scholarly journals Fungal Adaptation to the Advanced Stages of Wood Decomposition: Insights from the Steccherinum ochraceum

2019 ◽  
Vol 7 (11) ◽  
pp. 527 ◽  
Author(s):  
Konstantin V. Moiseenko ◽  
Olga A. Glazunova ◽  
Natalia V. Shakhova ◽  
Olga S. Savinova ◽  
Daria V. Vasina ◽  
...  
Keyword(s):  
De Novo ◽  
White Rot ◽  
Wood Decomposition ◽  
Carbohydrate Active Enzymes ◽  
Climatic Zones ◽  
Substrate Preferences ◽  
The World ◽  
Advanced Stages ◽  
Fungal Adaptation ◽  
Enzymatic Mechanisms

Steccherinum ochraceum is a white rot basidiomycete with wide ecological amplitude. It occurs in different regions of Russia and throughout the world, occupying different climatic zones. S. ochraceum colonizes stumps, trunks, and branches of various deciduous (seldom coniferous) trees. As a secondary colonizing fungus, S. ochraceum is mainly observed at the late decay stages. Here, we present the de novo assembly and annotation of the genome of S. ochraceum, LE-BIN 3174. This is the 8th published genome of fungus from the residual polyporoid clade and the first from the Steccherinaceae family. The obtained genome provides a first glimpse into the genetic and enzymatic mechanisms governing adaptation of S. ochraceum to an ecological niche of pre-degraded wood. It is proposed that increased number of carbohydrate-active enzymes (CAZymes) belonging to the AA superfamily and decreased number of CAZymes belonging to the GH superfamily reflects substrate preferences of S. ochraceum. This proposition is further substantiated by the results of the biochemical plate tests and exoproteomic study, which demonstrates that S. ochraceum assumes the intermediate position between typical primary colonizing fungi and litter decomposers or humus saprotrophs. Phylogenetic analysis of S. ochraceum laccase and class II peroxidase genes revealed the distinct evolutional origin of these genes in the Steccherinaceae family.

scholarly journals Quantitative comparison of the biomass-degrading enzyme repertoires of five filamentous fungi

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Magnus Ø. Arntzen ◽  
Oskar Bengtsson ◽  
Anikó Várnai ◽  
Francesco Delogu ◽  
Geir Mathiesen ◽  
...  
Keyword(s):  
Filamentous Fungi ◽  
Large Scale ◽  
Aspergillus Terreus ◽  
Quantitative Comparison ◽  
Biofuel Production ◽  
White Rot ◽  
Carbohydrate Active Enzymes ◽  
Proteomics Approach ◽  
Polysaccharide Monooxygenases ◽  
Fungal Adaptation

AbstractThe efficiency of microorganisms to degrade lignified plants is of great importance in the Earth’s carbon cycle, but also in industrial biorefinery processes, such as for biofuel production. Here, we present a large-scale proteomics approach to investigate and compare the enzymatic response of five filamentous fungi when grown on five very different substrates: grass (sugarcane bagasse), hardwood (birch), softwood (spruce), cellulose and glucose. The five fungi included the ascomycetes Aspergillus terreus, Trichoderma reesei, Myceliophthora thermophila, Neurospora crassa and the white-rot basidiomycete Phanerochaete chrysosporium, all expressing a diverse repertoire of enzymes. In this study, we present comparable quantitative protein abundance values across five species and five diverse substrates. The results allow for direct comparison of fungal adaptation to the different substrates, give indications as to the substrate specificity of individual carbohydrate-active enzymes (CAZymes), and reveal proteins of unknown function that are co-expressed with CAZymes. Based on the results, we present a quantitative comparison of 34 lytic polysaccharide monooxygenases (LPMOs), which are crucial enzymes in biomass deconstruction.

scholarly journals Identifying molecules as biosignatures with assembly theory and mass spectrometry

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Stuart M. Marshall ◽  
Cole Mathis ◽  
Emma Carrick ◽  
Graham Keenan ◽  
Geoffrey J. T. Cooper ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
De Novo ◽  
Outer Space ◽  
Molecular Assembly ◽  
Detection Experiment ◽  
Complex Molecules ◽  
The World ◽  
Life Detection ◽  
Molecular Complexity ◽  
The Universe

AbstractThe search for alien life is hard because we do not know what signatures are unique to life. We show why complex molecules found in high abundance are universal biosignatures and demonstrate the first intrinsic experimentally tractable measure of molecular complexity, called the molecular assembly index (MA). To do this we calculate the complexity of several million molecules and validate that their complexity can be experimentally determined by mass spectrometry. This approach allows us to identify molecular biosignatures from a set of diverse samples from around the world, outer space, and the laboratory, demonstrating it is possible to build a life detection experiment based on MA that could be deployed to extraterrestrial locations, and used as a complexity scale to quantify constraints needed to direct prebiotically plausible processes in the laboratory. Such an approach is vital for finding life elsewhere in the universe or creating de-novo life in the lab.

scholarly journals AGROCLIMATIC ZONING OF EUROPEAN AND ASIAN PEAR CULTIVARS WITH POTENTIAL FOR COMMERCIAL PLANTING IN SOUTHERN BRAZIL

2017 ◽  
Vol 39 (2) ◽  
Author(s):  
MARCOS SILVEIRA WREGE ◽  
IVAN DAGOBERTO FAORO ◽  
FLÁVIO GILBERTO HERTER ◽  
CRISTINA PANDOLFO ◽  
IVAN RODRIGUES DE ALMEIDA ◽  
...  
Keyword(s):  
Fruit Quality ◽  
Climate Risk ◽  
Southern Brazil ◽  
Climatic Zones ◽  
Local Conditions ◽  
Asian Pear ◽  
Commercial Interest ◽  
The World ◽  
Chilling Hours ◽  
Production Problems

ABSTRACT Pear is among the fruits of major commercial interest in the world and one of the most imported in Brazil. Brazilian production is very small and the fruit quality is low, due to production problems. The success of culture in the country, among other factors, may be linked to the choice of cultivars, pollinating and rootstocks better adapted to local conditions, and thus depend on the particulars of an agricultural zoning. The aim of this study was to identify, in southern Brazil, homogeneous climatic zones with potential for growing of European and Asian pears, through climate risk studies. The regions were defined by the seasonal availability of chilling hours (<7.2 °C) accumulated during the period from May to September and the monthly risk of drought. The analysis allowed the recognition of four homogeneous areas for the production of pears in southern Brazil.

scholarly journals Machine learning approaches to predict the Plant-associated phenotype of Xanthomonas strains

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Dennie te Molder ◽  
Wasin Poncheewin ◽  
Peter J. Schaap ◽  
Jasper J. Koehorst
Keyword(s):  
Machine Learning ◽  
Plant Pathogens ◽  
De Novo ◽  
Classification Algorithms ◽  
Learning Approaches ◽  
Enabling Factors ◽  
Essential Step ◽  
The World ◽  
Genome Content

Abstract Background The genus Xanthomonas has long been considered to consist predominantly of plant pathogens, but over the last decade there has been an increasing number of reports on non-pathogenic and endophytic members. As Xanthomonas species are prevalent pathogens on a wide variety of important crops around the world, there is a need to distinguish between these plant-associated phenotypes. To date a large number of Xanthomonas genomes have been sequenced, which enables the application of machine learning (ML) approaches on the genome content to predict this phenotype. Until now such approaches to the pathogenomics of Xanthomonas strains have been hampered by the fragmentation of information regarding pathogenicity of individual strains over many studies. Unification of this information into a single resource was therefore considered to be an essential step. Results Mining of 39 papers considering both plant-associated phenotypes, allowed for a phenotypic classification of 578 Xanthomonas strains. For 65 plant-pathogenic and 53 non-pathogenic strains the corresponding genomes were available and de novo annotated for the presence of Pfam protein domains used as features to train and compare three ML classification algorithms; CART, Lasso and Random Forest. Conclusion The literature resource in combination with recursive feature extraction used in the ML classification algorithms provided further insights into the virulence enabling factors, but also highlighted domains linked to traits not present in pathogenic strains.

scholarly journals IMPACT OF GREEN ROOF ON HEATING AND COOLING IN CONTEXT OF DIFFERENT CLIMATIC ZONES IN INDIA

2021 ◽  
pp. 436-440
Author(s):  
Ar. Ankur Bhardwaj ◽  
Dr. Shweta Chaudhary ◽  
Ar.Kirti Varandani
Keyword(s):  
Urban Areas ◽  
Green Roof ◽  
Green Roofs ◽  
Climatic Zones ◽  
Sustainable Living ◽  
Secondary Sources ◽  
Heating And Cooling ◽  
The World ◽  
Depth Study ◽  
Rainwater Runoff

The ecological, social and visual commitments that green roofs can make towards sustainable living in more intensified urban centres are generally recognized around the world. Green roof is one such sustainable methodology, utilization of which causes us in insulating the buildings and, subsequently contributing to better energy proficient execution of the same. Green roofs additionally give environment to various species, lessen the rainwater runoff and better deal with the carbon-dioxide cycle. In spite of these advantages, Green roofs are not as basic an element in India as they are in other European and American urban areas. In this paper an attempt has been made to enhance the advantages of this innovation in India. Green roofs systems looks simple in terms of setting up, but actually very complex in maintaining and achieving sustainability. In depth study of green roofs, historic background, climatic zones, impacts of green roofs on heating and cooling, benefits, problems and opportunities is done with the help of data taken from secondary sources like books, magazines and published literature (articles, journals, conference proceedings) form various e-libraries and other online platforms. KEY WORDS: Heating, Cooling, Green Roof, Sustainability)

Ulex europaeus (gorse).

2021 ◽  
Author(s):  
Julissa Rojas-Sandoval ◽  
Nick Pasiecznik
Keyword(s):  
Fire Risk ◽  
Ecosystem Processes ◽  
Tree Seedlings ◽  
Climatic Zones ◽  
Ulex Europaeus ◽  
The World ◽  
Tall Shrub ◽  
Noxious Weed ◽  
Disturbed Habitats ◽  
Grassland Habitats

Abstract U. europaeus was spread intentionally through most of the world in the 1800s and 1900s as a hedge plant, an ornamental and as a forage, although it is unlikely that it will be distributed to new areas for these purposes in future. It has large seeds and there is a threat from inadvertent introduction, but this is not high. U. europaeus was already declared a noxious weed 100 years ago in Australia and New Zealand, and is now a serious weed in many other countries, and poses a threat elsewhere where it is present but not yet invasive. It is an aggressive colonizer of disturbed habitats, and the risk from continued invasion in suitable climatic zones in countries where present is high. It is a tough, spiny, long-lived, tall shrub with a long-lived seed bank and is difficult to control. Thickets displace vegetation in grassland habitats, and outgrow and supplant tree seedlings in plantation forests. Heavy infestations modify soil and hydrological conditions, and so modify ecosystem processes. This plant poses a serious fire risk for indigenous ecosystems as well as managed habitats and human habitations.

Clinico-pathologic characteristics and outcomes of the World Health Organization (WHO) provisional entity de novo acute myeloid leukemia with mutated RUNX1

2020 ◽  
Vol 33 (9) ◽  
pp. 1678-1689
Author(s):  
Andrés E. Quesada ◽  
Guillermo Montalban-Bravo ◽  
Rajyalakshmi Luthra ◽  
Keyur P. Patel ◽  
Koji Sasaki ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
World Health Organization ◽  
Myeloid Leukemia ◽  
De Novo ◽  
World Health ◽  
The World ◽  
Health Organization ◽  
Acute Myeloid

scholarly journals Locations and contributions of the phosphotransferases EPT1 and CEPT1 to the biosynthesis of ethanolamine phospholipids

2020 ◽  
Vol 61 (8) ◽  
pp. 1221-1231 ◽  
Author(s):  
Yasuhiro Horibata ◽  
Hiromi Ando ◽  
Hiroyuki Sugimoto
Keyword(s):  
Fatty Acids ◽  
De Novo ◽  
Brefeldin A ◽  
Hek293 Cells ◽  
Intracellular Location ◽  
De Novo Biosynthesis ◽  
Substrate Preferences ◽  
Ethanolamine Phosphate ◽  
Immunohistochemical Analyses

The final step of the CDP-ethanolamine pathway is catalyzed by ethanolamine phosphotransferase 1 (EPT1) and choline/EPT1 (CEPT1). These enzymes are likely involved in the transfer of ethanolamine phosphate from CDP-ethanolamine to lipid acceptors such as 1,2-diacylglycerol (DAG) for PE production and 1-alkyl-2-acyl-glycerol (AAG) for the generation of 1-alkyl-2-acyl-glycerophosphoethanolamine. Here, we investigated the intracellular location and contribution to ethanolamine phospholipid (EP) biosynthesis of EPT1 and CEPT1 in HEK293 cells. Immunohistochemical analyses revealed that EPT1 localizes to the Golgi apparatus and CEPT1 to the ER. We created EPT1-, CEPT1-, and EPTI-CEPT1-deficient cells, and labeling of these cells with radio- or deuterium-labeled ethanolamine disclosed that EPT1 is more important for the de novo biosynthesis of 1-alkenyl-2-acyl-glycerophosphoethanolamine than is CEPT1. EPT1 also contributed to the synthesis of PE species containing the fatty acids 36:1, 36:4, 38:5, 38:4, 38:3, 40:6, 40:5, and 40:4. In contrast, CEPT1 was important for PE formation from shorter fatty acids such as 32:2, 32:1, 34:2, and 34:1. Brefeldin A treatment did not significantly affect the levels of the different PE species, indicating that the subcellular localization of the two enzymes is not responsible for their substrate preferences. In vitro enzymatic analysis revealed that EPT1 prefers AAG 16–20:4 > DAG 18:0–20:4 > DAG 16:0–18:1 = AAG 16–18:1 as lipid acceptors and that CEPT1 greatly prefers DAG 16:0–18:1 to other acceptors. These results suggest that EPT1 and CEPT1 differ in organelle location and are responsible for the biosynthesis of distinct EP species.

II. Dutch Views and Uses of British Policy in India around 1800

Itinerario ◽  
1988 ◽  
Vol 12 (1) ◽  
pp. 17-32
Author(s):  
Robert van Niel
Keyword(s):  
De Novo ◽  
The State ◽  
Final Report ◽  
Total Change ◽  
Group Of Seven ◽  
East Indies ◽  
The World ◽  
The Hague ◽  
The Republic ◽  
The Government

On August 31, 1803, a group of seven men, comprising the Commission for East Indies Affairs (Commissie tot de Oost-Indische Zaken), submitted the final report of its deliberations to the Government of the State of the Batavian Republic (Staatsbewind der Bataafsche Republiek) in The Hague. This Commission had been called into existence in November 1802 to make recommendations on how best to administer and conduct trade with the nation's possessions in the East Indies in a fashion that would render the greatest advantage to the nation's finances and profit to its commerce. Only a couple of years earlier Holland's monopolistic United East Indies Company (VOC) had been terminated by the Republic, and its assets and liabilities assumed by the State. The liabilities were immediately identifiable, for they consisted of debts which had to be paid in hard cash. The assets, on the other hand, consisted of territories – most of which had fallen under English control – and factories that somehow had to be made profitable, but seemed, given the then-existing conditions in the world, to be almost out of reach. The Commission was supposed to make recommendations as to how the remaining, territories of the VOC should be managed and how the trade with the East Indies and Asia in general was to be made profitable. This was no small task, so it may appear somewhat wondrous that the Commission was able to complete its work in less than ten months. The dispatch with which the Commission's work was completed, however, is more understandable if it is realised that the financial collapse of the VOC had been openly recognised since 1786, and various proposals for either reform or total change of the Company's system had been presented and discussed. These alternative proposals were well known to the members of the Commission. Their work, therefore, involved striking a balance among these proposals rather than creating a system de novo.

scholarly journals Nonalcoholic steatohepatitis in posttransplantation liver: Review article

2018 ◽  
Vol 64 (2) ◽  
pp. 187-194 ◽  
Author(s):  
Antônio Ricardo Cardia Ferraz de Andrade ◽  
Helma P. Cotrim ◽  
Paulo L. Bittencourt ◽  
Carolina G. Almeida ◽  
Ney Christian Amaral Boa Sorte
Keyword(s):  
Nonalcoholic Steatohepatitis ◽  
Clinical Characteristics ◽  
Metabolic Disorders ◽  
Patient Survival ◽  
De Novo ◽  
Review Article ◽  
Liver Transplants ◽  
The Third ◽  
High Prevalence ◽  
The World

Summary Introduction: Nonalcoholic steatohepatitis (NASH) associated or not with cirrhosis is the third leading indication for liver transplantation (LT) around the world. After transplants, NASH has a high prevalence and occurs as both recurrent and de novo manifestations. De novo NASH can also occur in allografts of patients transplanted for non-NASH liver disease. Objective: To evaluate recurrent or de novo NASH in post-LT patients. Method: A literature review was performed using search engines of indexed scientific material, including Medline (by PubMed), Scielo and Lilacs, to identify articles published in Portuguese and English until August 2016. Eligible studies included: place and year of publication, prevalence, clinical characteristics, risk factors and survival. Results: A total of 110 articles were identified and 63 were selected. Most of the studies evaluated recurrence and survival after LT. Survival reached 90-100% in 1 year and 52-100% in 5 years. Recurrence of NAFLD (steatosis) was described in 15-100% and NASH, in 4-71%. NAFLD and de novo NASH were observed in 18-67% and 3-17%, respectively. Metabolic syndrome, diabetes mellitus, dyslipidemia and hypertension were seen in 45-58%, 18-59%, 25-66% and 52-82%, respectively. Conclusion: After liver transplants, patients present a high prevalence of recurrent and de novo NASH. They also show a high frequence of metabolic disorders. Nevertheless, these alterations seem not to influence patient survival.

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