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Open AccessArticle
Whole-Genome Re-Alignment Facilitates Development of Specific Molecular Markers for Races 1 and 4 of Xanthomonas campestris pv. campestris, the Cause of Black rot Disease in Brassica oleracea
Int. J. Mol. Sci. 2017, 18(12), 2523; doi:10.3390/ijms18122523 (registering DOI) -
Abstract
Black rot, caused by Xanthomonas campestris pv. campestris (Xcc),is a seed borne disease of Brassicaceae. Eleven pathogenic races have been identified based on the phenotype interaction pattern of differential brassica cultivars inoculated with different strains. Race 1 and 4
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Black rot, caused by Xanthomonas campestris pv. campestris (Xcc),is a seed borne disease of Brassicaceae. Eleven pathogenic races have been identified based on the phenotype interaction pattern of differential brassica cultivars inoculated with different strains. Race 1 and 4 are the two most frequent races found in Brassica oleracea crops.In this study,a PCR molecular diagnostic tool was developed for the identification of Xcc races 1 and 4 of this pathogen. Whole genomic sequences of races 1, 3, 4 and 9 and sequences of three other Xanthomonas pathovars/species (X. campestris pv. incanae (Xci), X. campestris pv. raphani (Xcr)and X. euvesicatoria(Xev) were aligned to identify variable regions among races. To develop specific markers for races 1 and 4, primers were developed from a region where sequences were dissimilar in other races. Sequence-characterized amplified regions (SCAR) and insertion or deletion of bases (InDel) were used to develop each specific set of primers. The specificity of the selected primers was confirmed by PCR tests using genomic DNA of seven different Xcc races, two strains of X. campestris pathovars and other species of bacteria. Bacterial samples of the races 1 and 4 isolates were collected from artificially inoculated cabbage leaves to conduct bio-PCR. Bio-PCR successfully detected the two Xcc isolates. By using our race-specific markers, a potential race 1 strain from the existing Korean Xcc collection was identified. The Xcc race 1 and 4-specific markers developed in this study are novel and can potentially be used for rapid detection of Xcc races through PCR. Full article
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Open AccessReview
Epigenetic Basis of Cellular Senescence and Its Implications in Aging
Genes 2017, 8(12), 343; doi:10.3390/genes8120343 (registering DOI) -
Abstract
Cellular senescence is a tumor suppressive response that has become recognized as a major contributor of tissue aging. Senescent cells undergo a stable proliferative arrest that protects against neoplastic transformation, but acquire a secretory phenotype that has long-term deleterious effects. Studies are still
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Cellular senescence is a tumor suppressive response that has become recognized as a major contributor of tissue aging. Senescent cells undergo a stable proliferative arrest that protects against neoplastic transformation, but acquire a secretory phenotype that has long-term deleterious effects. Studies are still unraveling the effector mechanisms that underlie these senescence responses with the goal to identify therapeutic interventions. Such effector mechanisms have been linked to the dramatic remodeling in the epigenetic and chromatin landscape that accompany cellular senescence. We discuss these senescence-associated epigenetic changes and their impact on the senescence phenotypes, notably the proliferative arrest and senescence associated secretory phenotype (SASP). We also explore possible epigenetic targets to suppress the deleterious effects of senescent cells that contribute towards aging. Full article
Open AccessReview
The POZ/BTB and AT-Hook Containing Zinc Finger 1 (PATZ1) Transcription Regulator: Physiological Functions and Disease Involvement
Int. J. Mol. Sci. 2017, 18(12), 2524; doi:10.3390/ijms18122524 (registering DOI) -
Abstract
PATZ1 is a zinc finger protein, belonging to the POZ domain Krüppel-like zinc finger (POK) family of architectural transcription factors, first discovered in 2000 by three independent groups. Since that time accumulating evidences have shown its involvement in a variety of biological processes
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PATZ1 is a zinc finger protein, belonging to the POZ domain Krüppel-like zinc finger (POK) family of architectural transcription factors, first discovered in 2000 by three independent groups. Since that time accumulating evidences have shown its involvement in a variety of biological processes (i.e., embryogenesis, stemness, apoptosis, senescence, proliferation, T-lymphocyte differentiation) and human diseases. Here we summarize these studies with a focus on the PATZ1 emerging and controversial role in cancer, where it acts as either a tumor suppressor or an oncogene. Finally, we give some insight on clinical perspectives using PATZ1 as a prognostic marker and therapeutic target. Full article
Open AccessReview
Clavine Alkaloids Gene Clusters of Penicillium and Related Fungi: Evolutionary Combination of Prenyltransferases, Monooxygenases and Dioxygenases
Genes 2017, 8(12), 342; doi:10.3390/genes8120342 (registering DOI) -
Abstract
The clavine alkaloids produced by the fungi of the Aspergillaceae and Arthrodermatacea families differ from the ergot alkaloids produced by Claviceps and Neotyphodium. The clavine alkaloids lack the extensive peptide chain modifications that occur in lysergic acid derived ergot alkaloids. Both clavine
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The clavine alkaloids produced by the fungi of the Aspergillaceae and Arthrodermatacea families differ from the ergot alkaloids produced by Claviceps and Neotyphodium. The clavine alkaloids lack the extensive peptide chain modifications that occur in lysergic acid derived ergot alkaloids. Both clavine and ergot alkaloids arise from the condensation of tryptophan and dimethylallylpyrophosphate by the action of the dimethylallyltryptophan synthase. The first five steps of the biosynthetic pathway that convert tryptophan and dimethylallyl-pyrophosphate (DMA-PP) in chanoclavine-1-aldehyde are common to both clavine and ergot alkaloids. The biosynthesis of ergot alkaloids has been extensively studied and is not considered in this article. We focus this review on recent advances in the gene clusters for clavine alkaloids in the species of Penicillium, Aspergillus (Neosartorya), Arthroderma and Trychophyton and the enzymes encoded by them. The final products of the clavine alkaloids pathways derive from the tetracyclic ergoline ring, which is modified by late enzymes, including a reverse type prenyltransferase, P450 monooxygenases and acetyltransferases. In Aspergillus japonicus, a α-ketoglutarate and Fe2+-dependent dioxygenase is involved in the cyclization of a festuclavine-like unknown type intermediate into cycloclavine. Related dioxygenases occur in the biosynthetic gene clusters of ergot alkaloids in Claviceps purpurea and also in the clavine clusters in Penicillium species. The final products of the clavine alkaloid pathway in these fungi differ from each other depending on the late biosynthetic enzymes involved. An important difference between clavine and ergot alkaloid pathways is that clavine producers lack the enzyme CloA, a P450 monooxygenase, involved in one of the steps of the conversion of chanoclavine-1-aldehyde into lysergic acid. Bioinformatic analysis of the sequenced genomes of the Aspergillaceae and Arthrodermataceae fungi showed the presence of clavine gene clusters in Arthroderma species, Penicillium roqueforti, Penicillium commune, Penicillium camemberti, Penicillium expansum, Penicillium steckii and Penicillium griseofulvum. Analysis of the gene clusters in several clavine alkaloid producers indicates that there are gene gains, gene losses and gene rearrangements. These findings may be explained by a divergent evolution of the gene clusters of ergot and clavine alkaloids from a common ancestral progenitor six genes cluster although horizontal gene transfer of some specific genes may have occurred more recently. Full article
Open AccessArticle
New Scheme for Validating Remote-Sensing Land Surface Temperature Products with Station Observations
Remote Sens. 2017, 9(12), 1210; doi:10.3390/rs9121210 (registering DOI) -
Abstract
Continuous land-surface temperature (LST) observations from ground-based stations are an important reference dataset for validating remote-sensing LST products. However, a lack of evaluations of the representativeness of station observations limits the reliability of validation results. In this study, a new practical validation scheme
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Continuous land-surface temperature (LST) observations from ground-based stations are an important reference dataset for validating remote-sensing LST products. However, a lack of evaluations of the representativeness of station observations limits the reliability of validation results. In this study, a new practical validation scheme is presented for validating remote-sensing LST products that includes a key step: assessing the spatial representativeness of ground-based LST measurements. Three indicators, namely, the dominant land-cover type (DLCT), relative bias (RB), and average structure scale (ASS), are established to quantify the representative levels of station observations based on the land-cover type (LCT) and LST reference maps with high spatial resolution. We validated MODIS LSTs using station observations from the Heihe River Basin (HRB) in China. The spatial representative evaluation steps show that the representativeness of observations greatly differs among stations and varies with different vegetation growth and other factors. Large differences in the validation results occur when using different representative level observations, which indicates a large potential for large error during the traditional T-based validation scheme. Comparisons show that the new validation scheme greatly improves the reliability of LST product validation through high-level representative observations. Full article
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Open AccessFeature PaperArticle
Aminated Polyethylene Terephthalate (PET) Nanofibers for the Selective Removal of Pb(II) from Polluted Water
Materials 2017, 10(12), 1352; doi:10.3390/ma10121352 (registering DOI) -
Abstract
Electrospun nanofibers have been successfully applied to remove toxic and carcinogenic contaminants such as heavy metals from polluted water. In this study, an efficient adsorbent based on poly(ethylene terephthalate) (PET) nanofibers was developed following a cheap, versatile and scalable process. PET nanofibers were
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Electrospun nanofibers have been successfully applied to remove toxic and carcinogenic contaminants such as heavy metals from polluted water. In this study, an efficient adsorbent based on poly(ethylene terephthalate) (PET) nanofibers was developed following a cheap, versatile and scalable process. PET nanofibers were first produced by electrospinning, and their surface was chemically functionalized using a simple aminolysis process. The capacity of the resulting material to adsorb Pb(II) from synthetic solutions was evaluated as a function of the contact time, pH, and initial metal ion concentration. The adsorbent system presented a quick kinetic adsorption, reaching an extremely high maximum adsorption capacity of about 50 millimol (mmol) of Pb(II) per gram of adsorbent system after just 30 min. Moreover, the effect of competing metal ions, such as Ni(II), Cd(II) and Cu(II), was studied at different molar ratios. Finally, when tested in continuous flow mode, aminated PET (APET) nanofibers were able to remove 97% of Pb(II) ions in solution, demonstrating their potential for the remediation of heavy metal-contaminated water. Full article
Open AccessFeature PaperArticle
Castanea sativa Bur: An Undervalued By-Product but a Promising Cosmetic Ingredient
Cosmetics 2017, 4(4), 50; doi:10.3390/cosmetics4040050 (registering DOI) -
Abstract
Castanea sativa fruit processing generates high amounts of by-products, mostly bur. Currently, the cosmetic industry has a great interest in natural extracts as antioxidant sources. In the present study, C. sativa bur extract was used as the active ingredient, in different amounts, in
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Castanea sativa fruit processing generates high amounts of by-products, mostly bur. Currently, the cosmetic industry has a great interest in natural extracts as antioxidant sources. In the present study, C. sativa bur extract was used as the active ingredient, in different amounts, in topical hydrogels. The formulations were characterized regarding total phenolic and flavonoid contents (TPC and TFC, respectively), antioxidant activity (DPPH radical scavenging capacity and ferric reducing antioxidant power (FRAP)) and technological and microbiological properties. The same parameters were evaluated after 30 days of storage at 4 °C (T30/4 °C) and 20 °C (T30/20 °C). At time 0 (T0), the TPC ranged between 0.79 and 9.65 mg of gallic acid equivalents (GAE)/g gel, while TFC varied from 0.05 to 1.23 mg of catechin equivalents (CAE)/g gel. Antioxidant activity was high for both assays, with values at T0 ranging between 98.41 and 1013.43 µmol of ferrous sulphate equivalents (FSE)/g gel and varying between 431.96 and 990.84 µg of Trolox equivalents (TE)/g gel for FRAP and DPPH assays, respectively. No formulation exceeded the defined criteria in microbiological counts. All formulations showed similar technological profiles but particular attention should be given to pH. The gel with 50% of extract (F3) was selected as the best one for potential cosmetic applications. Full article
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Open AccessFeature PaperReview
Intrinsic Disorder in Proteins with Pathogenic Repeat Expansions
Molecules 2017, 22(12), 2027; doi:10.3390/molecules22122027 (registering DOI) -
Abstract
Intrinsically disordered proteins and proteins with intrinsically disordered regions have been shown to be highly prevalent in disease. Furthermore, disease-causing expansions of the regions containing tandem amino acid repeats often push repetitive proteins towards formation of irreversible aggregates. In fact, in disease-relevant proteins,
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Intrinsically disordered proteins and proteins with intrinsically disordered regions have been shown to be highly prevalent in disease. Furthermore, disease-causing expansions of the regions containing tandem amino acid repeats often push repetitive proteins towards formation of irreversible aggregates. In fact, in disease-relevant proteins, the increased repeat length often positively correlates with the increased aggregation efficiency and the increased disease severity and penetrance, being negatively correlated with the age of disease onset. The major categories of repeat extensions involved in disease include poly-glutamine and poly-alanine homorepeats, which are often times located in the intrinsically disordered regions, as well as repeats in non-coding regions of genes typically encoding proteins with ordered structures. Repeats in such non-coding regions of genes can be expressed at the mRNA level. Although they can affect the expression levels of encoded proteins, they are not translated as parts of an affected protein and have no effect on its structure. However, in some cases, the repetitive mRNAs can be translated in a non-canonical manner, generating highly repetitive peptides of different length and amino acid composition. The repeat extension-caused aggregation of a repetitive protein may represent a pivotal step for its transformation into a proteotoxic entity that can lead to pathology. The goals of this article are to systematically analyze molecular mechanisms of the proteinopathies caused by the poly-glutamine and poly-alanine homorepeat expansion, as well as by the polypeptides generated as a result of the microsatellite expansions in non-coding gene regions and to examine the related proteins. We also present results of the analysis of the prevalence and functional roles of intrinsic disorder in proteins associated with pathological repeat expansions. Full article
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Open AccessArticle
Overtopping of Coastal Structures by Tsunami Waves
Geosciences 2017, 7(4), 121; doi:10.3390/geosciences7040121 (registering DOI) -
Abstract
Following the 2011 Tohoku Earthquake and Tsunami, Japanese tsunami protection guidelines stipulate that coastal defences should ensure that settlements are shielded from the coastal inundation that would result from Level 1 tsunami events (with return periods in the order of about 100
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Following the 2011 Tohoku Earthquake and Tsunami, Japanese tsunami protection guidelines stipulate that coastal defences should ensure that settlements are shielded from the coastal inundation that would result from Level 1 tsunami events (with return periods in the order of about 100 years). However, the overtopping mechanism and leeward inundation heights of tsunami bores as they hit coastal structures has received little attention in the past. To ascertain this phenomenon, the authors conducted physical experiments using a dam-break mechanism, which could generate bores that overtopped different types of structures. The results indicate that it is necessary to move away from only considering the tsunami inundation height at the beach, and also consider the bore velocity as it approaches the onshore area. The authors also prepared a simple, conservative method of estimating the inundation height after a structure of a given height, provided that the incident bore velocity and height are known. Full article
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