scholarly journals Predicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes

Pathogens ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 807
Author(s):  
Daniel Gómez-Pérez ◽  
Eric Kemen
Keyword(s):  
High Accuracy ◽  
Biological Processes ◽  
Diverse Range ◽  
Functional Annotations ◽  
Selective Pressures ◽  
The Core ◽  
Niche Shifts ◽  
Phenotypic Diversification ◽  
High Degree ◽  
Core Metabolism

As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome.

scholarly journals Predicting lifestyle and host from positive selection data and genome properties in oomycetes

2021 ◽  
Author(s):  
Daniel Gómez-Pérez ◽  
Eric Kemen
Keyword(s):  
High Accuracy ◽  
Emerging Diseases ◽  
Comparative Genomic ◽  
Biological Processes ◽  
Selective Pressures ◽  
Genomic Approach ◽  
Niche Shifts ◽  
Phenotypic Diversification ◽  
High Degree ◽  
Core Metabolism

AbstractBackgroundHost and niche shifts are a source of genomic and phenotypic diversification as evidenced in parasitism. Most characteristic is core metabolism reduction as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of such organisms are not fully understood.ResultsHere, we developed a comparative genomic approach to study underlying adaptive trends in oomycetes, a eukaryote phylum with a broad range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes inhabiting similar niches. We find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaption in oomycetes.DiscussionGiven the high correlation of lifestyle to genome properties in our oomycete dataset and the convergent evolution of fungal and oomycete genomes, we have developed a model that predicts plant pathogen lifestyles with high accuracy. Understanding how genomes and selective pressures correlate with lifestyle may be crucial to identify new emerging diseases and pandemic threats.

scholarly journals Predicting Lifestyle and Host From Positive Selection Data and Genome Properties in Oomycetes

2021 ◽  
Author(s):  
Daniel Gómez-Pérez ◽  
Eric Kemen
Keyword(s):  
Convergent Evolution ◽  
High Accuracy ◽  
Emerging Diseases ◽  
Comparative Genomic ◽  
Biological Processes ◽  
Selective Pressures ◽  
Genomic Approach ◽  
Niche Shifts ◽  
High Degree ◽  
Core Metabolism

Abstract Background: Host and niche shifts are a source of genomic and phenotypic diversi_cation as evidenced in parasitism. Most characteristic is core metabolism reduction as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversi_cation. However, selective pressures acting on the genome of such organisms are not fully understood. Results: Here, we developed a comparative genomic approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a broad range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes inhabiting similar niches. We _nd that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaption in oomycetes. Discussion: Given the high correlation of lifestyle to genome properties in our oomycete dataset and the convergent evolution of fungal and oomycete genomes, we have developed a model that predicts plant pathogen lifestyles with high accuracy. Understanding how genomes and selective pressures correlate with lifestyle may be crucial to identify new emerging diseases and pandemic threats.

Exploring the Mechanism of Lingzhu San in Treating Febrile Seizures by Using Network Pharmacology

2020 ◽  
Vol 23 ◽  
Author(s):  
Xiao Zhou ◽  
Xiao-Fei Zhang ◽  
Dong-Yan Guo ◽  
Yan-Jun Yang ◽  
Lin Liu ◽  
...  
Keyword(s):  
Febrile Seizures ◽  
Network Pharmacology ◽  
Biological Processes ◽  
Active Compounds ◽  
Potential Core ◽  
R Language ◽  
The Core ◽  
Multiple Factors ◽  
Therapeutic Mechanism

Objective: Lingzhu San (LZS) is a traditional Chinese medicine (TCM) prescription which can be effective in treating febrile seizures (FS) and has few researches on the mechanisms. In order to better guide the clinical use of LZS, we used the research ideas and methods of network pharmacology to find the potential core compounds, targets and pathways of LZS in the complex TCM system for the treatment of FS, and predict the mechanism. Materials and Methods: Databases such as BATMAN, TCMSP, TCMID, and SWISS TARGET are used to mine the active compounds and targets of LZS, and the target information of FS was obtained through GENECARDS and OMIM. Using Venny2.1.0 and Cytoscape software to locked the potential core compounds and targets of FS. The R language and ClusterProfiler software package were adopt to enrich and analyze the KEGG and GO pathways of the core targets and the biological processes and potential mechanisms of the core targets were revealed. Results: 187 active compounds and 2113 target proteins of LZS were collected. And 38 potential core compounds, 35 core targets and 775 metabolic and functional pathways were screened which involved in mediating FS. Finally, the role of the core compounds, targets and pivotal pathways of LZS regulated FS in the pathogenesis and therapeutic mechanism of FS was discussed and clarified. Conclusions: In this paper, the multi-compounds, multi-targets and multi-pathways mechanism of LZS in the treatment of FS was preliminarily revealed through the analysis of network pharmacology data, which is consistent with the principle of multi-compounds compatibility of TCM prescriptions and unified treatment of diseases from multiple angles, and it provides a new way for TCM to treat complex diseases caused by multiple factors.

scholarly journals NetCleave: an open-source algorithm for predicting C-terminal antigen processing for MHC-I and MHC-II

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Pep Amengual-Rigo ◽  
Victor Guallar
Keyword(s):  
Open Source ◽  
Antigen Processing ◽  
High Accuracy ◽  
Biological Processes ◽  
Mhc I ◽  
Mhc Ii ◽  
Prediction Tools ◽  
Immunogenic Peptides ◽  
Physicochemical Descriptors ◽  
Peptide Presentation

AbstractAntigens presented on the cell surface have been subjected to multiple biological processes. Among them, C-terminal antigen processing constitutes one of the main bottlenecks of the peptide presentation pathways, as it delimits the peptidome that will be subjected downstream. Here, we present NetCleave, an open-source and retrainable algorithm for the prediction of the C-terminal antigen processing for both MHC-I and MHC-II pathways. NetCleave architecture consists of a neural network trained on 46 different physicochemical descriptors of the cleavage site amino acids. Our results demonstrate that prediction of C-terminal antigen processing achieves high accuracy on MHC-I (AUC of 0.91), while it remains challenging for MHC-II (AUC of 0.66). Moreover, we evaluated the performance of NetCleave and other prediction tools for the evaluation of four independent immunogenicity datasets (H2-Db, H2-Kb, HLA-A*02:01 and HLA-B:07:02). Overall, we demonstrate that NetCleave stands out as one of the best algorithms for the prediction of C-terminal processing, and we provide one of the first evidence that C-terminal processing predictions may help in the discovery of immunogenic peptides.

scholarly journals Comparative genomics reveals new functional insights in uncultured MAST species

2021 ◽  
Author(s):  
Aurelie Labarre ◽  
David López-Escardó ◽  
Francisco Latorre ◽  
Guy Leonard ◽  
François Bucchini ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Genomic Data ◽  
Proton Pumps ◽  
Functional Annotations ◽  
The Core ◽  
Unicellular Eukaryotes ◽  
Microbial Eukaryotes ◽  
Core Energy ◽  
Marine Surface ◽  
Environmental Sequences

AbstractHeterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.

Gebruiksaspecten van het uitroeppartikel wat in het Nederlands en Fries

2020 ◽  
Vol 136 (4) ◽  
pp. 189-209
Author(s):  
Henk Wolf
Keyword(s):  
The Core ◽  
The Difference ◽  
Lexical Phrase ◽  
High Degree ◽  
Lexical Phrases

Abstract Both Dutch and (West) Frisian make use of the exclamative particle wat (‘how’), that adds an element of surprise about a high degree of something to the semantics of the sentence. In this paper I will first show the similarities between the use of the particle in the two languages. I will demonstrate that, in Dutch, its use is largely confined to constructions that are semantically scalable, whereas in Frisian this restriction is far less strict. I will explain the difference by showing that Dutch wat is a syntactic amplifier of lexical phrases, whereas Frisian wat has developed into a pragmatic amplifier of the core predicate. I will try to account for that difference by showing how homophonous words absent in Dutch are likely to have influenced the use of Frisian wat, and how Dutch prosody strengthens the connection between wat and the amplified lexical phrase, whereas Frisian prosody weakens it. Finally, I will show that the system described as ‘Frisian’ is occasionally found in varieties of Dutch too

Synthetic and Biological Attributes of Pyrimidine Derivatives: A Recent update

2021 ◽  
Vol 18 ◽  
Author(s):  
Meenu Devi ◽  
Shivangi Jaiswal ◽  
Sonika Jain ◽  
Navjeet Kaur ◽  
Jaya Dwivedi
Keyword(s):  
Biological Activities ◽  
Structural Diversity ◽  
Therapeutic Agents ◽  
Pyrimidine Derivatives ◽  
Diverse Range ◽  
Biological Attributes ◽  
Synthetic Approaches ◽  
High Degree ◽  
Therapeutic Activities ◽  
Anti Hiv

: Nitrogen-containing heterocycles attract the attention of chemists due to their multifarious activities. Amongst all, pyrimidine plays a central role and exhibits a broad spectrum of biological activities. Literature is replete with the various aspects of synthetic development in pyrimidine chemistry for a wide array of applications. It aroused our interest to compile various novel and efficient synthetic approaches towards the synthesis of pyrimidine and its derivatives. Pyrimidine derivatives are broadly useful as therapeutic agents, owing to their high degree of structural diversity. They have been recorded to possess a diverse range of therapeutic activities, viz. anticancer, anti-inflammatory, anti-HIV etc.

scholarly journals GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background

2020 ◽  
Author(s):  
Nasa Sinnott-Armstrong ◽  
Sahin Naqvi ◽  
Manuel Rivas ◽  
Jonathan K Pritchard
Keyword(s):  
Complex Traits ◽  
Genetic Basis ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Biological Processes ◽  
Uk Biobank ◽  
The Core ◽  
Genome Wide ◽  
Core Genes

SummaryGenome-wide association studies (GWAS) have been used to study the genetic basis of a wide variety of complex diseases and other traits. However, for most traits it remains difficult to interpret what genes and biological processes are impacted by the top hits. Here, as a contrast, we describe UK Biobank GWAS results for three molecular traits—urate, IGF-1, and testosterone—that are biologically simpler than most diseases, and for which we know a great deal in advance about the core genes and pathways. Unlike most GWAS of complex traits, for all three traits we find that most top hits are readily interpretable. We observe huge enrichment of significant signals near genes involved in the relevant biosynthesis, transport, or signaling pathways. We show how GWAS data illuminate the biology of variation in each trait, including insights into differences in testosterone regulation between females and males. Meanwhile, in other respects the results are reminiscent of GWAS for more-complex traits. In particular, even these molecular traits are highly polygenic, with most of the variance coming not from core genes, but from thousands to tens of thousands of variants spread across most of the genome. Given that diseases are often impacted by many distinct biological processes, including these three, our results help to illustrate why so many variants can affect risk for any given disease.

Critical Security Studies and Global Health

2018 ◽  
pp. 160-177
Author(s):  
João Nunes
Keyword(s):  
Global Health ◽  
Security Studies ◽  
Health Issues ◽  
Regional Stability ◽  
Health Security ◽  
Diverse Range ◽  
Critical Security Studies ◽  
The Core ◽  
Core Concepts ◽  
Political Dimensions

This chapter argues that Critical Security Studies (CSS), a diverse range of approaches that have questioned traditional ways of conceiving security, can provide a useful set of tools for understanding global health. CSS enables rich analyses of how health problems emerge as matters of security and allows one to discern the underlying conditions that make this possible, as well as the effects of framing diseases as threats. It also shows how health security can be conceived as a layered phenomenon, encompassing not just state and regional stability but also the everyday lives of individuals and groups. The chapter contextualizes and lays out the core tenets of CSS, then shows how some of the core concepts in the CSS literature can be applied to analysis of health issues. Finally, the chapter demonstrates how CSS can function as a privileged entry point into the political dimensions of the current global health regime.

On improving the ability of senior administrators in public policy-making

1986 ◽  
Vol 1 (0) ◽  
pp. 94-106
Author(s):  
Moon Hwa Chung
Keyword(s):  
Public Policy ◽  
Policy Making ◽  
Civil Servants ◽  
Senior Administrators ◽  
Diverse Range ◽  
Effective Training ◽  
Operational Systems ◽  
Professional Degree ◽  
High Degree

The involvement of civil servants in formulating public policy is ever expanding. Consequently, in order to effectively respond to rapid changes of the administrative environment, and to resolve the increasing conflicts which are bound to occur in greater frequency among various parties, government administration must be developed to a professional degree. Thus, it is important to restructure policy making processes and to improve the relations with each environmental factor which affects the orderly operation of the overall policy making mechanism. It is even more critical to develop the quality of those civil servants who influence the policy making procedure. In order to realize the above goals, first, government recruiting and staffing systems must be improved to attract and retain competent, capable personnel from the labor market; It is important to develop and preserve a personnel system which is based on the merit principle in order to maintain a high degree of motivation and benefit from the full capacities of employees; Finally, it is imperative to make use of a diverse range of effective training programs, techniques, and operational systems which will equip civil servants with the skills and knowledge necessary to cope with ever increasing administrative demands and develop in them progressive oriented attitudes.

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