that is most recognized for its role as an intermediate of nicotinamide adenine dinucleotide (NAD+) biosynthesis. Although the biosynthetic pathway of NMN varies between eukaryote and prokaryote, two pathways are mainly followed in case of eukaryotic human—one is through the salvage pathway using nicotinamide while the other follows phosphorylation of nicotinamide riboside. Due to the unavailability of a suitable transporter, NMN enters inside the mammalian cell in the form of nicotinamide riboside followed by its subsequent conversion to NMN and NAD+. This particular molecule has demonstrated several beneficial pharmacological activities in preclinical studies, which suggest its potential therapeutic use. Mostly mediated by its involvement in NAD+ biosynthesis, the pharmacological activities of NMN include its role in cellular biochemical functions, cardioprotection, diabetes, Alzheimer’s disease, and complications associated with obesity. The recent groundbreaking discovery of anti-ageing activities of this chemical moiety has added a valuable essence in the research involving this molecule. This review focuses on the biosynthesis of NMN in mammalian and prokaryotic cells and mechanism of absorption along with the reported pharmacological activities in murine model. Full article
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Open AccessArticle Cord-Blood Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes
Biomolecules 2019, 9(1), 33; https://doi.org/10.3390/biom9010033
Received: 7 December 2018 / Revised: 8 January 2019 / Accepted: 15 January 2019 / Published: 21 January 2019
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Abstract
Previous studies suggest that children who progress to type 1 diabetes (T1D) later in life already have an altered serum lipid molecular profile at birth. Here, we compared cord blood lipidome across the three study groups: children who progressed to T1D (PT1D; n [...] Read more.
Previous studies suggest that children who progress to type 1 diabetes (T1D) later in life already have an altered serum lipid molecular profile at birth. Here, we compared cord blood lipidome across the three study groups: children who progressed to T1D (PT1D; n = 30), children who developed at least one islet autoantibody but did not progress to T1D during the follow-up (P1Ab; n = 33), and their age-matched controls (CTR; n = 38). We found that phospholipids, specifically sphingomyelins, were lower in T1D progressors when compared to P1Ab and the CTR. Cholesterol esters remained higher in PT1D when compared to other groups. A signature comprising five lipids was predictive of the risk of progression to T1D, with an area under the receiver operating characteristic curve (AUROC) of 0.83. Our findings provide further evidence that the lipidomic profiles of newborn infants who progress to T1D later in life are different from lipidomic profiles in P1Ab and CTR. Full article
(This article belongs to the Special Issue Lipidomics)
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Open AccessArticle Histone Acetylation Promotes Neutrophil Extracellular Trap Formation
Biomolecules 2019, 9(1), 32; https://doi.org/10.3390/biom9010032
Received: 19 December 2018 / Revised: 14 January 2019 / Accepted: 15 January 2019 / Published: 18 January 2019
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Abstract
Neutrophils undergo a unique form of cell death to generate neutrophil extracellular traps (NETs). It is well established that citrullination of histones (e.g., CitH3) facilitates chromatin decondensation during NET formation (NETosis), particularly during calcium-induced NETosis that is independent of nicotinamide adenine dinucleotide phosphate [...] Read more.
Neutrophils undergo a unique form of cell death to generate neutrophil extracellular traps (NETs). It is well established that citrullination of histones (e.g., CitH3) facilitates chromatin decondensation during NET formation (NETosis), particularly during calcium-induced NETosis that is independent of nicotinamide adenine dinucleotide phosphate (NADPH) oxidase (NOX) activation. However, the importance of other forms of histone modifications in NETosis has not been established. We considered that acetylation of histones would also facilitate NETosis. To test this hypothesis, we induced NOX-dependent NETosis in human neutrophils with phorbol myristate acetate or lipopolysaccharide (from Escherichia coli 0128), and NOX-independent NETosis with calcium ionophores A23187 or ionomycin (from Streptomyces conglobatus) in the presence or absence of two pan histone deacetylase inhibitors (HDACis), belinostat and panobinostat (within their half maximal inhibitory concentration (IC50) range). The presence of these inhibitors increased histone acetylation (e.g., AcH4) in neutrophils. Histone acetylation was sufficient to cause a significant increase (~20%) in NETosis in resting neutrophils above baseline values. When acetylation was promoted during NOX-dependent or -independent NETosis, the degree of NETosis additively increased (~15–30%). Reactive oxygen species (ROS) production is essential for baseline NETosis (mediated either by NOX or mitochondria); however, HDACis did not promote ROS production. The chromatin decondensation step requires promoter melting and transcriptional firing in both types of NETosis; consistent with this point, suppression of transcription prevented the NETosis induced by the acetylation of histones. Collectively, this study establishes that histone acetylation (e.g., AcH4) promotes NETosis at baseline, and when induced by both NOX-dependent or -independent pathway agonists, in human neutrophils. Therefore, we propose that acetylation of histone is a key component of NETosis. Full article
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Open AccessArticle BIOFACQUIM: A Mexican Compound Database of Natural Products
Biomolecules 2019, 9(1), 31; https://doi.org/10.3390/biom9010031
Received: 29 November 2018 / Revised: 28 December 2018 / Accepted: 15 January 2019 / Published: 17 January 2019
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Abstract
Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds with natural origins is increasing. Several countries, Brazil, France, Panama and, recently, Vietnam, have initiatives [...] Read more.
Compound databases of natural products have a major impact on drug discovery projects and other areas of research. The number of databases in the public domain with compounds with natural origins is increasing. Several countries, Brazil, France, Panama and, recently, Vietnam, have initiatives in place to construct and maintain compound databases that are representative of their diversity. In this proof-of-concept study, we discuss the first version of BIOFACQUIM, a novel compound database with natural products isolated and characterized in Mexico. We discuss its construction, curation, and a complete chemoinformatic characterization of the content and coverage in chemical space. The profile of physicochemical properties, scaffold content, and diversity, as well as structural diversity based on molecular fingerprints is reported. BIOFACQUIM is available for free. Full article
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Open AccessReview A Review on Bioactivities of Tobacco Cembranoid Diterpenes
Biomolecules 2019, 9(1), 30; https://doi.org/10.3390/biom9010030
Received: 9 December 2018 / Revised: 27 December 2018 / Accepted: 14 January 2019 / Published: 16 January 2019
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Abstract
Cembranoids are carbocyclic diterpenes comprising four isoprene units and are natural products with a parent skeleton consisting of a 14-membered ring. They have gained wide interest in recent years and are a major hotspot in the research of natural product chemistry. Since 1962, [...] Read more.
Cembranoids are carbocyclic diterpenes comprising four isoprene units and are natural products with a parent skeleton consisting of a 14-membered ring. They have gained wide interest in recent years and are a major hotspot in the research of natural product chemistry. Since 1962, various tobacco cembranoid diterpenes have been identified. This review systematically discusses and summarises the excellent antimicrobial, insecticidal, cytotoxic and neuroprotective activities of tobacco cembranoid diterpenes. These compounds show potential to be developed as botanical fungicides, cytotoxic drugs and drugs for the treatment of human immunodeficiency virus, Alzheimer’s disease, Parkinson’s disease, and other neurodegenerative diseases. However, there are relatively few studies on the structure–activity relationship (SAR) of tobacco cembranoid diterpenes. Therefore, future studies should focus on their structural modification, SAR and biogenic relationships. Full article
(This article belongs to the Special Issue Evaluation and formulation of Bioactive Terpenes)
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Open AccessReview Impact of p85α Alterations in Cancer
Biomolecules 2019, 9(1), 29; https://doi.org/10.3390/biom9010029
Received: 7 December 2018 / Revised: 7 January 2019 / Accepted: 11 January 2019 / Published: 15 January 2019
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Abstract
The phosphatidylinositol 3-kinase (PI3K) pathway plays a central role in the regulation of cell signaling, proliferation, survival, migration and vesicle trafficking in normal cells and is frequently deregulated in many cancers. The p85α protein is the most characterized regulatory subunit of the class [...] Read more.
The phosphatidylinositol 3-kinase (PI3K) pathway plays a central role in the regulation of cell signaling, proliferation, survival, migration and vesicle trafficking in normal cells and is frequently deregulated in many cancers. The p85α protein is the most characterized regulatory subunit of the class IA PI3Ks, best known for its regulation of the p110-PI3K catalytic subunit. In this review, we will discuss the impact of p85α mutations or alterations in expression levels on the proteins p85α is known to bind and regulate. We will focus on alterations within the N-terminal half of p85α that primarily regulate Rab5 and some members of the Rho-family of GTPases, as well as those that regulate PTEN (phosphatase and tensin homologue deleted on chromosome 10), the enzyme that directly counteracts PI3K signaling. We highlight recent data, mapping the interaction surfaces of the PTEN–p85α breakpoint cluster region homology (BH) domain, which sheds new light on key residues in both proteins. As a multifunctional protein that binds and regulates many different proteins, p85α mutations at different sites have different impacts in cancer and would necessarily require distinct treatment strategies to be effective. Full article
(This article belongs to the Special Issue Phosphoinositide 3-kinase, a Field in Transition)
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Open AccessReview Aurora A Protein Kinase: To the Centrosome and Beyond
Biomolecules 2019, 9(1), 28; https://doi.org/10.3390/biom9010028
Received: 7 December 2018 / Revised: 9 January 2019 / Accepted: 9 January 2019 / Published: 15 January 2019
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Abstract
Accurate chromosome segregation requires the perfect spatiotemporal rearrangement of the cellular cytoskeleton. Isolated more than two decades ago from Drosophila, Aurora A is a widespread protein kinase that plays key roles during cell division. Numerous studies have described the localisation of Aurora [...] Read more.
Accurate chromosome segregation requires the perfect spatiotemporal rearrangement of the cellular cytoskeleton. Isolated more than two decades ago from Drosophila, Aurora A is a widespread protein kinase that plays key roles during cell division. Numerous studies have described the localisation of Aurora A at centrosomes, the mitotic spindle, and, more recently, at mitotic centromeres. In this review, we will summarise the cytoskeletal rearrangements regulated by Aurora A during cell division. We will also discuss the recent discoveries showing that Aurora A also controls not only the dynamics of the cortical proteins but also regulates the centromeric proteins, revealing new roles for this kinase during cell division. Full article
(This article belongs to the Special Issue Cytoskeleton and Regulation of Mitosis)
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Open AccessArticle Enzymatic Synthesis and Characterization of a Novel α-1→6-Glucosyl Rebaudioside C Derivative Sweetener
Biomolecules 2019, 9(1), 27; https://doi.org/10.3390/biom9010027
Received: 14 December 2018 / Revised: 31 December 2018 / Accepted: 4 January 2019 / Published: 14 January 2019
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Abstract
Zero-calorie high-intensity sweeteners from natural sources perform very well in the market place. This has encouraged food scientists to continue the effort to search for novel natural ingredients to satisfy consumer demand. Rebaudioside C (reb C) is the third most prevalent steviol glycoside [...] Read more.
Zero-calorie high-intensity sweeteners from natural sources perform very well in the market place. This has encouraged food scientists to continue the effort to search for novel natural ingredients to satisfy consumer demand. Rebaudioside C (reb C) is the third most prevalent steviol glycoside in the leaves of the Stevia rebaudiana Bertoni plant, but has limited applications in food and beverage products due to its low sweetness and high lingering bitterness compared to other major steviol glycosides, such as rebaudioside A (reb A). Here we present a new enzyme modification strategy to improve the taste profile of reb C by using Cargill’s propriety enzyme and sucrose as a glucose donor. A novel α-1→6-glucosyl reb C derivative was produced and its structure was elucidated by mass spectrometry and NMR spectroscopy. Sensory analysis demonstrated that this new reb C derivative has improved sweetness, reduced bitterness, and enhanced solubility in water. Full article
(This article belongs to the Special Issue Evaluation and formulation of Bioactive Terpenes)
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Open AccessArticle Foliar Accumulation of Melatonin Applied to the Roots of Maize (Zea mays) Seedlings
Biomolecules 2019, 9(1), 26; https://doi.org/10.3390/biom9010026
Received: 16 December 2018 / Revised: 8 January 2019 / Accepted: 9 January 2019 / Published: 12 January 2019
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Abstract
Plants absorb melatonin from the environments as well as they synthesize the regulatory molecule. We applied melatonin to the roots of maize (Zea mays) seedlings and examined its accumulation in the leaves. Melatonin accumulation in the leaves was proportional to the [...] Read more.
Plants absorb melatonin from the environments as well as they synthesize the regulatory molecule. We applied melatonin to the roots of maize (Zea mays) seedlings and examined its accumulation in the leaves. Melatonin accumulation in the leaves was proportional to the exogenously applied concentrations up to 5 mM, without saturation. Time-course analysis of the accumulated melatonin content did not show an adaptable (or desensitizable) uptake system over a 24-h period. Melatonin accumulation in the leaves was reduced significantly by the plant hormones abscisic acid (ABA) and salicylic acid (SA), which commonly cause stomatal closure. The application of ABA and benzo-18-crown-6 (18-CR, a stomata-closing agent) induced stomatal closure and simultaneously decreased melatonin content in the leaves. When plants were shielded from airflow in the growth chamber, melatonin accumulation in the leaves decreased, indicating the influence of reduced transpiration. We conclude that melatonin applied exogenously to the root system is absorbed, mobilized upward according to the transpirational flow, and finally accumulated in the leaves. Full article
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Open AccessArticle The Effect of Arabic Gum on Renal Function in Reversible Unilateral Ureteric Obstruction
Biomolecules 2019, 9(1), 25; https://doi.org/10.3390/biom9010025
Received: 5 November 2018 / Revised: 7 January 2019 / Accepted: 8 January 2019 / Published: 11 January 2019
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Abstract
Arabic gum (AG) has antioxidant and anti-inflammatory properties. However, the effect of AG in ureteric obstruction (UO) has not been investigated yet. Male rats underwent reversible left unilateral UO (UUO) for 72 h. Group AG-1 (n = 12) received AG 15 g/kg/day [...] Read more.
Arabic gum (AG) has antioxidant and anti-inflammatory properties. However, the effect of AG in ureteric obstruction (UO) has not been investigated yet. Male rats underwent reversible left unilateral UO (UUO) for 72 h. Group AG-1 (n = 12) received AG 15 g/kg/day dissolved in drinking water starting seven days before and continuing throughout the period of the UUO, whereas group Vx-1 (n = 8) had only water. Group AG-2 (n = 12) and Vx-2 (n = 8) had similar protocols as AG-1 and Vx-1, respectively, but underwent terminal experiments to measure renal functions, six days post-UUO reversal. Arabic gum significantly attenuated the UUO-induced increase in the tissue level of malonedialdehyde and superoxide dismutase and the rise in the gene expression of TNF-α, TGF-β1, and p53 in AG-1 compared to Vx-1. It also attenuated the severity of tubular dilatation. However, AG did not affect the alterations in the renal blood flow or glomerular filtration rate. The fractional sodium excretion was lower in AG-2 but did not reach statistical significance (0.40 ± 0.11 vs 0.74 ± 0.12, p = 0.07). AG attenuated the UUO-induced rise in oxidative stress markers and proinflammatory and profibrotic cytokines and the degree of renal tubular dilatation, indicating a protective effect in obstructive nephropathy. Full article
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Open AccessArticle Plasma Zonulin Levels as a Non-Invasive Biomarker of Intestinal Permeability in Women with Gestational Diabetes Mellitus
Biomolecules 2019, 9(1), 24; https://doi.org/10.3390/biom9010024
Received: 22 November 2018 / Revised: 4 January 2019 / Accepted: 7 January 2019 / Published: 11 January 2019
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Abstract
Objective: We aimed to compare the levels of plasma zonulin, a non-invasive biomarker of increased intestinal permeability, between pregnant subjects, with and without gestational diabetes mellitus (GDM), at 24–28 gestational weeks. The eighty-five consecutive pregnant subjects that presented to our hospital’s obstetrics outpatient [...] Read more.
Objective: We aimed to compare the levels of plasma zonulin, a non-invasive biomarker of increased intestinal permeability, between pregnant subjects, with and without gestational diabetes mellitus (GDM), at 24–28 gestational weeks. The eighty-five consecutive pregnant subjects that presented to our hospital’s obstetrics outpatient clinic and were diagnosed with GDM, for the first time by an oral glucose tolerance test (OGTT), formed the GDM group; 90 consecutive subjects that were not diagnosed with GDM by OGTT, formed the control group. The diagnosis of GDM was made by an OGTT performed between the 24th and 28th weeks of gestation, and in compliance with the American Diabetes Association (ADA) criteria. Plasma zonulin levels were measured by the enzyme-linked immunosorbent assay (ELISA) methods. The Plasma zonulin level was significantly higher in the GDM group than the control group (p < 0.001). A correlation analysis showed that plasma zonulin level was positively correlated to body mass index (BMI), creatinine, fasting plasma glucose, baseline, first hour, and two hours glucose levels and the OGTT, hemoglobin A1C (HbA1C), homeostatic model assessment for insulin resistance (HOMA-IR), and alanine aminotransferase (ALT) levels. Our findings suggest that zonulin may be a non-invasive biomarker involved in the pathogenesis of GDM. Further large-scale studies are needed on this subject. Full article
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Open AccessReview Bio-Molecular Applications of Recent Developments in Optical Tweezers
Biomolecules 2019, 9(1), 23; https://doi.org/10.3390/biom9010023
Received: 23 November 2018 / Revised: 2 January 2019 / Accepted: 2 January 2019 / Published: 11 January 2019
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Abstract
In the past three decades, the ability to optically manipulate biomolecules has spurred a new era of medical and biophysical research. Optical tweezers (OT) have enabled experimenters to trap, sort, and probe cells, as well as discern the structural dynamics of proteins and [...] Read more.
In the past three decades, the ability to optically manipulate biomolecules has spurred a new era of medical and biophysical research. Optical tweezers (OT) have enabled experimenters to trap, sort, and probe cells, as well as discern the structural dynamics of proteins and nucleic acids at single molecule level. The steady improvement in OT’s resolving power has progressively pushed the envelope of their applications; there are, however, some inherent limitations that are prompting researchers to look for alternatives to the conventional techniques. To begin with, OT are restricted by their one-dimensional approach, which makes it difficult to conjure an exhaustive three-dimensional picture of biological systems. The high-intensity trapping laser can damage biological samples, a fact that restricts the feasibility of in vivo applications. Finally, direct manipulation of biological matter at nanometer scale remains a significant challenge for conventional OT. A significant amount of literature has been dedicated in the last 10 years to address the aforementioned shortcomings. Innovations in laser technology and advances in various other spheres of applied physics have been capitalized upon to evolve the next generation OT systems. In this review, we elucidate a few of these developments, with particular focus on their biological applications. The manipulation of nanoscopic objects has been achieved by means of plasmonic optical tweezers (POT), which utilize localized surface plasmons to generate optical traps with enhanced trapping potential, and photonic crystal optical tweezers (PhC OT), which attain the same goal by employing different photonic crystal geometries. Femtosecond optical tweezers (fs OT), constructed by replacing the continuous wave (cw) laser source with a femtosecond laser, promise to greatly reduce the damage to living samples. Finally, one way to transcend the one-dimensional nature of the data gained by OT is to couple them to the other large family of single molecule tools, i.e., fluorescence-based imaging techniques. We discuss the distinct advantages of the aforementioned techniques as well as the alternative experimental perspective they provide in comparison to conventional OT. Full article
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Open AccessReview Combination of Cell-Penetrating Peptides with Nanoparticles for Therapeutic Application: A Review
Biomolecules 2019, 9(1), 22; https://doi.org/10.3390/biom9010022
Received: 17 December 2018 / Revised: 3 January 2019 / Accepted: 3 January 2019 / Published: 10 January 2019
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Abstract
Cell-penetrating peptides (CPPs), also known as protein translocation domains, membrane translocating sequences or Trojan peptides, are small molecules of 6 to 30 amino acid residues capable of penetrating biological barriers and cellular membranes. Furthermore, CPP have become an alternative strategy to overcome some [...] Read more.
Cell-penetrating peptides (CPPs), also known as protein translocation domains, membrane translocating sequences or Trojan peptides, are small molecules of 6 to 30 amino acid residues capable of penetrating biological barriers and cellular membranes. Furthermore, CPP have become an alternative strategy to overcome some of the current drug limitations and combat resistant strains since CPPs are capable of delivering different therapeutic molecules against a wide range of diseases. In this review, we address the recent conjugation of CPPs with nanoparticles, which constitutes a new class of delivery vectors with high pharmaceutical potential in a variety of diseases. Full article
(This article belongs to the Special Issue Multidrug Combinations)
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Open AccessArticle Doxorubicin Is Key for the Cardiotoxicity of FAC (5-Fluorouracil + Adriamycin + Cyclophosphamide) Combination in Differentiated H9c2 Cells
Biomolecules 2019, 9(1), 21; https://doi.org/10.3390/biom9010021
Received: 4 October 2018 / Revised: 28 December 2018 / Accepted: 3 January 2019 / Published: 10 January 2019
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Currently, a common therapeutic approach in cancer treatment encompasses a drug combination to attain an overall better efficacy. Unfortunately, it leads to a higher incidence of severe side effects, namely cardiotoxicity. This work aimed to assess the cytotoxicity of doxorubicin (DOX, also known [...] Read more.
Currently, a common therapeutic approach in cancer treatment encompasses a drug combination to attain an overall better efficacy. Unfortunately, it leads to a higher incidence of severe side effects, namely cardiotoxicity. This work aimed to assess the cytotoxicity of doxorubicin (DOX, also known as Adriamycin), 5-fluorouracil (5-FU), cyclophosphamide (CYA), and their combination (5-Fluorouracil + Adriamycin + Cyclophosphamide, FAC) in H9c2 cardiac cells, for a better understanding of the contribution of each drug to FAC-induced cardiotoxicity. Differentiated H9c2 cells were exposed to pharmacological relevant concentrations of DOX (0.13–5 μM), 5-FU (0.13–5 μM), CYA (0.13–5 μM) for 24 or 48 h. Cells were also exposed to FAC mixtures (0.2, 1 or 5 μM of each drug and 50 μM 5-FU + 1 μM DOX + 50 μM CYA). DOX was the most cytotoxic drug, followed by 5-FU and lastly CYA in both cytotoxicity assays (reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and neutral red (NR) uptake). Concerning the equimolar combination with 1 or 5 μM, FAC caused similar cytotoxicity to DOX alone. Even in the presence of higher concentrations of 5-FU and CYA (50 μM 5-FU + 1 μM DOX + 50 μM CYA), 1 μM DOX was still a determinant for the cardiotoxicity observed in the cytotoxicity assays, phase contrast morphological evaluation, and mitochondrial potential depolarization evaluation. To the best of our knowledge, this was the first in vitro work with this combination regimen, DOX being the most toxic drug and key to the toxicity of FAC. Full article
(This article belongs to the Special Issue Multidrug Combinations)
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Open AccessReview Versatility of Cyclophilins in Plant Growth and Survival: A Case Study in Arabidopsis
Biomolecules 2019, 9(1), 20; https://doi.org/10.3390/biom9010020
Received: 19 November 2018 / Revised: 22 December 2018 / Accepted: 2 January 2019 / Published: 10 January 2019
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Abstract
Cyclophilins (CYPs) belong to a peptidyl-prolyl cis-trans isomerase family, and were first characterized in mammals as a target of an immunosuppressive drug, cyclosporin A, preventing proinflammatory cytokine production. In Arabidopsis, 29 CYPs and CYP-like proteins are found across all subcellular compartments, involved [...] Read more.
Cyclophilins (CYPs) belong to a peptidyl-prolyl cis-trans isomerase family, and were first characterized in mammals as a target of an immunosuppressive drug, cyclosporin A, preventing proinflammatory cytokine production. In Arabidopsis, 29 CYPs and CYP-like proteins are found across all subcellular compartments, involved in various physiological processes including transcriptional regulation, organogenesis, photosynthetic and hormone signaling pathways, stress adaptation and defense responses. These important but diverse activities of CYPs must be reflected by their versatility as cellular and molecular modulators. However, our current knowledge regarding their mode of actions is still far from complete. This review will briefly revisit recent progresses on the roles and mechanisms of CYPs in Arabidopsis studies, and information gaps within, which help understanding the phenotypic and environmental plasticity of plants. Full article
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Open AccessArticle Annatto (Bixa orellana) δ-TCT Supplementation Protection against Embryonic Malformations through Alterations in PI3K/Akt-Cyclin D1 Pathway
Biomolecules 2019, 9(1), 19; https://doi.org/10.3390/biom9010019
Received: 31 October 2018 / Revised: 20 December 2018 / Accepted: 20 December 2018 / Published: 10 January 2019
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Protective action by annatto-derived delta-tocotrienol (δ-TCT) and soy-derived alpha-tocopherol (α-TOC) through the regulation of the PI3K/Akt-cyclin D1 pathway against nicotine-induced DNA damage is the focus of the present study. Nicotine, which has been widely reported to have numerous adverse effects on the reproductive [...] Read more.
Protective action by annatto-derived delta-tocotrienol (δ-TCT) and soy-derived alpha-tocopherol (α-TOC) through the regulation of the PI3K/Akt-cyclin D1 pathway against nicotine-induced DNA damage is the focus of the present study. Nicotine, which has been widely reported to have numerous adverse effects on the reproductive system, was used as a reproductive toxicant. 48 female balb/c mice (6–8 weeks) (23–25 g) were randomly divided into eight groups (Grp.1–Grp.8; n = 6) and treated with either nicotine or/and annatto δ-TCT/soy α-TOC for seven consecutive days. On Day 8, the females were superovulated and mated before euthanization for embryo collection (46 h post-coitum). Fifty 2-cell embryos from each group were used in gene expression analysis using Affymetrix QuantiGene Plex2.0 assay. Findings indicated that nicotine (Grp.2) significantly decreased (p < 0.05) the number of produced 2-cell embryos compared to the control (Grp.1). Intervention with mixed annatto δ-TCT (Grp.3) and pure annatto δ-TCT (Grp.4) significantly increased the number of produced 2-cell embryos by 127% and 79%, respectively compared to Grp.2, but these were lower than Grp.1. Concurrent treatment with soy α-TOC (Grp.5) decreased embryo production by 7%. Supplementations with δ-TCT and α-TOC alone (Grp.6-Grp.8) significantly increased (p < 0.05) the number of produced 2-cell embryos by 50%, 36%, and 41%, respectively, compared to control (Grp.1). These results were found to be associated with alterations in the PI3K/Akt-Cyclin D1 genes expressions, indicating the inhibitory effects of annatto δ-TCT and soy α-TOC against nicotinic embryonic damage. To our knowledge, this is the first attempt in studying the benefits of annatto δ-TCT on murine preimplantation 2-cell embryos. Full article
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Open AccessArticle Longitudinal Study of Delta-Aminolevulinate Dehydratase Activity and Oxidative Profile in Healthy Pregnant Women
Biomolecules 2019, 9(1), 18; https://doi.org/10.3390/biom9010018
Received: 5 December 2018 / Revised: 28 December 2018 / Accepted: 2 January 2019 / Published: 9 January 2019
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Abstract
Pregnancy is characterized by changes in various organs, triggering changes in the use of energy substrates and increased oxygen consumption. In addition, gestation is an oxidative event that can be assessed by the relationship between free radicals and antioxidants produced by the body. [...] Read more.
Pregnancy is characterized by changes in various organs, triggering changes in the use of energy substrates and increased oxygen consumption. In addition, gestation is an oxidative event that can be assessed by the relationship between free radicals and antioxidants produced by the body. Excessive production of free radicals has detrimental effects such as damage to enzymes, carbohydrates, and DNA. Thus, the objective of this study was to evaluate the oxidative status and antioxidant responses throughout pregnancy through a longitudinal study. Reactive oxygen species were analyzed by means of thiobarbituric acid reactive substances and nitric oxide, the antioxidant system through vitamin C, sulfhydryl groups, total antioxidant capacity, and ferric reducing ability of plasma as well as enzymes such as catalase and delta-aminolevulinate-dehydratase in pregnant women in the three gestational trimesters (n = 30). According to the results, the markers of oxidative damage showed significant differences in the different gestational trimesters where they were increased in the second trimester when compared to the first trimester. The antioxidant defenses responded differently in each gestational trimester, suggesting a response pattern to try to combat the damage caused by free radicals, in order to stabilize the increase of oxidative stress caused in the second gestational trimester. Full article
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Open AccessReview Specialized Roles for Actin in Osteoclasts: Unanswered Questions and Therapeutic Opportunities
Biomolecules 2019, 9(1), 17; https://doi.org/10.3390/biom9010017
Received: 10 December 2018 / Revised: 3 January 2019 / Accepted: 4 January 2019 / Published: 9 January 2019
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Abstract
Osteoclasts are cells of the hematopoietic lineage that are specialized to resorb bone. In osteoclasts, the actin cytoskeleton engages in at least two unusual activities that are required for resorption. First, microfilaments form a dynamic and structurally elaborate actin ring. Second, microfilaments bind [...] Read more.
Osteoclasts are cells of the hematopoietic lineage that are specialized to resorb bone. In osteoclasts, the actin cytoskeleton engages in at least two unusual activities that are required for resorption. First, microfilaments form a dynamic and structurally elaborate actin ring. Second, microfilaments bind vacuolar H+-ATPase (V-ATPase) and are involved in forming the V-ATPase-rich ruffled plasma membrane. The current review examines these two specialized functions with emphasis on the identification of new therapeutic opportunities. The actin ring is composed of substructures called podosomes that are interwoven to form a cohesive superstructure. Studies examining the regulation of the formation of actin rings and its constituent proteins are reviewed. Areas where there are gaps in the knowledge are highlighted. Microfilaments directly interact with the V-ATPase through an actin binding site in the B2-subunit of V-ATPase. This binding interaction is required for ruffled membrane formation. Recent studies show that an inhibitor of the interaction blocks bone resorption in pre-clinical animal models, including a model of post-menopausal osteoporosis. Because the unusual actin-based resorption complex is unique to osteoclasts and essential for bone resorption, it is likely that deeper understanding of its underlying mechanisms will lead to new approaches to treat bone disease. Full article
(This article belongs to the Special Issue Key Biomolecules in Bone Resorption)
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Open AccessArticle High Glucose Represses the Anti-Proliferative and Pro-Apoptotic Effect of Metformin in Triple Negative Breast Cancer Cells
Biomolecules 2019, 9(1), 16; https://doi.org/10.3390/biom9010016
Received: 20 November 2018 / Revised: 26 December 2018 / Accepted: 3 January 2019 / Published: 8 January 2019
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Abstract
Metformin, the most widely prescribed anti-diabetic drug, is shown to possess anti-cancer potential in treatment of cancers, including breast cancer; decreases breast cancer risk; and improves overall survival. However, reports suggest that higher glucose concentrations may negatively impact the anti-cancer efficacy of metformin. [...] Read more.
Metformin, the most widely prescribed anti-diabetic drug, is shown to possess anti-cancer potential in treatment of cancers, including breast cancer; decreases breast cancer risk; and improves overall survival. However, reports suggest that higher glucose concentrations may negatively impact the anti-cancer efficacy of metformin. Therefore, we examined the anti-cancer potential of metformin in triple-negative breast cancer cells (TNBCs) exposed to different glucose (25 mM, 5.5 mM and zero glucose/glucose-starved) conditions. Our data indicates that a high glucose (25 mM) concentration (mimicking diabetes) significantly abrogated the effect of metformin on cell proliferation, cell death and cell cycle arrest in addition to loss of efficacy in inhibition of the mTOR pathway, a key metabolic pathway in TNBC cells. The mTOR pathway is activated in TNBCs compared to other subtypes of breast cancer, regulates the synthesis of proteins that are critical for the growth and survival of cancer cells and its activation is correlated to poor outcomes among TNBC patients, while also contributing to metastatic progression and development of resistance to chemotherapy/radiotherapy. Our studies were performed in two different types of TNBCs, MDA-MB-231 cells (mesenchymal stem cell-like (MSL)) and MDA-MB-468 (basal like-1 (BL-1)). Interestingly, lower concentrations of metformin (50, 100, 250, and 500 μM) significantly increased cell proliferation in 25 mM glucose exposed MDA-MB-231 cells, an effect which was not observed in MDA-MB-468 cells, indicating that the effective concentration of metformin when used as anti-cancer drug in TNBCs may have to be determined based on cell type and blood glucose concentration. Our data indicates that metformin treatment was most effective under zero glucose/glucose-starved conditions in MDA-MB-468 with a significant increase in the apoptotic population (62.3 ± 1.5%; p-value < 0.01). Under 5.5 mM glucose conditions in both MDA-MB-231 and MDA-MB-468 cells our data showed reduced viability of 73.56 ± 2.53%; p-value < 0.05 and 70.49 ± 1.68%; p-value < 0.001, respectively, along with a significant increase in apoptotic populations of both cell types. Furthermore, metformin (2 mM) inhibited the mTOR pathway and its downstream components under zero glucose/glucose-starved conditions indicating that using metformin in combination with agents that inhibit the glycolytic pathway should be more beneficial for the treatment of triple-negative breast cancers in diabetic individuals. Full article
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Open AccessReview Sporadic Inclusion Body Myositis: An Acquired Mitochondrial Disease with Extras
Biomolecules 2019, 9(1), 15; https://doi.org/10.3390/biom9010015
Received: 21 November 2018 / Revised: 19 December 2018 / Accepted: 19 December 2018 / Published: 7 January 2019
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Abstract
The sporadic form of inclusion body myositis (IBM) is the most common late-onset myopathy. Its complex pathogenesis includes degenerative, inflammatory and mitochondrial aspects. However, which of those mechanisms are cause and which effect, as well as their interrelations, remain partly obscured to this [...] Read more.
The sporadic form of inclusion body myositis (IBM) is the most common late-onset myopathy. Its complex pathogenesis includes degenerative, inflammatory and mitochondrial aspects. However, which of those mechanisms are cause and which effect, as well as their interrelations, remain partly obscured to this day. In this review the nature of the mitochondrial dysregulation in IBM muscle is explored and comparison is made with other muscle disorders. Mitochondrial alterations in IBM are evidenced by histological and serum biomarkers. Muscular mitochondrial dynamics is disturbed, with deregulated organelle fusion leading to subsequent morphological alterations and muscle displays abnormal mitophagy. The tissue increases mitochondrial content in an attempt to compensate dysfunction, yet mitochondrial DNA (mtDNA) alterations and mild mtDNA depletion are also present. Oxidative phosphorylation defects have repeatedly been shown, most notably a reduction in complex IV activities and levels of mitokines and regulatory RNAs are perturbed. Based on the cumulating evidence of mitochondrial abnormality as a disease contributor, it is therefore warranted to regard IBM as a mitochondrial disease, offering a feasible therapeutic target to be developed for this yet untreatable condition. Full article
(This article belongs to the Special Issue Mitochondrial Diseases)
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Open AccessArticle Toxicity Mechanism of Low Doses of NaGdF4:Yb3+,Er3+ Upconverting Nanoparticles in Activated Macrophage Cell Lines
Biomolecules 2019, 9(1), 14; https://doi.org/10.3390/biom9010014
Received: 20 November 2018 / Revised: 15 December 2018 / Accepted: 21 December 2018 / Published: 3 January 2019
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Abstract
Gadolinium-doped nanoparticles (NPs) are regarded as promising luminescent probes. In this report, we studied details of toxicity mechanism of low doses of NaGdF4-based fluorescent nanoparticles in activated RAW264.7, J774A.1 macrophages. These cell lines were specifically sensitive to the treatment with nanoparticles. [...] Read more.
Gadolinium-doped nanoparticles (NPs) are regarded as promising luminescent probes. In this report, we studied details of toxicity mechanism of low doses of NaGdF4-based fluorescent nanoparticles in activated RAW264.7, J774A.1 macrophages. These cell lines were specifically sensitive to the treatment with nanoparticles. Using nanoparticles of three different sizes, but with a uniform zeta potential (about −11 mV), we observed rapid uptake of NPs by the cells, resulting in the increased lysosomal compartment and subsequent superoxide induction along with a decrease in mitochondrial potential, indicating the impairment of mitochondrial homeostasis. At the molecular level, this led to upregulation of proapoptotic Bax and downregulation of anti-apoptotic Bcl-2, which triggered the apoptosis with phosphatidylserine externalization, caspase-3 activation and DNA fragmentation. We provide a time frame of the toxicity process by presenting data from different time points. These effects were present regardless of the size of nanoparticles. Moreover, despite the stability of NaGdF4 nanoparticles at low pH, we identified cell acidification as an essential prerequisite of cytotoxic reaction using acidification inhibitors (NH4Cl or Bafilomycin A1). Therefore, approaching the evaluation of the biocompatibility of such materials, one should keep in mind that toxicity could be revealed only in specific cells. On the other hand, designing gadolinium-doped NPs with increased resistance to harsh conditions of activated macrophage phagolysosomes should prevent NP decomposition, concurrent gadolinium release, and thus the elimination of its toxicity. Full article
(This article belongs to the Special Issue Nanoparticles for Cancer Therapy)
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Open AccessReview Non-Curcuminoids from Turmeric and Their Potential in Cancer Therapy and Anticancer Drug Delivery Formulations
Biomolecules 2019, 9(1), 13; https://doi.org/10.3390/biom9010013
Received: 21 November 2018 / Revised: 14 December 2018 / Accepted: 17 December 2018 / Published: 2 January 2019
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Abstract
Over the past decades curcuminoids have been extensively studied for their biological activities such as antiulcer, antifibrotic, antiviral, antibacterial, antiprotozoal, antimutagenic, antifertility, antidiabetic, anticoagulant, antivenom, antioxidant, antihypotensive, antihypocholesteremic, and anticancer activities. With the perception of limited toxicity and cost, these compounds forms an [...] Read more.
Over the past decades curcuminoids have been extensively studied for their biological activities such as antiulcer, antifibrotic, antiviral, antibacterial, antiprotozoal, antimutagenic, antifertility, antidiabetic, anticoagulant, antivenom, antioxidant, antihypotensive, antihypocholesteremic, and anticancer activities. With the perception of limited toxicity and cost, these compounds forms an integral part of cancer research and is well established as a potential anticancer agent. However, only few studies have focused on the other bioactive molecules of turmeric, known as non-curcuminoids, which are also equally potent as curcuminoids. This review aims to explore the comprehensive potency including the identification, physicochemical properties, and anticancer mechanism inclusive of molecular docking studies of non-curcuminoids such as turmerones, elemene, furanodiene (FN), bisacurone, germacrone, calebin A (CA), curdione, and cyclocurcumin. An insight into the clinical studies of these curcumin-free compounds are also discussed which provides ample evidence that favors the therapeutic potential of these compounds. Like curcuminoids, limited solubility and bioavailability are the most fragile domain, which circumscribe further applications of these compounds. Thus, this review credits the encapsulation of non-curcuminoid components in diverse drug delivery systems such as co-crystals, solid lipid nanoparticles, liposomes, microspheres, polar-non-polar sandwich (PNS) technology, which help abolish their shortcomings and flaunt their ostentatious benefits as anticancer activities. Full article
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Open AccessArticle Integrated Transcriptome Analysis Reveals Plant Hormones Jasmonic Acid and Salicylic Acid Coordinate Growth and Defense Responses upon Fungal Infection in Poplar
Biomolecules 2019, 9(1), 12; https://doi.org/10.3390/biom9010012
Received: 18 November 2018 / Revised: 20 December 2018 / Accepted: 21 December 2018 / Published: 2 January 2019
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Abstract
Plants have evolved a sophisticated system to respond to various stresses. Fungal attack or infection is one of the most important biotic stresses for most plants. During the defense response to fungal infection, the plant hormones jasmonic acid (JA) and salicylic acid (SA) [...] Read more.
Plants have evolved a sophisticated system to respond to various stresses. Fungal attack or infection is one of the most important biotic stresses for most plants. During the defense response to fungal infection, the plant hormones jasmonic acid (JA) and salicylic acid (SA) play critical roles. Here, gene expression data on JA/SA treatments and Melampsora larici-populina (MLP) infection were generated. Integrated transcriptome analyses of these data were performed, and 943 genes in total were identified as common responsive genes (CRG). Gene ontology (GO) term analysis revealed that the genes from CRG are generally involved in the processes of stress responses, metabolism, and growth and development. The further cluster analysis of the CRG identified a set of core genes that are involved in the JA/SA-mediated response to fungal defense with distinct gene expression profiles upon JA/SA treatment, which highlighted the different effects of these two hormones on plant fungal defenses. The modifications of several pathways relative to metabolism, biotic stress, and plant hormone signal pathways suggest the possible roles of JA/SA on the regulation of growth and defense responses. Co-expression modules (CMs) were also constructed using the poplar expression data on JA, SA, M. larici-populina, Septoria musiva, and Marssonina brunnea treatment or infection. A total of 23 CMs were constructed, and different CMs clearly exhibited distinct biological functions, which conformably regulated the concerted processes in response to fungal defense. Furthermore, the GO term analysis of different CMs confirmed the roles of JA and SA in regulating growth and defense responses, and their expression profiles suggested that the growth ability was reduced when poplar deployed defense responses. Several transcription factors (TFs) among the CRG in the co-expression network were proposed as hub genes in regulating these processes. According to this study, our data finely uncovered the possible roles of JA/SA in regulating the balance between growth and defense responses by integrating multiple hormone signaling pathways. We were also able to provide more knowledge on how the plant hormones JA/SA are involved in the regulation of the balance between growth and plant defense. Full article
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Open AccessFeature PaperArticle Delineating the Dynamic Transcriptome Response of mRNA and microRNA during Zebrafish Heart Regeneration
Biomolecules 2019, 9(1), 11; https://doi.org/10.3390/biom9010011
Received: 30 November 2018 / Revised: 19 December 2018 / Accepted: 21 December 2018 / Published: 28 December 2018
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Abstract
Heart diseases are the leading cause of death for the vast majority of people around the world, which is often due to the limited capability of human cardiac regeneration. In contrast, zebrafish have the capacity to fully regenerate their hearts after cardiac injury. [...] Read more.
Heart diseases are the leading cause of death for the vast majority of people around the world, which is often due to the limited capability of human cardiac regeneration. In contrast, zebrafish have the capacity to fully regenerate their hearts after cardiac injury. Understanding and activating these mechanisms would improve health in patients suffering from long-term consequences of ischemia. Therefore, we monitored the dynamic transcriptome response of both mRNA and microRNA in zebrafish at 1–160 days post cryoinjury (dpi). Using a control model of sham-operated and healthy fish, we extracted the regeneration specific response and further delineated the spatio-temporal organization of regeneration processes such as cell cycle and heart function. In addition, we identified novel (miR-148/152, miR-218b and miR-19) and previously known microRNAs among the top regulators of heart regeneration by using theoretically predicted target sites and correlation of expression profiles from both mRNA and microRNA. In a cross-species effort, we validated our findings in the dynamic process of rat myoblasts differentiating into cardiomyocytes-like cells (H9c2 cell line). Concluding, we elucidated different phases of transcriptomic responses during zebrafish heart regeneration. Furthermore, microRNAs showed to be important regulators in cardiomyocyte proliferation over time. Full article
(This article belongs to the Special Issue Biomolecules for Translational Approaches in Cardiology)
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Open AccessFeature PaperArticle Delayed Chromosome Alignment to the Spindle Equator Increases the Rate of Chromosome Missegregation in Cancer Cell Lines
Biomolecules 2019, 9(1), 10; https://doi.org/10.3390/biom9010010
Received: 27 November 2018 / Revised: 20 December 2018 / Accepted: 21 December 2018 / Published: 28 December 2018
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Abstract
For appropriate chromosome segregation, kinetochores on sister chromatids have to attach to microtubules from opposite spindle poles (bi-orientation). Chromosome alignment at the spindle equator, referred to as congression, can occur through the attachment of kinetochores to the lateral surface of spindle microtubules, facilitating [...] Read more.
For appropriate chromosome segregation, kinetochores on sister chromatids have to attach to microtubules from opposite spindle poles (bi-orientation). Chromosome alignment at the spindle equator, referred to as congression, can occur through the attachment of kinetochores to the lateral surface of spindle microtubules, facilitating bi-orientation establishment. However, the contribution of this phenomenon to mitotic fidelity has not been clarified yet. Here, we addressed whether delayed chromosome alignment to the spindle equator increases the rate of chromosome missegregation. Cancer cell lines depleted of Kid, a chromokinesin involved in chromosome congression, showed chromosome alignment with a slight delay, and increased frequency of lagging chromosomes. Delayed chromosome alignment concomitant with an increased rate of lagging chromosomes was also seen in cells depleted of kinesin family member 4A (KIF4A), another chromokinesin. Cells that underwent chromosome missegregation took relatively longer time to align chromosomes in both control and Kid/KIF4A-depleted cells. Tracking of late-aligning chromosomes showed that they exhibit a higher rate of lagging chromosomes. Intriguingly, the metaphase of cells that underwent chromosome missegregation was shortened, and delaying anaphase onset ameliorated the increased chromosome missegregation. These data suggest that late-aligning chromosomes do not have sufficient time to establish bi-orientation, leading to chromosome missegregation. Our data imply that delayed chromosome alignment is not only a consequence, but also a cause of defective bi-orientation establishment, which can lead to chromosomal instability in cells without severe mitotic defects. Full article
(This article belongs to the Special Issue Cytoskeleton and Regulation of Mitosis)
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Open AccessArticle UPLC–MS Triglyceride Profiling in Sunflower and Rapeseed Seeds
Biomolecules 2019, 9(1), 9; https://doi.org/10.3390/biom9010009
Received: 20 November 2018 / Revised: 12 December 2018 / Accepted: 13 December 2018 / Published: 27 December 2018
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Abstract
Sunflower and rapeseed are among the most important sources of vegetable oil for food and industry. The main components of vegetable oil are triglycerides (TAGs) (about 97%). Ultra- performance liquid chromatography coupled with mass spectrometry (UPLC–MS) profiling of TAGs in sunflower and rapeseed [...] Read more.
Sunflower and rapeseed are among the most important sources of vegetable oil for food and industry. The main components of vegetable oil are triglycerides (TAGs) (about 97%). Ultra- performance liquid chromatography coupled with mass spectrometry (UPLC–MS) profiling of TAGs in sunflower and rapeseed has been performed and the TAG profiles obtained for these species have been compared. It has been identified that 34 TAGs are shared by sunflower and rapeseed. It was demonstrated that TAGs 52:2, 52:5, 52:6, 54:3; 54:4, 54:7, 56:3, 56:4, and 56:5 had the highest variability levels between sunflower and rapeseed with the higher presence in rapeseed. TAGs 50:2, 52:3, 52:4, 54:5, and 54:6 also showed high variability, but were the most abundant in sunflower. Moreover, the differences in TAG composition between the winter-type and spring-type rapeseed have been revealed, which may be associated with freezing tolerance. It was shown that winter-type rapeseed seeds contain TAGs with a lower degree of saturation, while in spring-type rapeseed highly saturated lipids are the most abundant. These findings may give new insights into the cold resistance mechanisms in plants the understanding of which is especially important in terms of global climate changes. Full article
(This article belongs to the Special Issue Lipidomics)
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Open AccessReview Modulation of Measles Virus NTAIL Interactions through Fuzziness and Sequence Features of Disordered Binding Sites
Biomolecules 2019, 9(1), 8; https://doi.org/10.3390/biom9010008
Received: 22 November 2018 / Revised: 10 December 2018 / Accepted: 18 December 2018 / Published: 27 December 2018
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Abstract
In this paper we review our recent findings on the different interaction mechanisms of the C-terminal domain of the nucleoprotein (N) of measles virus (MeV) NTAIL, a model viral intrinsically disordered protein (IDP), with two of its known binding partners, i.e., [...] Read more.
In this paper we review our recent findings on the different interaction mechanisms of the C-terminal domain of the nucleoprotein (N) of measles virus (MeV) NTAIL, a model viral intrinsically disordered protein (IDP), with two of its known binding partners, i.e., the C-terminal X domain of the phosphoprotein of MeV XD (a globular viral protein) and the heat-shock protein 70 hsp70 (a globular cellular protein). The NTAIL binds both XD and hsp70 via a molecular recognition element (MoRE) that is flanked by two fuzzy regions. The long (85 residues) N-terminal fuzzy region is a natural dampener of the interaction with both XD and hsp70. In the case of binding to XD, the N-terminal fuzzy appendage of NTAIL reduces the rate of α-helical folding of the MoRE. The dampening effect of the fuzzy appendage on XD and hsp70 binding depends on the length and fuzziness of the N-terminal region. Despite this similarity, NTAIL binding to XD and hsp70 appears to rely on completely different requirements. Almost any mutation within the MoRE decreases XD binding, whereas many of them increase the binding to hsp70. In addition, XD binding is very sensitive to the α-helical state of the MoRE, whereas hsp70 is not. Thus, contrary to hsp70, XD binding appears to be strictly dependent on the wild-type primary and secondary structure of the MoRE. Full article
(This article belongs to the Special Issue Intrinsically Disordered Proteins and Chronic Diseases)
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Open AccessArticle Total Fatty Acid Analysis of Human Blood Samples in One Minute by High-Resolution Mass Spectrometry
Biomolecules 2019, 9(1), 7; https://doi.org/10.3390/biom9010007
Received: 24 November 2018 / Revised: 13 December 2018 / Accepted: 17 December 2018 / Published: 27 December 2018
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Abstract
Total fatty acid analysis is a routine method in many areas, including lipotyping of individuals in personalized medicine, analysis of foodstuffs, and optimization of oil production in biotechnology. This analysis is commonly done by converting fatty acyl (FA) chains of intact lipids into [...] Read more.
Total fatty acid analysis is a routine method in many areas, including lipotyping of individuals in personalized medicine, analysis of foodstuffs, and optimization of oil production in biotechnology. This analysis is commonly done by converting fatty acyl (FA) chains of intact lipids into FA methyl esters (FAMEs) and monitoring these by gas-chromatography (GC)-based methods, typically requiring at least 15 min of analysis per sample. Here, we describe a novel method that supports fast, precise and accurate absolute quantification of total FA levels in human plasma and serum samples. The method uses acid-catalyzed transesterification with 18O-enriched H2O (i.e., H218O) to convert FA chains into 18O-labeled free fatty acids. The resulting “mass-tagged” FA analytes can be specifically monitored with improved signal-to-background by 1 min of high resolution Fourier transform mass spectrometry (FTMS) on an Orbitrap-based mass spectrometer. By benchmarking to National Institute of Standards and Technology (NIST) certified standard reference materials we show that the performance of our method is comparable, and at times superior, to that of gold-standard GC-based methods. In addition, we demonstrate that the method supports the accurate quantification of FA differences in samples obtained in dietary intervention studies and also affords specific monitoring of ingested stable isotope-labeled fatty acids (13C16-palmitate) in normoinsulinemic and hyperinsulinemic human subjects. Overall, our novel high-throughput method is generic and suitable for many application areas, spanning basic research to personalized medicine, and is particularly useful for laboratories equipped with high resolution mass spectrometers, but lacking access to GC-based instrumentation. Full article
(This article belongs to the Special Issue Lipidomics)
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