scholarly journals Frequent birth-and-death events throughout perforin-1 evolution

2020 ◽  
Author(s):  
Miguel Araujo-Voces ◽  
Victor Quesada
Keyword(s):  
Preliminary Analysis ◽  
Large Scale ◽  
Mammalian Species ◽  
Genomic Data ◽  
Start Codon ◽  
High Similarity ◽  
Gene Encoding ◽  
Coding Sequences ◽  
Copy Numbers ◽  
Multiple Species

Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

scholarly journals Frequent birth-and-death events throughout perforin-1 evolution

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Miguel Araujo-Voces ◽  
Víctor Quesada
Keyword(s):  
Preliminary Analysis ◽  
Large Scale ◽  
Mammalian Species ◽  
Genomic Data ◽  
Start Codon ◽  
High Similarity ◽  
Gene Encoding ◽  
Coding Sequences ◽  
Copy Numbers ◽  
Multiple Species

Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

scholarly journals Frequent birth-and-death events throughout perforin-1 evolution

2020 ◽  
Author(s):  
Miguel Araujo-Voces ◽  
Victor Quesada
Keyword(s):  
Preliminary Analysis ◽  
Large Scale ◽  
Mammalian Species ◽  
Genomic Data ◽  
Start Codon ◽  
High Similarity ◽  
Gene Encoding ◽  
Coding Sequences ◽  
Copy Numbers ◽  
Multiple Species

Abstract Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci with important variations in the number of copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.

High-level expression of Bacillus subtilis tryptophanyl-tRNA synthetase in Escherichia coli

1990 ◽  
Vol 68 (2) ◽  
pp. 492-495 ◽  
Author(s):  
Wen Shi ◽  
King-Chuen Chow ◽  
J. Tze-Fei Wong
Keyword(s):  
Escherichia Coli ◽  
Bacillus Subtilis ◽  
Large Scale ◽  
Trna Synthetase ◽  
Start Codon ◽  
Temperature Sensitive ◽  
Gene Encoding ◽  
Scale Preparation ◽  
High Level

The trpS gene encoding Bacillus subtilis tryptophanyl-tRNA synthetase (TrpRS) was prepared from the pUC8-derived pTSQ2 plasmid, mutagenized to introduce an EcoRI site immediately in front of the ATG start codon, and inserted into the pKK223-3 vector downstream to the tac promoter to yield the pKSW1 plasmid. Upon induction with isopropyl-β-D-thiogalactopyranoside, Escherichia coli JM109[pKSW1] cells synthesized TrpRS to a level corresponding to 45% of total cell proteins. This high level of gene expression facilitates large scale preparation of TrpRS for physical studies, detection of in vivo degradation of mutant forms of TrpRS, and comparative assays of TrpRS by [3H]Trp-tRNA formation and by Trp-hydroxamate formation for the purpose of mutant characterization. Finally, since pKSW1 could complement the temperature-sensitive TrpRS mutation on E. coli trpS 10343 cells, defective mutations of the trpS gene on pKSW1 would be detectible on the basis of complementation testing.Key words: tryptophan-tRNA, aminoacyl-tRNA synthetase, Bacillus subtilis.

scholarly journals Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

2008 ◽  
Vol 40 (7) ◽  
pp. 854-861 ◽  
Author(s):  
Jun Zhu ◽  
Bin Zhang ◽  
Erin N Smith ◽  
Becky Drees ◽  
Rachel B Brem ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Large Scale ◽  
Genomic Data ◽  
Functional Genomic ◽  
Functional Genomic Data

Dog Models of Aging

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Audrey Ruple ◽  
Evan MacLean ◽  
Noah Snyder-Mackler ◽  
Kate E. Creevy ◽  
Daniel Promislow
Keyword(s):  
Large Scale ◽  
Mammalian Species ◽  
Annual Review ◽  
Publication Date ◽  
Companion Dogs ◽  
Age Related ◽  
Key Concepts ◽  
Similarities And Differences ◽  
Laboratory Models ◽  
Unique Potential

As the most phenotypically diverse mammalian species that shares human environments and access to sophisticated healthcare, domestic dogs have unique potential to inform our understanding of the determinants of aging. Here we outline key concepts in the study of aging and illustrate the value of research with dogs, which can improve dog health and support translational discoveries. We consider similarities and differences in aging and age-related diseases in dogs and humans and summarize key advances in our understanding of genetic and environmental risk factors for morbidity and mortality in dogs. We address health outcomes ranging from cancer to cognitive function and highlight emerging research opportunities from large-scale cohort studies in companion dogs. We conclude that studying aging in dogs could overcome many limitations of laboratory models, most notably, the ability to assess how aging-associated pathways influence aging in real-world environments similar to those experienced by humans. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 10 is February 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

scholarly journals The theory on and software simulating large-scale genomic data for genotype-by-environment interactions

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiujin Li ◽  
Hailiang Song ◽  
Zhe Zhang ◽  
Yunmao Huang ◽  
Qin Zhang ◽  
...  
Keyword(s):  
Large Scale ◽  
Simulated Data ◽  
Genomic Data ◽  
Efficient Tool ◽  
Phenotypic Data ◽  
Genotype By Environment Interactions ◽  
Genotype By Environment ◽  
Threshold Trait ◽  
Genome Wide ◽  
Increasing Demand

Abstract Background With the emphasis on analysing genotype-by-environment interactions within the framework of genomic selection and genome-wide association analysis, there is an increasing demand for reliable tools that can be used to simulate large-scale genomic data in order to assess related approaches. Results We proposed a theory to simulate large-scale genomic data on genotype-by-environment interactions and added this new function to our developed tool GPOPSIM. Additionally, a simulated threshold trait with large-scale genomic data was also added. The validation of the simulated data indicated that GPOSPIM2.0 is an efficient tool for mimicking the phenotypic data of quantitative traits, threshold traits, and genetically correlated traits with large-scale genomic data while taking genotype-by-environment interactions into account. Conclusions This tool is useful for assessing genotype-by-environment interactions and threshold traits methods.

scholarly journals EXPLORATION OF BROTH CHICKEN GUT AS GROWTH MEDIA OF Escherichia coli BL21 pET-Endo FOR ENDO-Β-1,4-D-XYLANASE PRODUCTION

2017 ◽  
Vol 13 (2) ◽  
pp. 191
Author(s):  
Anak Agung Istri Ratnadewi ◽  
Moch. Yoris Alidion ◽  
Agung Budi Santoso ◽  
Ika Oktavianawatia
Keyword(s):  
Large Scale ◽  
Incubation Temperature ◽  
Specific Activity ◽  
Hydrolytic Enzyme ◽  
Optimal Growth ◽  
Good Alternative ◽  
Growth Media ◽  
Gene Encoding ◽  
Xylanase Production ◽  
E Coli

<p>Endo-β-1,4-D-xylanase is a hydrolytic enzyme that breakdown the 1.4 chain of xylan polysaccharide. We have succes to transform the plasmid pET-Endo gene encoding endo-1,4-β-D-xylanase from Bacillus sp. originally from termites abdominal to E. coli BL21. The clone was ready for large scale of enzyme production. To reduce production cost, we look for subtitute media for the expensive Luria Berthani broth. Chicken guts broth is good alternative while rich of protein and very cheap. The content of N dissolved chicken guts broth reaches 87 % of LB broth. Growth of E. Coli BL21 in Chicken guts broth and LB broth (as control) was observed by Optical Density (OD) using spectrofotometer. Concentration of glucose added in broth and incubation temperature was varied. The result showed that optimal growth was in addition of 1.5 % glucose and incubated at  37 <sup>o</sup>C for 16 h. This optimal condition was used to grow E. coli BL21 pET-Endo for xylanase production. Enzyme purification was done by Ni-NTA affinity chromatography. Highest protein yield was 0.076 mg/mL obtained in 100 mM imidazole elucidation. The activity and specific activity of xylanase were estimated as 0.042 U/mL and 0.556 U/µg, respectively. The purification factor was 3.16 time and the molecular weight of enzyme was ± 30, 000 Dalton</p>

scholarly journals Integrating multiple species criteria and species hypotheses in subterranean biology

2018 ◽  
Vol 1 ◽  
Author(s):  
Florian Malard ◽  
Philippe Grison ◽  
David Eme ◽  
Cene Fiser ◽  
Jean-François Flot ◽  
...  
Keyword(s):  
Large Scale ◽  
Species Concept ◽  
Genetic Isolation ◽  
Scientific Rigor ◽  
Geographic Range Size ◽  
Biodiversity Science ◽  
Multiple Species ◽  
Methodological Advance ◽  
New Generation ◽  
Scientific Hypotheses

Decades of debates around the species problem have resulted in the emergence of a unified species concept with multiple criteria to delimit species taxa. Many biologists now agree to consider species as separately evolving segments of metapopulation lineages (i.e. the species concept), and to consider species taxa (i.e. the elementary units used in biodiversity science) as scientific hypotheses of separately evolving entities. In this framework, sets of species hypotheses are generated using different criteria (i.e. morphological distinguishability, genetic isolation) that mirror the properties expressed by species at different times and sequential orders during the extended and heterogeneous process of speciation. This conceptual and methodological advance in taxonomy has several implications for biodiversity science. First, species taxa represent a heterogeneous set of hypotheses whose properties are contingent on the heterogeneous, continuous and extended nature of speciation. Second, species databases need to integrate information on the diverse properties of species by attributing specimens to multiple species hypotheses generated using different delimitation criteria. Third, biodiversity science at large can provide novel insights into biodiversity processes by incorporating multiple species hypotheses into the analysis of biodiversity patterns. Here, we show how these implications have been taken into account by subterranean biologists. First, we briefly review the criteria and methods used to delimit species in subterranean biology and the diverse sets of species hypotheses they generated. Second, we present a new generation of species occurrence databases that integrate different species criteria and hypotheses while fully respecting the scientific rigor of taxonomy. Last, we show how incorporating multiple species hypotheses into macroecological analyses of European groundwater fauna bolsters our under­standing of the factors shaping large-scale patterns of species richness and geographic range size.

Preliminary Analysis of Sustainable Design Management for LSPB

2012 ◽  
Vol 472-475 ◽  
pp. 2385-2388
Author(s):  
Qian Shi ◽  
Rui Huang
Keyword(s):  
Interface Design ◽  
Preliminary Analysis ◽  
Large Scale ◽  
Development Theory ◽  
Design Management ◽  
Model Design ◽  
Design Environment ◽  
Public Building ◽  
Organization Model ◽  
Complex Design

Large-scale public building (LSPB) is different from general industrial and civil construction, so that some special management methods are attained to handling the complex design environment based on sustainable development theory. Including organization model, design checklist and some interface design management principles are raised in this analysis.

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