scholarly journals CAPRIB: a user-friendly tool to study amino acid changes and selection for the exploration of intra-genus evolution

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Juan F. Guerra Maldonado ◽  
Antony T. Vincent ◽  
Martin Chenal ◽  
Frederic J. Veyrier
Keyword(s):  
Amino Acid ◽  
Single Species ◽  
Graphical Interface ◽  
Genetic Changes ◽  
Phenotypic Differences ◽  
Phenotypic Divergence ◽  
Potential Impact ◽  
Evolutionary Paths ◽  
User Friendly ◽  
Slow Growing

Abstract Background The evolution of bacteria is shaped by different mechanisms such as mutation, gene deletion, duplication, or insertion of foreign DNA among others. These genetic changes can accumulate in the descendants as a result of natural selection. Using phylogeny and genome comparisons, evolutionary paths can be somehow retraced, with recent events being much easier to detect than older ones. For this reason, multiple tools are available to study the evolutionary events within genomes of single species, such as gene composition alterations, or subtler mutations such as SNPs. However, these tools are generally designed to compare similar genomes and require advanced skills in bioinformatics. We present CAPRIB, a unique tool developed in Java that allows to determine the amino acid changes, at the genus level, that correlate with phenotypic differences between two groups of organisms. Results CAPRIB has a user-friendly graphical interface and uses databases in SQL, making it easy to compare several genomes without the need for programming or thorough knowledge in bioinformatics. This intuitive software narrows down a list of amino acid changes that are concomitant with a given phenotypic divergence at the genus scale. Each permutation found by our software is associated with two already described statistical values that indicate its potential impact on the protein’s function, helping the user decide which promising candidates to further investigate. We show that CAPRIB is able to detect already known mutations and uncovers many more, and that this tool can be used to question molecular phylogeny. Finally, we exemplify the utility of CAPRIB by pinpointing amino acid changes that coincided with the emergence of slow-growing mycobacteria from their fast-growing counterparts. The software is freely available at https://github.com/BactSymEvol/Caprib. Conclusions CAPRIB is a new bioinformatics software aiming to make genus-scale comparisons accessible to all. With its intuitive graphical interface, this tool identifies key amino acid changes concomitant with a phenotypic divergence. By comparing fast and slow-growing mycobacteria, we shed light on evolutionary hotspots, such as the cytokinin pathway, that are interesting candidates for further experimentations.

SIR2004: an improved tool for crystal structure determination and refinement

2005 ◽  
Vol 38 (2) ◽  
pp. 381-388 ◽  
Author(s):  
Maria C. Burla ◽  
Rocco Caliandro ◽  
Mercedes Camalli ◽  
Benedetta Carrozzini ◽  
Giovanni L. Cascarano ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Structure Determination ◽  
Protein Structures ◽  
Medium Size ◽  
Graphical Interface ◽  
Asymmetric Unit ◽  
Density Maps ◽  
Data Resolution ◽  
User Friendly

SIR2004is the evolution of theSIR2002program [Burla, Camalli, Carrozzini, Cascarano, Giacovazzo, Polidori & Spagna (2003).J. Appl. Cryst.36, 1103]. It is devoted to the solution of crystal structures by direct and Patterson methods. Several new features implemented inSIR2004make this program efficient: it is able to solveab initioboth small/medium-size structures as well as macromolecules (up to 2000 atoms in the asymmetric unit). In favourable circumstances, the program is also able to solve protein structures with data resolution up to 1.4–1.5 Å, and to provide interpretable electron density maps. A powerful user-friendly graphical interface is provided.

scholarly journals Ecological specialisation and evolutionary reticulation in extant Hyaenidae

2020 ◽  
Author(s):  
M V Westbury ◽  
Diana Le Duc ◽  
David A. Duchêne ◽  
Arunkumar Krishnan ◽  
Stefan Prost ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Species ◽  
Spotted Hyena ◽  
Genetic Changes ◽  
Slow Decline ◽  
Extant Species ◽  
Phylogenetic Discordance ◽  
Population Sizes ◽  
Olfactory Receptor Genes ◽  
Striped Hyena

AbstractDuring the Miocene, Hyaenidae was a highly diverse family of Carnivora that has since been severely reduced to four extant genera, each of which contains only a single species. These species include the bone-cracking spotted, striped, and brown hyenas, and the specialised insectivorous aardwolf. Previous genome studies have analysed the evolutionary histories of the spotted and brown hyenas, but little is known about the remaining two species. Moreover, the genomic underpinnings of scavenging and insectivory, defining traits of the extant species, remain elusive. To tackle these questions, we generated an aardwolf genome and analysed it together with those from the other three species. We provide new insights into the evolutionary relationships between the species, the genomic underpinnings of their scavenging and insectivorous lifestyles, and their respective genetic diversities and demographic histories. High levels of phylogenetic discordance within the family suggest gene flow between the aardwolf lineage and the ancestral brown/striped hyena lineage. Genes related to immunity and digestion in the bone-cracking hyenas and craniofacial development in the aardwolf showed the strongest signals of selection in their respective lineages, suggesting putative key adaptations to carrion or termite feeding. We also found a family-wide expansion in olfactory receptor genes suggesting that an acute sense of smell was a key early adaptation for the Hyaenidae family. Finally, we report very low levels of genetic diversity within the brown and striped hyenas despite no signs of inbreeding, which we putatively link to their similarly slow decline in Neover the last ∼2 million years. We found much higher levels of genetic diversity in both the spotted hyena and aardwolf and more stable population sizes through time. Taken together, these findings highlight how ecological specialisation can impact the evolutionary history, demographics, and adaptive genetic changes of a lineage.

RES2INS: a graphical interface for theSHELXprogram suite

1998 ◽  
Vol 31 (6) ◽  
pp. 963-964
Author(s):  
Leonard J. Barbour ◽  
Jerry L. Atwood
Keyword(s):  
Operating System ◽  
Structural Model ◽  
Graphical Interface ◽  
Structure Solution ◽  
User Friendly

RES2INSruns under the MS-DOS operating system and allows the user to view graphically the results of successiveSHELXstructure solution and refinement runs. In addition, the structural model can be edited in a user-friendly manner and these changes can be carried through to a newSHELXinstruction file. The program is menu driven and extensive use is made of the mouse for the facilitation of operations on individual atoms.

scholarly journals Phenotypic and Genotypic Comparison of a Live-Attenuated Genotype I Japanese Encephalitis Virus SD12-F120 Strain with Its Virulent Parental SD12 Strain

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 552 ◽  
Author(s):  
Muhammad Naveed Anwar ◽  
Xin Wang ◽  
Muddassar Hameed ◽  
Abdul Wahaab ◽  
Chenxi Li ◽  
...  
Keyword(s):  
Amino Acid ◽  
Japanese Encephalitis Virus ◽  
Japanese Encephalitis ◽  
Clinical Symptoms ◽  
Encephalitis Virus ◽  
Amino Acid Substitutions ◽  
Genotype I ◽  
Genetic Changes ◽  
Genotypic Characteristics ◽  
Insight Into

The phenotypic and genotypic characteristics of a live-attenuated genotype I (GI) strain (SD12-F120) of Japanese encephalitis virus (JEV) were compared with its virulent parental SD12 strain to gain an insight into the genetic changes acquired during the attenuation process. SD12-F120 formed smaller plaque on BHK-21 cells and showed reduced replication in mouse brains compared with SD12. Mice inoculated with SD12-F120 via either intraperitoneal or intracerebral route showed no clinical symptoms, indicating a highly attenuated phenotype in terms of both neuroinvasiveness and neurovirulence. SD12-F120 harbored 29 nucleotide variations compared with SD12, of which 20 were considered silent nucleotide mutations, while nine resulted in eight amino acid substitutions. Comparison of the amino acid variations of SD12-F120 vs. SD12 pair with those from other four isogenic pairs of the attenuated and their virulent parental strains revealed that the variations at E138 and E176 positions of E protein were identified in four and three pairs, respectively, while the remaining amino acid variations were almost unique to their respective strain pairs. These observations suggest that the genetic changes acquired during the attenuation process were likely to be strain-specific and that the mechanisms associated with JEV attenuation/virulence are complicated.

scholarly journals Visualizing hematopoiesis as a stochastic process

2018 ◽  
Vol 2 (20) ◽  
pp. 2637-2645
Author(s):  
Jason Xu ◽  
Yiwen Wang ◽  
Peter Guttorp ◽  
Janis L. Abkowitz
Keyword(s):  
Stochastic Process ◽  
Cell Expansion ◽  
Visualization Tool ◽  
Graphical Interface ◽  
Human Cord Blood ◽  
Virtual Experiments ◽  
Clonal Hematopoiesis ◽  
Cord Blood Cell ◽  
Statistical Background ◽  
User Friendly

Abstract Stochastic simulation has played an important role in understanding hematopoiesis, but implementing and interpreting mathematical models requires a strong statistical background, often preventing their use by many clinical and translational researchers. Here, we introduce a user-friendly graphical interface with capabilities for visualizing hematopoiesis as a stochastic process, applicable to a variety of mammal systems and experimental designs. We describe the visualization tool and underlying mathematical model, and then use this to simulate serial transplantations in mice, human cord blood cell expansion, and clonal hematopoiesis of indeterminate potential. The outcomes of these virtual experiments challenge previous assumptions and provide examples of the flexible range of hypotheses easily testable via the visualization tool.

PreDICT: a graphical user interface to the DICVOL14 indexing software program for powder diffraction data

2019 ◽  
Vol 34 (3) ◽  
pp. 233-241 ◽  
Author(s):  
Justin R. Blanton ◽  
Robert J. Papoular ◽  
Daniel Louër
Keyword(s):  
Powder Diffraction ◽  
Laboratory Data ◽  
Graphical Interface ◽  
Powder Diffraction Data ◽  
X Ray ◽  
Moderate Number ◽  
Diffraction Patterns ◽  
User Friendly ◽  
Recent Version ◽  
Selection Of

A straightforward intuitive user-friendly compact graphical interface, PreDICT (Premier DICVOL Tool) has been developed to take full advantage of the new capabilities of the most recent version of the DICVOL14 Indexing Software. The latter, an updated version of DICVOL04, includes optimizations, e.g. for monoclinic and triclinic cases, a detailed review of the input data from the indexing solutions, cell centering tests, as well as the handling of a moderate number of impurity peaks. Among the most salient features of PreDICT, one can mention the ability (1) to use 2θ non-equistepped input 1D X-ray powder diffraction patterns as can be obtained from 2D detectors, (2) to strip laboratory data from its Kα2 contribution when present, (3) to generate 2θ equistepped output 1D X-ray powder diffraction patterns in both the “.XY” and “.GSA” formats. In addition, PreDICT allows for the following features: (1) full access to the native DICVOL14 input/output ASCII file system is retained, (2) for any selection of a DICVOL14 suggested unit cell, all predicted Bragg peaks up to a certain 2θMAX value are clearly displayed and indicated, thereby emphasizing the contribution of the unaccounted peaks (if any) to the 1D X-ray powder diffraction pattern under current investigation.

Brazilian-adapted soybean Bradyrhizobium strains uncover IS elements with potential impact on biological nitrogen fixation

2019 ◽  
Vol 366 (11) ◽  
Author(s):  
Gesiele Almeida Barros-Carvalho ◽  
Mariangela Hungria ◽  
Fabrício Martins Lopes ◽  
Marie-Anne Van Sluys
Keyword(s):  
Natural Variation ◽  
Bacterial Genomes ◽  
Phenotypic Differences ◽  
Is Elements ◽  
Local Impact ◽  
Potential Impact ◽  
Symbiotic Properties ◽  
Biological Nitrogen ◽  
Insertional Polymorphism ◽  
Commercial Inoculants

ABSTRACTBradyrhizobium diazoefficiens CPAC 7 and Bradyrhizobium japonicum CPAC 15 are broadly used in commercial inoculants in Brazil, contributing to most of the nitrogen required by the soybean crop. These strains differ in their symbiotic properties: CPAC 7 is more efficient in fixing nitrogen, whereas CPAC 15 is more competitive. Comparative genomics revealed many transposases close to genes associated with symbiosis in the symbiotic island of these strains. Given the importance that insertion sequences (IS) elements have to bacterial genomes, we focused on identifying the local impact of these elements in the genomes of these and other related Bradyrhizobium strains to further understand their phenotypic differences. Analyses were performed using bioinformatics approaches. We found IS elements disrupting and inserted at regulatory regions of genes involved in symbiosis. Further comparative analyses with 21 Bradyrhizobium genomes revealed insertional polymorphism with distinguishing patterns between B. diazoefficiens and B. japonicum lineages. Finally, 13 of these potentially impacted genes are differentially expressed under symbiotic conditions in B. diazoefficiens USDA 110. Thus, IS elements are associated with the diversity of Bradyrhizobium, possibly by providing mechanisms for natural variation of symbiotic effectiveness.

New insights into the regulation of inducible nitric oxide synthesis

1994 ◽  
Vol 266 (6) ◽  
pp. E829-E839 ◽  
Author(s):  
S. M. Morris ◽  
T. R. Billiar
Keyword(s):  
Nitric Oxide ◽  
Amino Acid ◽  
Host Response ◽  
Cell Types ◽  
Nitric Oxide Synthesis ◽  
Arginine Metabolism ◽  
Anatomic Site ◽  
Nitrogen Donor ◽  
Potential Impact ◽  
Inducible Nitric Oxide

Recent studies have identified the induction of nitric oxide (NO) synthesis in many cell types as part of the host response to sepsis and inflammation. Induced NO can have a variety of effects which may be detrimental or beneficial during sepsis or inflammation, depending on amount, duration, and anatomic site of synthesis. As arginine is the only physiological nitrogen donor for NO synthesis, metabolism of this amino acid may play an important role in regulation of NO synthesis during sepsis. This review will discuss the roles NO plays in sepsis and the potential impact of arginine metabolism on NO synthesis.

scholarly journals Identifying biochemical phenotypic differences between cryptic species

2014 ◽  
Vol 10 (9) ◽  
pp. 20140615 ◽  
Author(s):  
Manuel Liebeke ◽  
Michael W. Bruford ◽  
Robert K. Donnelly ◽  
Timothy M. D. Ebbels ◽  
Jie Hao ◽  
...  
Keyword(s):  
Cryptic Species ◽  
Molecular Genetic ◽  
Single Species ◽  
Functional Trait ◽  
Species Group ◽  
Lumbricus Rubellus ◽  
Phenotypic Differences ◽  
Functional Differences ◽  
High Concentrations ◽  
Metabolomic Approach

Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus . There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as N ε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status.

The side effects of translational omics: overtesting, overdiagnosis, overtreatment

2016 ◽  
Vol 54 (3) ◽  
Author(s):  
Eleftherios P. Diamandis ◽  
Michelle Li
Keyword(s):  
False Positive ◽  
Research Groups ◽  
Pilot Projects ◽  
Genetic Changes ◽  
Screening Programs ◽  
Unknown Significance ◽  
Disease Predisposition ◽  
Low Costs ◽  
Slow Growing ◽  
Positive Results

AbstractHigh-throughput technologies such as next-generation genomics, transcriptomics and proteomics are capable of generating massive amounts of data quickly, and at relatively low costs. It is tempting to use this data for various medical applications including preclinical disease detection and for prediction of disease predisposition. Pilot projects, initiated by various research groups and Google, are currently underway, but results with not be available for a few years. We here summarize some possible difficulties with these approaches, by using examples from already tried cancer and other screening programs. Population screening, especially with multiparametric algorithms, will identify at least some false positive parameters and screening programs will identify abnormal results in otherwise healthy individuals. Whole genome sequencing will identify genetic changes of unknown significance and may not predict accurately future disease predisposition if the disease is also influenced by environmental factors. In screening programs, if the disease is rare, the positive predictive value of the test will be low, even if the test has excellent sensitivity and specificity. False positive results may require invasive procedures to delineate. Furthermore, screening programs are not effective if the cancer grows quickly, and will identify indolent forms of the disease with slow-growing tumors. It has also been recently shown that for some cancers, more intensive and radical treatments do not usually lead to better clinical outcomes. We conclude that new omics testing technologies should avoid overdiagnosis and overtreatment and need to be evaluated for overall clinical benefit before introduction to the clinic.

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