scholarly journals Precise Excision and Self-Integration of a Composite Transposon as a Model for Spontaneous Large-Scale Chromosome Inversion/Deletion of the Staphylococcus haemolyticus Clinical Strain JCSC1435

2007 ◽  
Vol 189 (7) ◽  
pp. 2921-2925 ◽  
Author(s):  
Shinya Watanabe ◽  
Teruyo Ito ◽  
Yuh Morimoto ◽  
Fumihiko Takeuchi ◽  
Keiichi Hiramatsu
Keyword(s):  
Large Scale ◽  
Chromosome Rearrangements ◽  
Clinical Strain ◽  
Beta Lactam ◽  
Chromosome Inversion ◽  
Chromosomal Inversions ◽  
Precise Excision ◽  
Staphylococcus Haemolyticus ◽  
Drug Free ◽  
Chromosomal Loci

ABSTRACT Large-scale chromosomal inversions (455 to 535 kbp) or deletions (266 to 320 kbp) were found to accompany spontaneous loss of beta-lactam resistance during drug-free passage of the multiresistant Staphylococcus haemolyticus clinical strain JCSC1435. Identification and sequencing of the rearranged chromosomal loci revealed that ISSha1 of S. haemolyticus is responsible for the chromosome rearrangements.

scholarly journals Review of the Studies in the Use of Biofeedback Therapy in Rehabilitation and Physiatrics of Neurological Patients

Doctor Ru ◽  
2021 ◽  
Vol 20 (9) ◽  
pp. 43-47
Author(s):  
E.Yu. Mozheyko ◽  
◽  
O.V. Petryaeva ◽  
◽  
◽  
...  
Keyword(s):  
Large Scale ◽  
Small Sample Size ◽  
Small Sample ◽  
Healthy Population ◽  
Biofeedback Therapy ◽  
Level Of Evidence ◽  
Double Blind ◽  
Key Points ◽  
Neurological Patients ◽  
Drug Free

Objective of the Review: To collect information, analyse and evaluate previous studies in the use of biofeedback in neurological patients. Key Points. Despite the wide practical application and a lot of available publications, the level of evidence of this method is low because of a small sample size and the challenges with biofeedback mechanism description. A review of various types of biocontrol, its mechanisms and developments shows that drug-free therapy using only patient’s resources (organic, psychological, emotional and volitional) can activate the mechanisms of neuroplasticity, which are poorly studied. Still, it does not prevent from using biocontrol for the therapy of patients and/or prevention of various diseases in healthy population. Conclusion. Biofeedback therapy has proven to be a safe, relatively efficient and easy-to-use method. However, organisation of a large-scale double blind randomized trial is one of the predominant directions in the future. Keywords: biofeedback, biocontrol, neurofeedback, biofeedback therapy.

scholarly journals A TEM-derived extended-spectrum beta-lactamase in Pseudomonas aeruginosa.

1996 ◽  
Vol 40 (11) ◽  
pp. 2488-2493 ◽  
Author(s):  
P Mugnier ◽  
P Dubrous ◽  
I Casin ◽  
G Arlet ◽  
E Collatz
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Clinical Strain ◽  
Beta Lactamase ◽  
Beta Lactam ◽  
Aminoglycoside Resistance ◽  
Double Mutation ◽  
Extended Spectrum Beta Lactamase ◽  
Beta Lactam Antibiotics ◽  
Extended Spectrum ◽  
High Level

A clinical strain of Pseudomonas aeruginosa, PAe1100, was found to be resistant to all antipseudomonal beta-lactam antibiotics and to aminoglycosides, including gentamicin, amikacin, and isepamicin. PAe1100 produced two beta-lactamases, TEM-2 (pI 5.6) and a novel, TEM-derived extended-spectrum beta-lactamase called TEM-42 (pI 5.8), susceptible to inhibition by clavulanate, sulbactam, and tazobactam. Both enzymes, as well as the aminoglycoside resistance which resulted from AAC(3)-IIa and AAC(6')-I production, were encoded by an 18-kb nonconjugative plasmid, pLRM1, that could be transferred to Escherichia coli by transformation. The gene coding for TEM-42 had four mutations that led to as many amino acid substitutions with respect to TEM-2: Val for Ala at position 42 (Ala42), Ser for Gly238, Lys for Glu240, and Met for Thr265 (Ambler numbering). The double mutation Ser for Gly238 and Lys for Glu240, which has so far only been described in SHV-type but not TEM-type enzymes, conferred concomitant high-level resistance to cefotaxime and ceftazidime. The novel, TEM-derived extended-spectrum beta-lactamase appears to be the first of its class to be described in P. aeruginosa.

scholarly journals Genomic Outcomes of Haploid Induction Crosses in Potato (Solanum tuberosum L.)

Genetics ◽  
2019 ◽  
Vol 214 (2) ◽  
pp. 369-380 ◽  
Author(s):  
Kirk R. Amundson ◽  
Benny Ordoñez ◽  
Monica Santayana ◽  
Ek Han Tan ◽  
Isabelle M. Henry ◽  
...  
Keyword(s):  
Solanum Tuberosum ◽  
Genetic Markers ◽  
Large Scale ◽  
Solanum Tuberosum L ◽  
Small Scale ◽  
Haploid Induction ◽  
Variation Patterns ◽  
Number Variation ◽  
Additional Chromosome ◽  
Chromosomal Loci

The challenges of breeding autotetraploid potato (Solanum tuberosum) have motivated the development of alternative breeding strategies. A common approach is to obtain uniparental dihaploids from a tetraploid of interest through pollination with S. tuberosum Andigenum Group (formerly S. phureja) cultivars. The mechanism underlying haploid formation of these crosses is unclear, and questions regarding the frequency of paternal DNA transmission remain. Previous reports have described aneuploid and euploid progeny that, in some cases, displayed genetic markers from the haploid inducer (HI). Here, we surveyed a population of 167 presumed dihaploids for large-scale structural variation that would underlie chromosomal addition from the HI, and for small-scale introgression of genetic markers. In 19 progeny, we detected 10 of the 12 possible trisomies and, in all cases, demonstrated the noninducer parent origin of the additional chromosome. Deep sequencing indicated that occasional, short-tract signals appearing to be of HI origin were better explained as technical artifacts. Leveraging recurring copy number variation patterns, we documented subchromosomal dosage variation indicating segregation of polymorphic maternal haplotypes. Collectively, 52% of the assayed chromosomal loci were classified as dosage variable. Our findings help elucidate the genomic consequences of potato haploid induction and suggest that most potato dihaploids will be free of residual pollinator DNA.

Organization of human class I homeobox genes

Genome ◽  
1989 ◽  
Vol 31 (2) ◽  
pp. 745-756 ◽  
Author(s):  
Edoardo Boncinelli ◽  
Dario Acampora ◽  
Maria Pannese ◽  
Maurizio D'Esposito ◽  
Renato Somma ◽  
...  
Keyword(s):  
Large Scale ◽  
Genomic Organization ◽  
Gene Evolution ◽  
Homeobox Gene ◽  
Peptide Sequence ◽  
Class I ◽  
Human Class ◽  
Single Complex ◽  
Complex Locus ◽  
Chromosomal Loci

We report the genomic organization of 20 human class I homeoboxes and the predicted primary sequence of the encoded homeodomains. These homeoboxes are clustered in four complex HOX loci on chromosomes 2, 7, 12, and 17. The homeoboxes of one HOX locus can be aligned to the homeoboxes of the other HOX loci so that corresponding homeodomains in all loci can share the maximal peptide sequence identity. This correspondence of individual homeoboxes in different chromosomal loci suggests the hypothesis of large-scale duplications of a single complex locus. The existence of an ancestral complex locus might have predated the divergence of vertebrates and invertebrates.Key words: development, homeobox, gene evolution.

scholarly journals Gene regulatory effects of a large chromosomal inversion in highland maize

2019 ◽  
Author(s):  
Taylor Crow ◽  
James Ta ◽  
Saghi Nojoomi ◽  
M. Rocío Aguilar-Rangel ◽  
Jorge Vladimir Torres Rodríguez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Zea Mays ◽  
Large Scale ◽  
Chromosomal Inversion ◽  
Experimental Conditions ◽  
Chromosomal Inversions ◽  
Functional Variants ◽  
Original Manuscript ◽  
Locally Adaptive ◽  
Highland Maize

AbstractChromosomal inversions play an important role in local adaptation. Inversions can capture multiple locally adaptive functional variants in a linked block by repressing recombination. However, this recombination suppression makes it difficult to identify the genetic mechanisms that underlie an inversion’s role in adaption. In this study, we explore how large-scale transcriptomic data can be used to dissect the functional importance of a 13 Mb inversion locus (Inv4m) found almost exclusively in highland populations of maize (Zea mays ssp. mays). Inv4m introgressed into highland maize from the wild relative Zea mays ssp. mexicana, also present in the highlands of Mexico, and is thought to be important for the adaptation of these populations to cultivation in highland environments. First, using a large publicly available association mapping panel, we confirmed that Inv4m is associated with locally adaptive agronomic phenotypes, but only in highland fields. Second, we created two families segregating for standard and inverted haplotypess of Inv4m in a isogenic B73 background, and measured gene expression variation association with Inv4m across 9 tissues in two experimental conditions. With these data, we quantified both the global transcriptomic effects of the highland Inv4m haplotype, and the local cis-regulatory variation present within the locus. We found diverse physiological effects of Inv4m, and speculate that the genetic basis of its effects on adaptive traits is distributed across many separate functional variants.Author SummaryChromosomal inversions are an important type of genomic structural variant. However, mapping causal alleles within their boundaries is difficult because inversions suppress recombination between homologous chromosomes. This means that inversions, regardless of their size, are inherited as a unit. We leveraged the high-dimensional phenotype of gene expression as a tool to study the genetics of a large chromosomal inversion found in highland maize populations in Mexico - Inv4m. We grew plants carrying multiple versions of Inv4m in a common genetic background, and quantified the transcriptional reprogramming induced by alternative alleles at the locus. Inv4m has been shown in previous studies to have a large effect on flowering, but we show that the functional variation within Inv4m affects many developmental and physiological processes.Author ContributionsT. Crow, R. Rellan-Alvarez, R. Sawers and D. Runcie conceived and designed the experiment. M. Aguilar-Rangel, J. Rodrǵuez, R. Rellan-Alvarez and R. Sawers generated the segregating families. T. Crow, J. Ta, S. Nojoomi, M. Aguilar-Rangel, J. Rodrǵuez D. Gates, D. Runcie performed the experiment. T. Crow, D. Gates, D. Runcie analyzed the data. T. Crow, D. Runcie wrote the original manuscript, and R. Rellan-Alvarez and R. Sawers provided review and editing.

scholarly journals Nano Drug Deliverer for Ampicillin, Clavulanic Acid, Imipenem, Penicillin G and Ticarcillin

2016 ◽  
Vol 13 (10) ◽  
pp. 7144-7155
Author(s):  
Maryam Derakhshandeh ◽  
Majid Monajjemi
Keyword(s):  
Drug Delivery ◽  
Clavulanic Acid ◽  
Large Scale ◽  
Penicillin G ◽  
Effect Of Temperature ◽  
Phenoxyacetic Acid ◽  
Scale Production ◽  
Electronic Effects ◽  
Beta Lactam ◽  
Gram Positive

Ampicillin, Clavulanic acid, Imipenem, Penicillin G and Ticarcillin properties for the drug delivery with binding to SWCNNTs and SWBNNTs have been studied. Penicillin and its alteration Penicillin G or phenoxyacetic acid for Penicillin V is used for large scale production. Penicillin and other cell wall inhibitors are primarily specific against Gram positive bacteria because of higher percentage of peptidoglycan in the cell walls of these organisms. Ampicillin belonging to the penicillin group of beta lactam antibiotics, ampicillin is able to penetrate Gram positive and some Gram-negative bacteria. Imipenem (Primaxin) is an intravenous β-lactam antibiotic discovered by Merck scientists Burton Christensen, William Leanza, and Kenneth Wildonger in 1980. It was the first member of the carbapenem class of antibiotics. Based on our previous works we have modeled and simulated a drug delivery system of those antibiotics. The investigation of those antibiotics in binding with single-walled carbon nanotube (SWCNT) and SWBNNTs have been studied by theoretical methods. It has been established the best structural and functional of those antibiotics. A number of computational chemistry studies carried out to understand the conformational preferences that may be attributed to stereo electronic effects. These results show the minimized structure of mentioned antibiotics with SWCNTs and SWBNNTs, calculated potential energy for important dihedral angles, and the effect of temperature on geometry of optimized structure. NMR by GIAO approximation, have been applied for determination of the situation in antibiotics-SWCNT and shifting. This model provides an atomistic analysis of the antibiotics-SWCNT strategy and its implications for further investigations of drugs.

scholarly journals A new (old) approach to genotype-based phylogenomic inference within species, with an example from the saguaro cactus (Carnegiea gigantea)

2020 ◽  
Author(s):  
Michael J. Sanderson ◽  
Alberto Búrquez ◽  
Dario Copetti ◽  
Michelle M. McMahon ◽  
Yichao Zeng ◽  
...  
Keyword(s):  
Large Scale ◽  
Sequence Data ◽  
Rooted Tree ◽  
Diploid Species ◽  
Morphological Characters ◽  
Data Sets ◽  
Genotype Data ◽  
Species Trees ◽  
Chromosome Inversion ◽  
Diploid Genotype

AbstractGenome sequence data are routinely being used to infer phylogenetic history within and between closely related diploid species, but few tree inference methods are specifically tailored to diploid genotype data. Here we re-examine the method of “polymorphism parsimony” (Inger 1967; Farris 1978; Felsenstein 1979), originally introduced to study morphological characters and chromosome inversion polymorphisms, to evaluate its utility for unphased diploid genotype data in large scale phylogenomic data sets. We show that it is equivalent to inferring species trees by minimizing deep coalescences—assuming an infinite sites model. Two potential advantages of this approach are scalability and estimation of a rooted tree. As with some other single nucleotide polymorphism (SNP) based methods, it requires thinning of data sets to statistically independent sites, and we describe a genotype-based test for phylogenetic independence. To evaluate this approach in genome scale data, we construct intraspecific phylogenies for 10 populations of the saguaro cactus using 200 Gbp of resequencing data, and then use these methods to test whether the population with highest genetic diversity corresponds to the root of the genotype trees. Results were highly congruent with the (unrooted) trees obtained using SVDquartets, a scalable alternative method of phylogenomic inference.

scholarly journals Microscopic Chromosomal Structural and Dynamical Origin of Cell Differentiation and Reprogramming

2020 ◽  
Author(s):  
Xiakun Chu ◽  
Jin Wang
Keyword(s):  
Cell Differentiation ◽  
Large Scale ◽  
Chromosome Structure ◽  
Structural Characteristics ◽  
Three Dimensional ◽  
Embryonic Stem ◽  
Switching Model ◽  
Somatic Cell Reprogramming ◽  
Fundamental Process ◽  
Chromosomal Loci

AbstractAs an essential and fundamental process of life, cell development involves large-scale reorganization of the three-dimensional genome architecture, which forms the basis of gene regulation. Here, we develop a landscape-switching model to explore the microscopic chromosomal structural origin of the embryonic stem cell (ESC) differentiation and the somatic cell reprogramming. We show that chromosome structure exhibits significant compartment-switching in the unit of topologically associating domain. We find that the chromosome during differentiation undergoes monotonic compaction with spatial re-positioning of active and inactive chromosomal loci towards the chromosome surface and interior, respectively. In contrast, an over-expanded chromosome, which exhibits universal localization of loci at the chromosomal surface with erasing the structural characteristics formed in the somatic cells, is observed during reprogramming. We suggest an early distinct differentiation pathway from the ESC to the terminally differentiated cell, giving rise to early bifurcation on the Waddington landscape for the ESC differentiation. Our theoretical model including the non-equilibrium effects, draws a picture of the highly irreversible cell differentiation and reprogramming processes, in line with the experiments. The predictions from our model provide a physical understanding of cell differentiation and reprogramming from the chromosomal structural and dynamical perspective and can be tested by future experiments.

scholarly journals An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Victoria Furió ◽  
Miguel Moreno-Molina ◽  
Álvaro Chiner-Oms ◽  
Luis M. Villamayor ◽  
Manuela Torres-Puente ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Large Scale ◽  
Resistance Mechanism ◽  
Clinical Strain ◽  
Resistance Mutations ◽  
Isoniazid Resistance ◽  
Resistance Determinants ◽  
Main Target ◽  
New Antibiotics ◽  
Candidate Regions

AbstractEfforts to eradicate tuberculosis are hampered by the rise and spread of antibiotic resistance. Several large-scale projects have aimed to specifically link clinical mutations to resistance phenotypes, but they were limited in both their explanatory and predictive powers. Here, we combine functional genomics and phylogenetic associations using clinical strain genomes to decipher the architecture of isoniazid resistance and search for new resistance determinants. This approach has allowed us to confirm the main target route of the antibiotic, determine the clinical relevance of redox metabolism as an isoniazid resistance mechanism and identify novel candidate genes harboring resistance mutations in strains with previously unexplained isoniazid resistance. This approach can be useful for characterizing how the tuberculosis bacilli acquire resistance to new antibiotics and how to forestall them.

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