scholarly journals GBRAP: a tool to retrieve, parse and analyze GenBank files of viral and bacterial species

2021 ◽  
Author(s):  
Chiara Vischioni ◽  
Valerio Giaccone ◽  
Paolo Catellani ◽  
Leonardo Alberghini ◽  
Riccardo Miotti Scapin ◽  
...  
Keyword(s):  
Topological Entropy ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Genomic Data ◽  
Command Line ◽  
Mathematical Methods ◽  
Entire Genome ◽  
Genomic Analyses ◽  
Living Organisms ◽  
Dna Strand

GenBank files contain genomic data of sequenced living organisms. Here, we present GBRAP (GenBank Retrieving, Analyzing and Parsing software), a tool written in Python 3 that can be used to easily download, parse and analyze viral and bacterial GenBank files, even when contain more than one genomic sequence for each species. GBRAP can analyze more files simultaneously through single command line parameters that give as output a single table showing the genomic characteristics of each organism. It is also able to calculate Shannon, LZSS (Lempel Ziv Storer Szymanski) and topological entropy for both the entire genome and its constitutive elements such as genes, rRNAs, tRNAs, tmRNAs and ncRNAs together with Chargaff's second parity rule scores obtained using different mathematical methods. Moreover, GBRAP can calculate, the number, the length and the nucleotides abundance of genomic components for each DNA strand and for the overlapping regions among the two complementary helixes. To our knowledge, this is the only software capable of providing this type of genomic analyses all together in a single tool, that, therefore can be used by the scientists interested in both genomics and evolutionary research.

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

scholarly journals The genomic sequence ofExiguobacterium chiriqhuchastr. N139 reveals a species that thrives in cold waters and extreme environmental conditions

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3162 ◽  
Author(s):  
Ana Gutiérrez-Preciado ◽  
Carlos Vargas-Chávez ◽  
Mariana Reyes-Prieto ◽  
Omar F. Ordoñez ◽  
Diego Santos-García ◽  
...  
Keyword(s):  
Acid Metabolism ◽  
High Salinity ◽  
Genomic Sequence ◽  
Ultraviolet B ◽  
Comparative Genomic ◽  
Ultraviolet B Radiation ◽  
Genomic Analyses ◽  
High Concentrations ◽  
And Coping ◽  
Cold Lake

We report the genome sequence ofExiguobacterium chiriqhuchastr. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of theExiguobacteriumgenomes available suggest that our strain belongs to the same species as the previously reportedE. pavilionensisstr. RW-2 andExiguobacteriumstr. GIC 31. We describe this species and propose thechiriqhuchaname to group them. ‘Chiri qhucha’ in Quechua means ‘cold lake’, which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bpE. chiriqhuchastr. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that conferE. chiriqhuchastr. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.

scholarly journals Bactopia: a flexible pipeline for complete analysis of bacterial genomes

2020 ◽  
Author(s):  
Robert A. Petit ◽  
Timothy D. Read
Keyword(s):  
Standard Procedure ◽  
Bacterial Species ◽  
Bacterial Genome ◽  
Complete Analysis ◽  
Comparative Genomic ◽  
Bacterial Genomes ◽  
Analysis Pipeline ◽  
Genomic Analyses ◽  
Conserved Genes ◽  
Downstream Analysis

AbstractSequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera. Bactopia consists of a dataset setup step (Bactopia Datasets; BaDs) where a series of customizable datasets are created for the species of interest; the Bactopia Analysis Pipeline (BaAP), which performs quality control, genome assembly and several other functions based on the available datasets and outputs the processed data to a structured directory format; and a series of Bactopia Tools (BaTs) that perform specific post-processing on some or all of the processed data. BaTs include pan-genome analysis, computing average nucleotide identity between samples, extracting and profiling the 16S genes and taxonomic classification using highly conserved genes. It is expected that the number of BaTs will increase to fill specific applications in the future. As a demonstration, we performed an analysis of 1,664 public Lactobacillus genomes, focusing on L. crispatus, a species that is a common part of the human vaginal microbiome. Bactopia is an open source system that can scale from projects as small as one bacterial genome to thousands that allows for great flexibility in choosing comparison datasets and options for downstream analysis. Bactopia code can be accessed at https://www.github.com/bactopia/bactopia.

scholarly journals New Genus Fibralongavirus in Siphoviridae Phages of Staphylococcus pseudintermedius

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1143
Author(s):  
Michal Zeman ◽  
Pavol Bárdy ◽  
Veronika Vrbovská ◽  
Pavel Roudnický ◽  
Zbyněk Zdráhal ◽  
...  
Keyword(s):  
New Genus ◽  
Bacterial Species ◽  
Gene Sequencing ◽  
Rpob Gene ◽  
Global Alignment ◽  
Significant Similarity ◽  
Staphylococcus Pseudintermedius ◽  
The Family ◽  
Genomic Analyses ◽  
Taxonomical Classification

Bacteriophages of the significant veterinary pathogen Staphylococcus pseudintermedius are rarely described morphologically and genomically in detail, and mostly include phages of the Siphoviridae family. There is currently no taxonomical classification for phages of this bacterial species. Here we describe a new phage designated vB_SpsS_QT1, which is related to phage 2638A originally described as a Staphylococcus aureus phage. Propagating strain S. aureus 2854 of the latter was reclassified by rpoB gene sequencing as S. pseudintermedius 2854 in this work. Both phages have a narrow but different host range determined on 54 strains. Morphologically, both of them belong to the family Siphoviridae, share the B1 morphotype, and differ from other staphylococcal phage genera by a single long fibre at the terminus of the tail. The complete genome of phage vB_SpsS_QT1 was sequenced with the IonTorrent platform and expertly annotated. Its linear genome with cohesive ends is 43,029 bp long and encodes 60 predicted genes with the typical modular structure of staphylococcal siphophages. A global alignment found the genomes of vB_SpsS_QT1 and 2638A to share 84% nucleotide identity, but they have no significant similarity of nucleotide sequences with other phage genomes available in public databases. Based on the morphological, phylogenetic, and genomic analyses, a novel genus Fibralongavirus in the family Siphoviridae is described with phage species vB_SpsS_QT1 and 2638A.

Cloning and molecular analysis of promoter-like sequences isolated from the chromosomal DNA ofLactobacillus acidophilusATCC 4356

1997 ◽  
Vol 43 (1) ◽  
pp. 61-69 ◽  
Author(s):  
G. Djordjevic ◽  
B. Bojovic ◽  
N. Miladinov ◽  
L. Topisirovic
Keyword(s):  
Lactococcus Lactis ◽  
Molecular Analysis ◽  
Lactobacillus Acidophilus ◽  
Promoter Activity ◽  
Lactobacillus Reuteri ◽  
Bacterial Species ◽  
Chromosomal Dna ◽  
Complementary Dna ◽  
E Coli ◽  
Dna Strand

Promoter-like sequences from the chromosomal DNA of thermophilic strain Lactobacillus acidophilus ATCC 4356 were cloned. Analysis of the three DNA fragments showing promoter activity, designated P3, P6, and P15, were performed in Lactobacillus reuteri, Lactococcus lactis, and E. coli. The reporter cat-86 gene was expressed in all three bacterial species under control of the fragments P3 and P6. Fragment P15 showed promoter activity only in Lactobacillus reuteri and E. coli but not in Lactococcus lactis. The three host-specific transcriptional start points (TSPs) were used when transcription of the cat-86 gene was controlled by fragment P3 in Lactobacillus reuteri, E. coli, and Lactococcus lactis. Similarly, fragment P15 initiated transcription of the cat-86 gene at two distinctive sites in Lactobacillus reuteri and E. coli. Only within fragment P6, a common TSP was used in Lactobacillus reuteri and E. coli, but different from that used in Lactococcus lactis. Each TSP was preceded by the putative −35 and −10 hexamers. Computer analysis of the fragment P3 sequence revealed the existence of divergent promoterlike sequence (P3rev) located on the complementary DNA strand. Fragments P6 and P15 were also functional in Lactobacillus acidophilus ATCC 4356 from which chromosomal DNA they were originally cloned.Key words: Lactobacillus acidophilus, promoter-like sequences, regulation.

scholarly journals CoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets

2020 ◽  
Author(s):  
Connor D Harris ◽  
Ellis L Torrance ◽  
Kasie Raymann ◽  
Louis-Marie Bobay
Keyword(s):  
Core Genome ◽  
Genomic Data ◽  
Data Sets ◽  
The Core ◽  
Genomic Analyses ◽  
Massive Accumulation ◽  
Genome Comparisons

Abstract The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.

scholarly journals Role of Water for Life

2019 ◽  
Vol 03 (01) ◽  
pp. 3-19
Author(s):  
Bengt Nordén
Keyword(s):  
Chemical Potential ◽  
Genetic Recombination ◽  
Solar Systems ◽  
Gene Recognition ◽  
Low Dielectric ◽  
Sexual Recombination ◽  
Dna Strand Exchange ◽  
Living Organisms ◽  
Dna Strand ◽  
Life On Earth

The behavior of benzoic acid in polyethylene inspired me to reflect on why water is a unique molecule that all living organisms depend upon. From properties of DNA in aqueous solution a seemingly counter-intuitive conjecture emerges: water is needed for the creation of certain dry low-dielectric nm-size environments where hydrogen bonding exerts strong recognition power. Such environments seem to be functionally crucial, and their interactions with other hydrophobic environments, or with hydrophobic agents that modulate the chemical potential of water, can cause structural transformations via ‘hydrophobic catalysis’. Possibly combined with an excluded volume osmosis effect (EVO), hydrophobic catalysis may have important biological roles, e.g., in genetic recombination. Hydrophobic agents are found to strongly accelerate spontaneous DNA strand exchange as well as certain other DNA rearrangement reactions. It is hypothesized that hydrophobic catalysis be involved in gene recognition and gene recombination mediated by bacterial RecA (one of the oldest proteins we know of) as well as in sexual recombination in higher organisms, by Rad51. Hydrophobically catalyzed unstacking fluctuations of DNA bases can favor elongated conformations, such as the recently proposed [Formula: see text]-DNA, with potential regulatory roles. That living cells can survive as dormant spores, with very low water content and in principle as such travel far in space is reflected upon: a random walk model with solar photon pressure as driving force indicates our life on earth could not have originated outside our galaxy but possibly from many solar systems within it — at some place, though, where there was plenty of liquid water.

scholarly journals The Radioprotective Effect of Procaine and Procaine-Derived Product Gerovital H3 in Lymphocytes from Young and Aged Individuals

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Anca Ungurianu ◽  
Denisa Margina ◽  
Claudia Borsa ◽  
Cristina Ionescu ◽  
Gudrun von Scheven ◽  
...  
Keyword(s):  
Mononuclear Cells ◽  
Low Density Lipoprotein ◽  
Density Lipoprotein ◽  
Chemical Compounds ◽  
Dna Strand Breaks ◽  
Peripheral Blood Mononuclear ◽  
Strand Breaks ◽  
Young Subjects ◽  
Living Organisms ◽  
Dna Strand

Ionizing radiation induces genomic instability in living organisms, and several studies reported an ageing-dependent radiosensitivity. Chemical compounds, such as scavengers, radioprotectors, and modifiers, contribute to reducing the radiation-associated toxicity. These compounds are often antioxidants, and therefore, in order to be effective, they must be present before or during exposure to radiation. However, not all antioxidants provide radioprotection. In this study, we investigated the effects of procaine and of a procaine-based product Gerovital H3 (GH3) on the formation of endogenous and X-ray-induced DNA strand breaks in peripheral blood mononuclear cells (PBMCs) isolated from young and elderly individuals. Interestingly, GH3 showed the strongest radioprotective effects in PBMCs from young subjects, while procaine reduced the endogenous amount of DNA strand breaks more pronounced in aged individuals. Both procaine and GH3 inhibited lipid peroxidation, but procaine was more effective in inhibiting mitochondria free radicals’ generation, while GH3 showed a higher antioxidant action on macrophage-induced low-density lipoprotein oxidation. Our findings provide new insights into the mechanisms underlying the distinct effects of procaine and GH3 on DNA damage.

scholarly journals Isolation and cloning of the raccoon (Procyon lotor) papillomavirus type 1 by using degenerate papillomavirus-specific primers

2005 ◽  
Vol 86 (7) ◽  
pp. 2029-2033 ◽  
Author(s):  
Annabel Rector ◽  
Koenraad Van Doorslaer ◽  
Mads Bertelsen ◽  
Ian K. Barker ◽  
Rolf-Arne Olberg ◽  
...  
Keyword(s):  
Genomic Sequence ◽  
Procyon Lotor ◽  
Cutaneous Lesion ◽  
Open Reading Frames ◽  
Coding Region ◽  
Specific Primers ◽  
Entire Genome ◽  
Early Proteins ◽  
Late Protein

Partial sequences of a novel papillomavirus were amplified from a cutaneous lesion biopsy of a raccoon (Procyon lotor), by using PCR with degenerate papillomavirus-specific primers. The Procyon lotor papillomavirus type 1 (PlPV-1) DNA was amplified with long template PCR in two overlapping fragments, together encompassing the entire genome, and the complete PlPV-1 genomic sequence was determined. The PlPV-1 genome consists of 8170 bp, and contains the typical papillomaviral open reading frames, encoding five early proteins and two late capsid proteins. Besides the classical non-coding region (NCR1) between the end of L1 and the start of E6, PlPV-1 contains an additional non-coding region (NCR2) of 1065 bp between the early and late protein region, which has previously also been described for the canine oral papillomavirus (COPV) and the Felis domesticus papillomavirus (FdPV-1). Phylogenetic analysis places PlPV-1 together with COPV and FdPV-1 in a monophyletic branch which encompasses the Lambda papillomavirus genus.

scholarly journals Lessons in Fundamental Mechanisms and Diverse Adaptations from the 2015 Bacterial Locomotion and Signal Transduction Meeting

2015 ◽  
Vol 197 (19) ◽  
pp. 3028-3040 ◽  
Author(s):  
Birgit M. Prüβ ◽  
Jun Liu ◽  
Penelope I. Higgs ◽  
Lynmarie K. Thompson
Keyword(s):  
Signal Transduction ◽  
Biofilm Formation ◽  
Cell Biology ◽  
Bacterial Species ◽  
Interacting Proteins ◽  
Mathematical Methods ◽  
Detailed Understanding ◽  
Rapid Changes ◽  
Functional Mechanisms ◽  
Insight Into

In response to rapid changes in their environment, bacteria control a number of processes, including motility, cell division, biofilm formation, and virulence. Research presented in January 2015 at the biennial Bacterial Locomotion and Signal Transduction (BLAST) meeting in Tucson, AZ, illustrates the elegant complexity of the nanoarrays, nanomachines, and networks of interacting proteins that mediate such processes. Studies employing an array of biophysical, genetic, cell biology, and mathematical methods are providing an increasingly detailed understanding of the mechanisms of these systems within well-studied bacteria. Furthermore, comparisons of these processes in diverse bacterial species are providing insight into novel regulatory and functional mechanisms. This review summarizes research presented at the BLAST meeting on these fundamental mechanisms and diverse adaptations, including findings of importance for applications involving bacteria of medical or agricultural relevance.

Sign in / Sign up

Export Citation Format

Share Document