scholarly journals Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sonam Gaba ◽  
Abha Kumari ◽  
Marnix Medema ◽  
Rajeev Kaushik
Keyword(s):  
Salt Concentration ◽  
Genome Analysis ◽  
Gene Tree ◽  
Halophilic Archaea ◽  
Variable Component ◽  
Last Common Ancestor ◽  
Ancestral State ◽  
The Core ◽  
Pan Genome ◽  
Wide Range

AbstractHalobacteria, a class of Euryarchaeota are extremely halophilic archaea that can adapt to a wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl. It consists of the orders: Halobacteriales, Haloferaciales and Natriabales. Pan-genome analysis of class Halobacteria was done to explore the core (300) and variable components (Softcore: 998, Cloud:36531, Shell:11784). The core component revealed genes of replication, transcription, translation and repair, whereas the variable component had a major portion of environmental information processing. The pan-gene matrix was mapped onto the core-gene tree to find the ancestral (44.8%) and derived genes (55.1%) of the Last Common Ancestor of Halobacteria. A High percentage of derived genes along with presence of transformation and conjugation genes indicate the occurrence of horizontal gene transfer during the evolution of Halobacteria. A Core and pan-gene tree were also constructed to infer a phylogeny which implicated on the new super-order comprising of Natrialbales and Halobacteriales.

scholarly journals First Steps in the Analysis of Prokaryotic Pan-Genomes

2020 ◽  
Vol 14 ◽  
pp. 117793222093806
Author(s):  
Sávio Souza Costa ◽  
Luís Carlos Guimarães ◽  
Artur Silva ◽  
Siomar Castro Soares ◽  
Rafael Azevedo Baraúna
Keyword(s):  
Genome Analysis ◽  
Core Genome ◽  
Bacterial Species ◽  
Genomic Analysis ◽  
Gene Families ◽  
Specific Group ◽  
The Core ◽  
Pan Genome ◽  
Research Areas ◽  
Key Concepts

Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.

scholarly journals Roary: Rapid large-scale prokaryote pan genome analysis

2015 ◽  
Author(s):  
Andrew J Page ◽  
Carla A Cummins ◽  
Martin Hunt ◽  
Vanessa K Wong ◽  
Sandra Reuter ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Genome Analysis ◽  
Large Scale ◽  
The Core ◽  
Pan Genome ◽  
Accessory Genes ◽  
Multiple Processors ◽  
Prokaryotic Genomes ◽  
Accuracy Of Results

A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors.

scholarly journals Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 477 ◽  
Author(s):  
Vikas Sharma ◽  
Fauzul Mobeen ◽  
Tulika Prakash
Keyword(s):  
Core Genome ◽  
Size Variation ◽  
Genomic Islands ◽  
Genome Size Variation ◽  
Host Interactions ◽  
The Core ◽  
Pan Genome ◽  
Wide Range ◽  
Insertion Elements ◽  
Open Nature

Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.

scholarly journals Critical assessment of pan-genomics of metagenome-assembled genomes

2022 ◽  
Author(s):  
Tang Li ◽  
Yanbin Yin
Keyword(s):  
Genome Analysis ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Gene Loss ◽  
Core Gene ◽  
Critical Assessment ◽  
Major Influence ◽  
The Core ◽  
Pan Genome ◽  
Analysis Tools

Background: Large scale metagenome assembly and binning to generate metagenome-assembled genomes (MAGs) has become possible in the past five years. As a result, millions of MAGs have been produced and increasingly included in pan-genomics workflow. However, pan-genome analyses of MAGs may suffer from the known issues with MAGs: fragmentation, incompleteness, and contamination, due to mis-assembly and mis-binning. Here, we conducted a critical assessment of including MAGs in pan-genome analysis, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. Results: We found that incompleteness led to more significant core gene loss than fragmentation. Contamination had little effect on core genome size but had major influence on accessory genomes. The core gene loss remained when using different pan-genome analysis tools and when using a mixture of MAGs and complete genomes. Importantly, the core gene loss was partially alleviated by lowering the core gene threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The core gene loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Conclusions: We conclude that lowering core gene threshold and predicting genes in metagenome mode (as Anvio does with Prodigal) are necessary in pan-genome analysis of MAGs to alleviate the accuracy loss. Better quality control of MAGs and development of new pan-genome analysis tools specifically designed for MAGs are needed in future studies.

Duoethnography: A Polytheoretical Approach to (Re)Storing, (Re)Storying the Meanings That One Gives

2020 ◽  
pp. 396-423
Author(s):  
John Joseph Norris ◽  
Richard D. Sawyer
Keyword(s):  
Social Justice ◽  
Critical Theory ◽  
Third Space ◽  
The Third ◽  
The Core ◽  
Wide Range ◽  
Core Elements ◽  
Feminist Inquiry

This chapter summarizes the advancement of duoethnography throughout its fifteen-year history, employing examples from a variety of topics in education and social justice to provide a wide range of approaches that one may take when conducting a duoethnography. A checklist articulates what its cofounders consider the core elements of duoethnographies, additional features that may or may not be employed and how some studies purporting to be duoethnographies may not be so. The chapter indicates connections between duoethnography and a number of methodological concepts including the third space, the problematics of representation, feminist inquiry, and critical theory using published examples by several duoethnographers.

scholarly journals Influence of Salt on the Self-Organization in Solutions of Star-Shaped Poly-2-alkyl-2-oxazoline and Poly-2-alkyl-2-oxazine on Heating

Polymers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1152
Author(s):  
Tatyana Kirila ◽  
Anna Smirnova ◽  
Alla Razina ◽  
Andrey Tenkovtsev ◽  
Alexander Filippov
Keyword(s):  
Phase Separation ◽  
Salt Concentration ◽  
Monomer Unit ◽  
Salt Content ◽  
The Self ◽  
Self Organization ◽  
Phase Separation Temperature ◽  
The Core ◽  
Separation Temperature ◽  
Water Salt

The water–salt solutions of star-shaped six-arm poly-2-alkyl-2-oxazines and poly-2-alkyl-2-oxazolines were studied by light scattering and turbidimetry. The core was hexaaza[26]orthoparacyclophane and the arms were poly-2-ethyl-2-oxazine, poly-2-isopropyl-2-oxazine, poly-2-ethyl-2-oxazoline, and poly-2-isopropyl-2-oxazoline. NaCl and N-methylpyridinium p-toluenesulfonate were used as salts. Their concentration varied from 0–0.154 M. On heating, a phase transition was observed in all studied solutions. It was found that the effect of salt on the thermosensitivity of the investigated stars depends on the structure of the salt and polymer and on the salt content in the solution. The phase separation temperature decreased with an increase in the hydrophobicity of the polymers, which is caused by both a growth of the side radical size and an elongation of the monomer unit. For NaCl solutions, the phase separation temperature monotonically decreased with growth of salt concentration. In solutions with methylpyridinium p-toluenesulfonate, the dependence of the phase separation temperature on the salt concentration was non-monotonic with minimum at salt concentration corresponding to one salt molecule per one arm of a polymer star. Poly-2-alkyl-2-oxazine and poly-2-alkyl-2-oxazoline stars with a hexaaza[26]orthoparacyclophane core are more sensitive to the presence of salt in solution than the similar stars with a calix[n]arene branching center.

Dual-temperature and pH responsive (ethylene glycol)-based nanogels via structural design

2014 ◽  
Vol 5 (8) ◽  
pp. 3061-3070 ◽  
Author(s):  
Yohei Kotsuchibashi ◽  
Ravin Narain
Keyword(s):  
Carboxylic Acid ◽  
Ethylene Glycol ◽  
Salt Concentration ◽  
Structural Design ◽  
Solution Temperature ◽  
Ph Responsive ◽  
Solution Ph ◽  
Critical Solution Temperature ◽  
Carboxylic Acid Groups ◽  
The Core

Dual-temperature and pH responsive (ethylene glycol)-based nanogels were synthesized. Both the core and the shell of the nanogels showed a lower critical solution temperature (LCST) and the LCST of the shell was strongly affected by the solution pH and salt concentration due to the presence of carboxylic acid groups at the nanogel surface.

Measurements and Modeling of Ingress in a New 1.5-Stage Turbine Research Facility

2016 ◽  
Vol 139 (1) ◽  
Author(s):  
Marios Patinios ◽  
James A. Scobie ◽  
Carl M. Sangan ◽  
J. Michael Owen ◽  
Gary D. Lock
Keyword(s):  
Theoretical Model ◽  
Gas Turbines ◽  
Test Facility ◽  
Radial Clearance ◽  
Operating Life ◽  
The Core ◽  
Wide Range ◽  
Purge Flow ◽  
Rotor Disk ◽  
Engine Components

In gas turbines, hot mainstream flow can be ingested into the wheel-space formed between stator and rotor disks as a result of the circumferential pressure asymmetry in the annulus; this ingress can significantly affect the operating life, performance, and integrity of highly stressed, vulnerable engine components. Rim seals, fitted at the periphery of the disks, are used to minimize ingress and therefore reduce the amount of purge flow required to seal the wheel-space and cool the disks. This paper presents experimental results from a new 1.5-stage test facility designed to investigate ingress into the wheel-spaces upstream and downstream of a rotor disk. The fluid-dynamically scaled rig operates at incompressible flow conditions, far removed from the harsh environment of the engine which is not conducive to experimental measurements. The test facility features interchangeable rim-seal components, offering significant flexibility and expediency in terms of data collection over a wide range of sealing flow rates. The rig was specifically designed to enable an efficient method of ranking and quantifying the performance of generic and engine-specific seal geometries. The radial variation of CO2 gas concentration, pressure, and swirl is measured to explore, for the first time, the flow structure in both the upstream and downstream wheel-spaces. The measurements show that the concentration in the core is equal to that on the stator walls and that both distributions are virtually invariant with radius. These measurements confirm that mixing between ingress and egress is essentially complete immediately after the ingested fluid enters the wheel-space and that the fluid from the boundary layer on the stator is the source of that in the core. The swirl in the core is shown to determine the radial distribution of pressure in the wheel-space. The performance of a double radial-clearance seal is evaluated in terms of the variation of effectiveness with sealing flow rate for both the upstream and the downstream wheel-spaces and is found to be independent of rotational Reynolds number. A simple theoretical orifice model was fitted to the experimental data showing good agreement between theory and experiment for all cases. This observation is of great significance as it demonstrates that the theoretical model can accurately predict ingress even when it is driven by the complex unsteady pressure field in the annulus upstream and downstream of the rotor. The combination of the theoretical model and the new test rig with its flexibility and capability for detailed measurements provides a powerful tool for the engine rim-seal designer.

A new species of genus Hexacentrus Serville, 1831 from Taiwan (Orthoptera: Tettigoniidae: Hexacentrinae)

Zootaxa ◽  
2021 ◽  
Vol 4933 (4) ◽  
pp. 543-556
Author(s):  
PO-WEI CHEN ◽  
HUI-CONG XIE ◽  
XUE WU ◽  
CHU-ZE SHEN ◽  
ZHU-QING HE
Keyword(s):  
New Species ◽  
Gene Tree ◽  
Species Level ◽  
National Museum ◽  
Type Specimens ◽  
As Species ◽  
Wide Range ◽  
Similar Appearance ◽  
One New Species ◽  
A New Species

There are 29 species or subspecies in genus Hexacentrus occurring in Asia, Africa and Australia. Because of its similar appearance, it is not easy to distinguish them by traditional methods. In this study, we collected samples and sequenced COI genes from wide range. By reconstructing the gene tree, we found one new species, H. formosanus Chen et He sp. nov., from Taiwan. The new species is similar to H. expansus or H. inflatissimus, but differs from the former in male Cu2 vein of left tegmina curved and slender, and spectrum of male left tegmina slender and subsquare; differs from the later by body size smaller and female tegmina narrow and short. The type specimens are deposited in National Museum of Natural Science, Taichung, Taiwan (NMNS). H. japonicus hareyamai is treated as species level, H. hareyamai stat. nov. 

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