Completed Genomic Sequence of Bacillus thuringiensis HER1410 Reveals a Cry-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage

Abstract Background The spread of carbapenem-resistant Enterobacteriaceae is an important challenge and an increasing healthcare problem. OXA-48 is a class D carbapenemase that is usually localized on a conjugative plasmid belonging to the IncL incompatibility group. Methods In this study, we used a combination of short- and long-read WGS approaches and molecular typing techniques to characterize the genetic environment of the smallest reported 27 029 bp IncFII plasmid carrying blaOXA-48 (pLAU-OXA48). Results The plasmid recovered from a clinical Escherichia coli isolate was positive for blaOXA-48, which was located within the Tn6237 composite transposon. Primers targeting junctions between the IncF fragment and Tn6237 for the rapid identification of pLAU-OXA48-like plasmids were designed. Conclusions To our knowledge, this is the first report showing the complete sequence of an IncFII plasmid carrying blaOXA-48 within Tn6237 using hybrid assembly of long- and short-read sequencing.

Download Full-text

Characterization of the genomic sequence data around common cutworm resistance genes in soybean (Glycine max) using short- and long-read sequencing methods

Data in Brief ◽

10.1016/j.dib.2020.106577 ◽

2021 ◽

Vol 34 ◽

pp. 106577

Author(s):

Eri Ogiso-Tanaka ◽

Nobuhiko Oki ◽

Tsuyoshi Tanaka ◽

Takehiko Shimizu ◽

Masao Ishimoto ◽

...

Keyword(s):

Glycine Max ◽

Resistance Genes ◽

Genomic Sequence ◽

Sequence Data ◽

Common Cutworm ◽

Long Read

Download Full-text

The fully resolved genome of Bacillus thuringiensis HER1410 reveals a cry-containing chromosome, two megaplasmids & an integrative plasmidial prophage

10.1101/2020.05.05.080028 ◽

2020 ◽

Author(s):

Ana Lechuga ◽

Cédric Lood ◽

Margarita Salas ◽

V. Vera van Noort ◽

Rob Lavigne ◽

...

Keyword(s):

Bacillus Thuringiensis ◽

Conjugative Plasmid ◽

Extrachromosomal Elements ◽

As Species ◽

Long Reads ◽

Genomic Characterization ◽

Group Members ◽

Genomic Similarity

AbstractBacillus thuringiensis is the most used biopesticide in agriculture. Its entomopathogenic capacity stems from the possession of plasmid-borne insecticidal crystal genes (cry), traditionally used as discriminant taxonomic feature for that species. As such, crystal and plasmid identification are key to the characterization of this species. To date, about 600 B. thuringiensis genomes have been reported, but less than 5% have been resolved, while the other draft genomes are incomplete, precluding plasmid delineation. Here we present the complete genome of Bacillus thuringiensis HER1410, a strain closely related to B. thuringiensis entomocidus and a known host for a variety of Bacillus phages. The combination of short and long-reads techniques allowed fully resolving the genome and delineation of three plasmids. This enabled the accurate detection of an unusual location of a unique cry gene, cry1Ba4, located in a genomic island near the chromosome replication origin. Two megaplasmids, pLUSID1 and pLUSID2 could be delineated: pLUSID1 (368kb), a likely conjugative plasmid involved in virulence, and pLUSID2 potentially related to the sporulation process. A smaller plasmidial prophage pLUSID3, with a dual lifestyle whose integration within the chromosome, causes the disruption of a flagellar key component. Finally, phylogenetic analysis located this strain within a clade comprising members from the B. thuringiensis serovar thuringiensis and other serovars and with B.cereus s. s. This highlights the intermingled taxonomy of B. cereus sensu lato group, where genomics alone does not support the present taxonomy between B. cereus s. s. and B. thuringiensis as species designation currently relies solely on the presence of entomocidal genes.ImportanceBacillus cereus group species have been extensively studied due to their economical and clinical relevance. This importance originally set the basis for B. cereus group members classification which are commonly based on phenotypical criteria. Sequencing era has shed light about genomic characterization of these species, showing their chromosomal genomic similarity and highlighting the role of mobile genetic elements, especially megaplasmids, in the classification and characterization of this group. However, only the 5% of the sequenced B. thuringiensis genomes have been fully resolved. Thus, here we addressed efficiently the study B. thuringiensis HER1410 genomic features by the use of a combination of short and long-reads sequencing. This methodology resulted in the high-quality assembly, which led to the identification of an uncommon location of a cry gene close to the chromosomal origin, as well as three fully resolved extrachromosomal elements, two megaplasmids and an integrative plasmidial prophage.

Download Full-text

Molecular Characterization of Carbapenemase-Producing Pseudomonas aeruginosa of Czech Origin and Evidence for Clonal Spread of Extensively Resistant Sequence Type 357 Expressing IMP-7 Metallo-β-Lactamase

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01811-17 ◽

2017 ◽

Vol 61 (12) ◽

Cited By ~ 15

Author(s):

Costas C. Papagiannitsis ◽

Matej Medvecky ◽

Katerina Chudejova ◽

Anna Skalova ◽

Veronika Rotova ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Molecular Characterization ◽

Genomic Island ◽

Sequence Type ◽

The Other ◽

Sequencing Data ◽

Molecular Surveillance ◽

Content Type ◽

Clonal Spread

ABSTRACT The objective of this study was to perform molecular surveillance for assessing the spread of carbapenemase-producing Pseudomonas aeruginosa in Czech hospitals. One hundred thirty-six carbapenemase-producing isolates were recovered from 22 hospitals located throughout the country. Sequence type 357 (ST357) dominated (n = 120) among carbapenemase producers. One hundred seventeen isolates produced IMP-type (IMP-7 [n = 116] and IMP-1 [n = 1]) metallo-β-lactamases (MβLs), 15 produced the VIM-2 MβL, and the remaining isolates expressed the GES-5 enzyme. The bla IMP-like genes were located in three main integron types, with In-p110-like being the most prevalent (n = 115). The two other IMP-encoding integrons (In1392 and In1393) have not been described previously. bla VIM-2-carrying integrons included In59-like, In56, and a novel element (In1391). bla GES-5 was carried by In717. Sequencing data showed that In-p110-like was associated with a Tn4380-like transposon inserted in genomic island LESGI-3 in the P. aeruginosa chromosome. The other integrons were also integrated into the P. aeruginosa chromosome. These findings indicated the clonal spread of ST357 P. aeruginosa, carrying the IMP-7-encoding integron In-p110, in Czech hospitals. Additionally, the sporadic emergence of P. aeruginosa producing different carbapenemase types, associated with divergent or novel integrons, punctuated the ongoing evolution of these bacteria.

Download Full-text

A very rapid in situ Kikuchi technique to determine relative crystal misorientation

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100106211 ◽

1988 ◽

Vol 46 ◽

pp. 830-831

Author(s):

J. I. Bennetch

Keyword(s):

Electron Beam ◽

Analytical Techniques ◽

Superplastic Forming ◽

The Other ◽

Kikuchi Pattern ◽

Kikuchi Line ◽

Line Analysis

In a recent study of the superplastic forming (SPF) behavior of certain Al-Li-X alloys, the relative misorientation between adjacent (sub)grains proved to be an important parameter. It is well established that the most accurate way to determine misorientation across boundaries is by Kikuchi line analysis. However, the SPF study required the characterization of a large number of (sub)grains in each sample to be statistically meaningful, a very time-consuming task even for comparatively rapid Kikuchi analytical techniques.In order to circumvent this problem, an alternate, even more rapid in-situ Kikuchi technique was devised, eliminating the need for the developing of negatives and any subsequent measurements on photographic plates. All that is required is a double tilt low backlash goniometer capable of tilting ± 45° in one axis and ± 30° in the other axis. The procedure is as follows. While viewing the microscope screen, one merely tilts the specimen until a standard recognizable reference Kikuchi pattern is centered, making sure, at the same time, that the focused electron beam remains on the (sub)grain in question.

Download Full-text

Rapid Isolation of High Molecular Weight Urokinase from Native Human Urine

Thrombosis and Haemostasis ◽

10.1055/s-0038-1657167 ◽

1982 ◽

Vol 47 (03) ◽

pp. 197-202 ◽

Cited By ~ 23

Author(s):

Kurt Huber ◽

Johannes Kirchheimer ◽

Bernd R Binder

Keyword(s):

Molecular Weight ◽

High Molecular Weight ◽

Human Urine ◽

Gel Filtration ◽

Chain Structure ◽

The Other ◽

Single Chain ◽

Apparent Homogeneity ◽

Sequential Adsorption

SummaryUrokinase (UK) could be purified to apparent homogeneity starting from crude urine by sequential adsorption and elution of the enzyme to gelatine-Sepharose and agmatine-Sepharose followed by gel filtration on Sephadex G-150. The purified product exhibited characteristics of the high molecular weight urokinase (HMW-UK) but did contain two distinct entities, one of which exhibited a two chain structure as reported for the HMW-UK while the other one exhibited an apparent single chain structure. The purification described is rapid and simple and results in an enzyme with probably no major alterations. Yields are high enough to obtain purified enzymes for characterization of UK from individual donors.

Download Full-text

Analysis of the Mechanism by Which Glucose Inhibits Maltose Induction of MAL Gene Expression in Saccharomyces

Genetics ◽

10.1093/genetics/154.1.121 ◽

2000 ◽

Vol 154 (1) ◽

pp. 121-132

Author(s):

Zhen Hu ◽

Yingzi Yue ◽

Hua Jiang ◽

Bin Zhang ◽

Peter W Sherwood ◽

...

Keyword(s):

Gene Expression ◽

Glucose Repression ◽

Protein A ◽

The Other ◽

Maltose Permease ◽

Inducer Exclusion ◽

Glucose Inhibition ◽

Independent Mechanism ◽

Mal Genes

Abstract Expression of the MAL genes required for maltose fermentation in Saccharomyces cerevisiae is induced by maltose and repressed by glucose. Maltose-inducible regulation requires maltose permease and the MAL-activator protein, a DNA-binding transcription factor encoded by MAL63 and its homologues at the other MAL loci. Previously, we showed that the Mig1 repressor mediates glucose repression of MAL gene expression. Glucose also blocks MAL-activator-mediated maltose induction through a Mig1p-independent mechanism that we refer to as glucose inhibition. Here we report the characterization of this process. Our results indicate that glucose inhibition is also Mig2p independent. Moreover, we show that neither overexpression of the MAL-activator nor elimination of inducer exclusion is sufficient to relieve glucose inhibition, suggesting that glucose acts to inhibit induction by affecting maltose sensing and/or signaling. The glucose inhibition pathway requires HXK2, REG1, and GSF1 and appears to overlap upstream with the glucose repression pathway. The likely target of glucose inhibition is Snf1 protein kinase. Evidence is presented indicating that, in addition to its role in the inactivation of Mig1p, Snf1p is required post-transcriptionally for the synthesis of maltose permease whose function is essential for maltose induction.

Download Full-text

On a New Geometric Constant Related to the Euler-Lagrange Type Identity in Banach Spaces

Mathematics ◽

10.3390/math9020116 ◽

2021 ◽

Vol 9 (2) ◽

pp. 116

Author(s):

Qi Liu ◽

Yongjin Li

Keyword(s):

Banach Spaces ◽

Product Space ◽

Sufficient Conditions ◽

Normal Structure ◽

The Other ◽

Inner Product ◽

Equivalent Characterization ◽

Geometric Constant ◽

Geometric Constants

In this paper, we will introduce a new geometric constant LYJ(λ,μ,X) based on an equivalent characterization of inner product space, which was proposed by Moslehian and Rassias. We first discuss some equivalent forms of the proposed constant. Next, a characterization of uniformly non-square is given. Moreover, some sufficient conditions which imply weak normal structure are presented. Finally, we obtain some relationship between the other well-known geometric constants and LYJ(λ,μ,X). Also, this new coefficient is computed for X being concrete space.

Download Full-text

The development of body and organ shape

BMC Zoology ◽

10.1186/s40850-020-00063-5 ◽

2020 ◽

Vol 5 (1) ◽

Author(s):

Ansa E. Cobham ◽

Christen K. Mirth

Keyword(s):

Relative Position ◽

Body Shape ◽

Single Cells ◽

The Other ◽

Geometric Features ◽

Main Text ◽

Size Characterization ◽

Organ Shape ◽

The Many

Abstract Background Organisms show an incredibly diverse array of body and organ shapes that are both unique to their taxon and important for adapting to their environment. Achieving these specific shapes involves coordinating the many processes that transform single cells into complex organs, and regulating their growth so that they can function within a fully-formed body. Main text Conceptually, body and organ shape can be separated in two categories, although in practice these categories need not be mutually exclusive. Body shape results from the extent to which organs, or parts of organs, grow relative to each other. The patterns of relative organ size are characterized using allometry. Organ shape, on the other hand, is defined as the geometric features of an organ’s component parts excluding its size. Characterization of organ shape is frequently described by the relative position of homologous features, known as landmarks, distributed throughout the organ. These descriptions fall into the domain of geometric morphometrics. Conclusion In this review, we discuss the methods of characterizing body and organ shape, the developmental programs thought to underlie each, highlight when and how the mechanisms regulating body and organ shape might overlap, and provide our perspective on future avenues of research.

Download Full-text

AsaGEI2d: a new variant of a genomic island identified in a group of Aeromonas salmonicida subsp. salmonicida isolated from France, which bears the pAsa7 plasmid

FEMS Microbiology Letters ◽

10.1093/femsle/fnab021 ◽

2021 ◽

Author(s):

Antony T Vincent ◽

Laurent Intertaglia ◽

Victor Loyer ◽

Valérie E Paquet ◽

Émilie Adouane ◽

...

Keyword(s):

Genomic Island ◽

Insertion Site ◽

Aeromonas Salmonicida ◽

Genomic Islands ◽

The Other ◽

Fish Pathogen ◽

Integrase Gene ◽

New Variant ◽

Cat Gene ◽

Unique Genes

Abstract Genomic islands (Aeromonas salmonicida genomic islands, AsaGEIs) are found worldwide in many isolates of Aeromonas salmonicida subsp. salmonicida, a fish pathogen. To date, five variants of AsaGEI (1a, 1b, 2a, 2b and 2c) have been described. Here, we investigate a sixth AsaGEI, which was identified in France between 2016 and 2019 in 20 A. salmonicida subsp. salmonicida isolates recovered from sick salmon all at the same location. This new AsaGEI shares the same insertion site in the chromosome as the other AsaGEI2s as they all have a homologous integrase gene. This new AsaGEI was thus named AsaGEI2d, and has 5 unique genes compared to the other AsaGEIs. The isolates carrying AsaGEI2d also bear the plasmid pAsa7, which was initially found in an isolate from Switzerland. This plasmid provides resistance to chloramphenicol thanks to a cat gene. This study reveals more about the diversity of the AsaGEIs.

Download Full-text