Distribution and Abundance of Insertion Sequences Among Natural Isolates of Escherichia coli

ABSTRACT A reference collection of 71 natural isolates of Escherichia coli (the ECOR collection) has been studied with respect to the distribution and abundance of transposable insertion sequences using DNA hybridization. The data include 1173 occurrences of six unrelated insertion sequences (IS 1, IS2, IS3, IS4, IS5 and IS 30). The number of insertion elements per strain, and the sizes of DNA restriction fragments containing them, is highly variable and can be used to discriminate even among closely related strains. The occurrence and abundance of pairs of unrelated insertion sequences are apparently statistically independent, but significant correlations result from stratifications in the reference collection. However, there is a highly significant positive association among the insertion sequences considered in the aggregate. Nine branching process models, which differ in assumptions regarding the regulation of transposition and the effect of copy number on fitness, have been evaluated with regard to their fit of the observed distributions. No single model fits all copy number distributions. The best models incorporate no regulation of transposition and a moderate to strong decrease in fitness with increasing copy number for IS1 and IS5, strong regulation of transposition and a negligible to weak decrease in fitness with increasing copy number for IS3, and less than strong regulation of transposition for IS2, IS 4 and IS30.

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JOINT DISTRIBUTION OF INSERTION ELEMENTS IS4 AND IS5 IN NATURAL ISOLATES OF ESCHERICHIA COLI

Genetics ◽

10.1093/genetics/111.2.219 ◽

1985 ◽

Vol 111 (2) ◽

pp. 219-231

Author(s):

Daniel E Dykhuizen ◽

Stanley A Sawyer ◽

Louis Green ◽

Raymond D Miller ◽

Daniel L Hartl

Keyword(s):

Escherichia Coli ◽

Dna Sequences ◽

Significant Negative Correlation ◽

Single Copy ◽

Common Mechanism ◽

Reference Collection ◽

Insertion Elements ◽

Natural Isolates ◽

Dna Insertion ◽

Flanking Sequences

ABSTRACT A reference collection of natural isolates of Escherichia coli has been studied in order to determine the distribution, abundance and joint occurence of DNA insertion elements IS4 and IS5. Among these isolates, 36% were found to contain IS4 and 30% were found to contain IS5. Among strains containing IS4 the mean number of copies per strain was 4.4 ± 0.8; the comparable figure for IS5 was 3.7 ± 1.0. Although the presence of the elements among the isolates was independent, among those isolates containing both IS4 and IS5, there was a significant negative correlation in the number of copies of the elements.— The reference collection was also studied for the presence of the DNA sequences flanking the single copy of IS4 in the chromosome of E. coli K12. Homologous sequences were found in only 26% of the isolates. The sequences flanking the IS4 invariably occur together, and their presence is significantly correlated with the presence of IS4. In eight of the strains that carry these flanking sequences, an IS4 is located between them, and the sequences are present at the homologous position as in the K12 strain. We suggest that IS4 and its flanking sequences share a common mechanism of dissemination, such as plasmids, and we present evidence that they are included in a much larger transposable element.

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Why do unrelated insertion sequences occur together in the genome of Escherichia coli?

Genetics ◽

10.1093/genetics/118.3.537 ◽

1988 ◽

Vol 118 (3) ◽

pp. 537-541

Author(s):

D L Hartl ◽

S A Sawyer

Keyword(s):

Escherichia Coli ◽

Horizontal Transfer ◽

Process Model ◽

Insertion Sequence ◽

Branching Process ◽

Insertion Sequences ◽

Reference Collection ◽

Natural Isolates ◽

Positive Correlations

Abstract Natural isolates of Escherichia coli are polymorphic for the presence or absence of insertion sequences. Among the ECOR reference collection of 71 natural isolates studied for the number of copies of the insertion sequences IS1, IS2, IS3, IS4, IS5 and IS30, the number of strains containing no copies of the insertion sequences were 11, 28, 23, 43, 46 and 36, respectively. Significant correlations occur in the ECOR strains in the presence or absence of unrelated insertion sequences in the chromosome and plasmid complements. Strains containing any insertion sequence are more likely to contain additional, unrelated insertion sequences than would be expected by chance. We suggest that the positive correlations result from horizontal transfer mediated by plasmids. A branching-process model for the plasmid-mediated transmission of insertion sequences among hosts yields such a correlation, even in the absence of interactions affecting transposition or fitness. The predictions of the model are quantitatively in agreement with the observed correlations among insertion sequences.

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The evolution of DNA sequences in Escherichia coli

Philosophical Transactions of the Royal Society of London Series B Biological Sciences ◽

10.1098/rstb.1986.0001 ◽

1986 ◽

Vol 312 (1154) ◽

pp. 191-204 ◽

Cited By ~ 18

Keyword(s):

Escherichia Coli ◽

Transposable Elements ◽

Dna Sequences ◽

Insertion Sequence ◽

Horizontal Transmission ◽

Insertion Sequences ◽

Insertion Element ◽

Reference Collection ◽

Natural Isolates ◽

Chromosomal Copy

It is proposed that certain families of transposable elements originally evolved in plasmids and functioned in forming replicon fusions to aid in the horizontal transmission of non-conjugational plasmids. This hypothesis is supported by the finding that the transposable elements Tn 3 and γδ are found almost exclusively in plasmids, and also by the distribution of the unrelated insertion sequences IS4 and IS 5 among a reference collection of 67 natural isolates of Escherichia coli. Each insertion sequence was found to be present in only about one-third of the strains. Among the ten strains found to contain both insertion sequences, the number of copies of the elements was negatively correlated. With respect to IS 5 , approximately half of the strains containing a chromosomal copy of the insertion element also contained copies within the plasmid complement of the strain.

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IS103, a new insertion element in Escherichia coli: characterization and distribution in natural populations.

Genetics ◽

10.1093/genetics/121.3.423 ◽

1989 ◽

Vol 121 (3) ◽

pp. 423-431 ◽

Cited By ~ 2

Author(s):

B G Hall ◽

L L Parker ◽

P W Betts ◽

R F DuBose ◽

S A Sawyer ◽

...

Keyword(s):

Escherichia Coli ◽

Copy Number ◽

Insertion Sequence ◽

Natural Populations ◽

Single Copy ◽

Target Sequence ◽

Wild Type ◽

Insertion Element ◽

E Coli ◽

Natural Isolates

Abstract IS103 is a previously unknown insertion sequence found in Escherichia coli K12. We have sequenced IS103 and find that it is a 1441-bp element that consists of a 1395-bp core flanked by imperfect 23-bp inverted repeats. IS103 causes a 6-bp duplication of the target sequence into which it inserts. There is a single copy of IS103 present in wild-type E. coli K12 strain HfrC. In strain X342 and its descendents there are two additional copies, one of which is located within the bglF gene. IS103 is capable of excising from within bglF and restoring function of that gene. IS103 exhibits 44% sequence identity with IS3, suggesting that the two insertion sequences are probably derived from a common ancestor. We have examined the distribution of IS103 in the chromosomes and plasmids of the ECOR collection of natural isolates of E. coli. IS103 is found in 36 of the 71 strains examined, and it strongly tends to inhabit plasmids rather than chromosomes. Comparison of the observed distribution of IS103 with distributions predicted by nine different models for the regulation of transposition according to copy number and of the effects of copy number on fitness suggest that transposition of IS103 is strongly regulated and that it has only minor effects on fitness. The strong clustering of IS103 within one phylogenetic subgroup of the E. coli population despite its presence on plasmids suggests that plasmids tend to remain within closely related strains and that transfer to distantly related strains is inhibited.

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Perceived Overprotection and Its Association With Quality of Life in Dementia

GeroPsych ◽

10.1024/1662-9647/a000207 ◽

2019 ◽

Vol 32 (3) ◽

pp. 125-134

Author(s):

Mechthild Niemann-Mirmehdi ◽

Andreas Häusler ◽

Paul Gellert ◽

Johanna Nordheim

Keyword(s):

Quality Of Life ◽

Patient Autonomy ◽

Positive Association ◽

Well Being ◽

Negative Association ◽

Significant Positive Association ◽

Cross Sectional ◽

People With Dementia ◽

Mental Well Being

Abstract. To date, few studies have focused on perceived overprotection from the perspective of people with dementia (PwD). In the present examination, the association of perceived overprotection in PwD is examined as an autonomy-restricting factor and thus negative for their mental well-being. Cross-sectional data from the prospective DYADEM study of 82 patient/partner dyads (mean age = 74.26) were used to investigate the association between overprotection, perceived stress, depression, and quality of life (QoL). The analyses show that an overprotective contact style with PwD has a significant positive association with stress and depression, and has a negative association with QoL. The results emphasize the importance of avoiding an overprotective care style and supporting patient autonomy.

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The Nexus Between Urbanisation and Human Empowerment: Income Group Based Findings of Bidirectional Causality

Urban Development Issues ◽

10.2478/udi-2019-0019 ◽

2019 ◽

Vol 64 (1) ◽

pp. 5-15

Author(s):

Christos Kollias ◽

Panayiotis Tzeremes

Keyword(s):

Human Rights ◽

Positive Association ◽

Income Group ◽

Academic Discourse ◽

Access To Education ◽

Democratic Institutions ◽

Significant Positive Association ◽

Public Action ◽

Income Groups ◽

Democratic Rule

Abstract The economic and social drivers of democratisation and the emergence and establishment of democratic institutions are longstanding themes of academic discourse. Within this broad body of literature, it has been argued that the process of urbanisation is also conducive to the emergence and consolidation of democracy through a number of different channels. Cities offer better access to education and facilitate organised public action and the demand for more democratic rule and respect of human rights. The nexus between urbanisation and human rights is the theme that is taken up in the present paper. Using a sample of 123 countries for the period 1981–2011, the paper examines empirically the association between urbanisation and human empowerment using the Cingranelli-Richards Index. In broad terms, the findings reported herein do not point to a strong nexus across all income groups. Nevertheless, there is evidence suggesting the presence of such a statistically significant positive association in specific cases.

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Empirical analysis on corporate environmental performance and environmental disclosure in an emerging market context

International Journal of Emerging Markets ◽

10.1108/ijoem-04-2019-0255 ◽

2020 ◽

Vol 15 (6) ◽

pp. 1061-1082 ◽

Cited By ~ 1

Author(s):

Merve Acar ◽

Hüseyin Temiz

Keyword(s):

Environmental Performance ◽

Emerging Market ◽

Positive Association ◽

Corporate Environmental Performance ◽

Tobit Regression ◽

Environmental Reporting ◽

Environmental Disclosure ◽

Significant Positive Association ◽

Content Type ◽

Environmental Disclosures

PurposeThe purpose of this study is to investigate the association between environmental performance of firms and the level of voluntary environmental disclosure in emerging markets.Design/methodology/approachWe used tobit regression OLS and t-test methods to reveal the association between environmental performance and the level of voluntary environmental disclosure.FindingsWe find a significant positive association between the level of discretionary environmental disclosures and corporate environmental performance. The result is in line with the arguments of economics disclosure theory that argues environmentally good performers disclose more.Practical implicationsMany of the environmentally good firms in Turkey are also listed in the “BIST Sustainability Index,” and this situation can be the result of the relative power of external regulations. Accordingly, it can be suggested to increase the community and governmental pressures for environmental reporting but also gives importance to increase intrinsic motivations for companies to engage in disclosure practices.Originality/valueThis study shed light on relation between environmental performance and environmental disclosure in an emerging market context. Also, it is revisited that the relation between environmental performance and the level of environmental disclosure by testing two different predictions on the level of environmental disclosures.

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Can Anhedonia Be Considered a Suicide Risk Factor? A Review of the Literature

Medicina ◽

10.3390/medicina55080458 ◽

2019 ◽

Vol 55 (8) ◽

pp. 458 ◽

Cited By ~ 1

Author(s):

Bonanni ◽

Gualtieri ◽

Lester ◽

Falcone ◽

Nardella ◽

...

Keyword(s):

Suicidal Behavior ◽

Affective Disorders ◽

Suicide Attempts ◽

Positive Association ◽

Negative Association ◽

Schizophrenia Spectrum Disorders ◽

Post Traumatic Stress ◽

Significant Positive Association ◽

Search Terms ◽

Schizophrenia Spectrum

Background and Objectives: At present, data collected from the literature about suicide and anhedonia are controversial. Some studies have shown that low levels of anhedonia are associated with serious suicide attempts and death by suicide, while other studies have shown that high levels of anhedonia are associated with suicide. Materials and Methods: For this review, we searched PubMed, Medline, and ScienceDirect for clinical studies published from 1 January 1990 to 31 December 2018 with the following search terms used in the title or in the abstract: “anhedonia AND suicid*.” We obtained a total of 155 articles; 133 items were excluded using specific exclusion criteria, the remaining 22 articles included were divided into six groups based on the psychiatric diagnosis: mood disorders, schizophrenia spectrum disorders, post-traumatic stress disorder (PTSD), other diagnoses, attempted suicides, and others (healthy subjects). Results: The results of this review reveal inconsistencies. Some studies reported that high anhedonia scores were associated with suicidal behavior (regardless of the diagnosis), while other studies found that low anhedonia scores were associated with suicidal behavior, and a few studies reported no association. The most consistent association between anhedonia and suicidal behavior was found for affective disorders (7 of 7 studies reported a significant positive association) and for PTSD (3 of 3 studies reported a positive association). In the two studies of patients with schizophrenia, one found no association, and one found a negative association. For patients who attempted suicide (undiagnosed), one study found a positive association, one a positive association only for depressed attempters, and one a negative association. Conclusions: We found the most consistent positive association for patients with affective disorders and PTSD, indicating that the assessment of anhedonia may be useful in the evaluation of suicidal risk.

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Autophagic Markers in Chordomas: Immunohistochemical Analysis and Comparison with the Immune Microenvironment of Chordoma Tissues

Cancers ◽

10.3390/cancers13092169 ◽

2021 ◽

Vol 13 (9) ◽

pp. 2169

Author(s):

Georgia Karpathiou ◽

Maroa Dridi ◽

Lila Krebs-Drouot ◽

François Vassal ◽

Emmanuel Jouanneau ◽

...

Keyword(s):

Tumor Cell ◽

Immune Cells ◽

Immune Cell ◽

Positive Association ◽

Immunohistochemical Analysis ◽

Vascular Density ◽

Immune Microenvironment ◽

Significant Positive Association ◽

Sequestosome 1 ◽

Cell Expression

Chordomas are notably resistant to chemotherapy. One of the cytoprotective mechanisms implicated in chemoresistance is autophagy. There are indirect data that autophagy could be implicated in chordomas, but its presence has not been studied in chordoma tissues. Sixty-one (61) chordomas were immunohistochemically studied for autophagic markers and their expression was compared with the expression in notochords, clinicopathological data, as well as the tumor immune microenvironment. All chordomas strongly and diffusely expressed cytoplasmic p62 (sequestosome 1, SQSTM1/p62), whereas 16 (26.2%) tumors also showed nuclear p62 expression. LC3B (Microtubule-associated protein 1A/1B-light chain 3B) tumor cell expression was found in 44 (72.1%) tumors. Autophagy-related 16‑like 1 (ATG16L1) was also expressed by most tumors. All tumors expressed mannose-6-phosphate/insulin-like growth factor 2 receptor (M6PR/IGF2R). LC3B tumor cell expression was negatively associated with tumor size, while no other parameters, such as age, sex, localization, or survival, were associated with the immunohistochemical factors studied. LC3B immune cell expression showed a significant positive association with programmed death-ligand 1 (PD-L1)+ immune cells and with a higher vascular density. ATG16L1 expression was also positively associated with higher vascular density. Notochords (n = 5) showed different immunostaining with a very weak LC3B and M6PR expression, and no p62 expression. In contrast to normal notochords, autophagic factors such as LC3B and ATG16L1 are often present in chordomas, associated with a strong and diffuse expression of p62, suggesting a blocked autophagic flow. Furthermore, PD-L1+ immune cells also express LC3B, suggesting the need for further investigations between autophagy and the immune microenvironment.

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Association between Health Practice and Food Stockpiling for Disaster

Nutrients ◽

10.3390/nu13051414 ◽

2021 ◽

Vol 13 (5) ◽

pp. 1414

Author(s):

Moeka Harada ◽

Rie Kobayashi ◽

Jun Oka ◽

Nobuyo Tsuboyama-Kasaoka

Keyword(s):

High Risk ◽

Online Survey ◽

Positive Association ◽

Good Health ◽

Food Shortage ◽

Multivariable Logistic Regression Analysis ◽

Health Practices ◽

Health Practice ◽

Significant Positive Association ◽

Good Score

In this study investigated the association between health practices and food stockpiling for disasters in predicted areas with a high risk of food shortage due to the Nankai Trough earthquake. A survey was conducted during 18–20 December 2019 using a self-administered web-based questionnaire. In total, 1200 individuals registered with an online survey company participated in the study. The association between health practices and food stockpiling status was analyzed (n = 998). 59.1% of participants had a poor Breslow’s seven health practice scores (BHPS), 32.9% had a moderate score, and 8.0% had a good score. Multivariable logistic regression analysis revealed that higher BHPS had a significantly higher prevalence of food stockpiling. Additionally, the interrupted group had the highest percentage of participants with low BHPS. Lower BHPS was significantly associated with interrupted stockpiled in the adjusted models. Among the seven health practices, the odds ratio of the “eating breakfast” practice was high. There was a significant positive association between higher health practice scores and food stockpiling for disasters in areas with a high risk of food shortage due to the predicted earthquake. Particularly, it was clarified that individuals who had fewer good health practices were associated with ending up interrupting food stockpiling.

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