THE DNA OF CAENORHABDITIS ELEGANS

Abstract We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the β-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif r system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced >250 mutations leading to Rif r in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.

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Microdissection of and microcloning from the short arm of human chromosome 2.

Molecular and Cellular Biology ◽

10.1128/mcb.6.11.3826 ◽

1986 ◽

Vol 6 (11) ◽

pp. 3826-3830 ◽

Cited By ~ 38

Author(s):

G P Bates ◽

B J Wainwright ◽

R Williamson ◽

S D Brown

Keyword(s):

Human Chromosome ◽

Dna Sequences ◽

Chromosomal Location ◽

Genetic Diseases ◽

Repetitive Sequences ◽

Single Copy ◽

Chromosome 2 ◽

Insert Size ◽

Base Pairs ◽

The Mean

A bank of cloned DNA sequences from the distal half of the short arm of human chromosome 2 was generated by using microdissection and microcloning techniques. DNA was purified from 106 chromosomal fragments, manually dissected from peripheral lymphocytes in metaphase, and cloned into the EcoRI site of lambda gt10. A total of 257 putative recombinants were recovered, of which 41% were found to contain human inserts. The mean insert size was 380 base pairs (median size, 83 base pairs), and fewer than 10% of the clones contained highly repetitive sequences. All single-copy sequences examined were shown to map to the short arm of chromosome 2 by using hybrid panels. This technique provides a rapid method of isolating probes specific to a human subchromosomal region to generate linked markers to genetic diseases for which the chromosomal location is known.

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HOMOLOGOUS RECOMBINATION IN ESCHERICHIA COLI: DEPENDENCE ON SUBSTRATE LENGTH AND HOMOLOGY

Genetics ◽

10.1093/genetics/112.3.441 ◽

1986 ◽

Vol 112 (3) ◽

pp. 441-457 ◽

Cited By ~ 2

Author(s):

Ping Shen ◽

Henry V Huang

Keyword(s):

Dna Sequences ◽

Wild Type ◽

Base Pairs ◽

E Coli ◽

In Vivo Recombination ◽

Recombinant Frequency ◽

Genetic Length ◽

Efficient Processing ◽

Low Levels

ABSTRACT We studied the in vivo recombination between homologous DNA sequences cloned in phage lambda and a pBR322-derived plasmid by assaying for the formation of phage-plasmid cointegrates by a single (or an odd number of) reciprocal exchange. (1) Recombination proceeds by the RecBC pathway in wild-type cells and by low levels of a RecF-dependent pathway in recBC - cells. The RecE pathway appears not to generate phage-plasmid cointegrates. (2) Recombination is linearly dependent on the length of the homologous sequences. In both RecBC and RecF-dependent pathways there is a minimal length, called the minimal efficient processing segment (MEPS), below which recombination becomes inefficient. The length of MEPS is between 23-27 base pairs (bp) and between 44-90 bp for the RecBC- and RecF-dependent pathways, respectively. A model, based on overlapping MEPS, of the correlation of genetic length with physical length is presented. The bases for the different MEPS length of the two pathways are discussed in relationship to the enzymes specific to each pathway. (3) The RecBC and the RecF-dependent pathways are each very sensitive to substrate homology. In wild-type E. coli, reduction of homology from 100% to 90% decreases recombinant frequency over 40-fold. The homology dependence of the RecBC and RecF-dependent pathways are similar. This suggests that a component common to both, probably recA, is responsible for the recognition of homology.

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Cloning of promoter-like sequences from Lactobacillus paracasei subsp. paracasei CG11 and their expression in Escherichia coli, Lactococcus lactis, and Lactobacillus reuteri

Canadian Journal of Microbiology ◽

10.1139/m94-165 ◽

1994 ◽

Vol 40 (12) ◽

pp. 1043-1050 ◽

Cited By ~ 17

Author(s):

Gordana Djordjevic ◽

Bojana Bojovic ◽

Ana Banina ◽

Ljubisa Topisirovic

Keyword(s):

Escherichia Coli ◽

Lactococcus Lactis ◽

Dna Sequences ◽

Lactobacillus Reuteri ◽

Lactobacillus Paracasei ◽

Translational Efficiency ◽

Broad Host Range ◽

Chromosomal Dna ◽

Base Pairs ◽

E Coli

Fragments of chromosomal DNA from Lactobacillus paracasei subsp. paracasei CG11 (formerly Lactobacillus casei CG11) capable of functioning as promoters were isolated using the broad host range, promoter-probe vector pGKV210. Five such fragments designated P61, P79, P80, P116, and P144 were completely sequenced and analyzed. Fragment P61 had the highest transcriptional efficiency in Escherichia coli and Lactobacillus reuteri whereas P80 was the most active in Lactococcus lactis. In general, the orders of the transcriptional strengths were almost identical in E. coli and Lactobacillus reuteri but different from that in Lactococcus lactis. Mapping of the 5′ end of cat mRNA showed that different regions of fragments P79 and P144 were used as promoters in Lactococcus lactis than in E. coli and Lactobacillus reuteri. Analysis of these DNA sequences revealed that the putative −35 and −10 hexanucleotides resembled those of E. coli, Bacillus subtilis, and lactococci. The spacing between these two hexanucleotides and between the putative −10 hexanucleotide and the transcriptional start point (A residues predominated) ranged from 17 to 18 base pairs and from 5 to 7 base pairs, respectively. Each of the cloned Lactobacillus paracasei CG11 promoter-like fragments contained an AT-rich sequence upstream of the putative −35 region (from 60 to 73%).Key words: Lactobacillus, promoter-like sequences, transcriptional efficiency, translational efficiency.

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Superoxide dismutase 1 (SOD1) and cadmium: a three models approach to the comprehension of its neurotoxic effects

Biomedical Science and Engineering ◽

10.4081/bse.2021.157 ◽

2021 ◽

Vol 4 (s1) ◽

Author(s):

Federica Bovio ◽

Barbara Sciandrone ◽

Chiara Urani ◽

Paola Fusi ◽

Matilde Forcella ◽

...

Keyword(s):

Superoxide Dismutase ◽

Caenorhabditis Elegans ◽

Recombinant Protein ◽

Neuronal Cells ◽

Expression Level ◽

Superoxide Dismutase 1 ◽

Biological Models ◽

Nematode Caenorhabditis Elegans ◽

E Coli ◽

Neurotoxic Effects

In three different biological models, the recombinant protein expressed in E. coli, the neuronal cells SH-SY5Y and the nematode Caenorhabditis elegans, cadmium inhibits SOD1 activity without affecting its expression level.

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SPECTROPHOTOMETRIC METHOD TO ESTIMATE GLYCOGEN LEVELS IN THE MODEL NEMATODE CAENORHABDITIS ELEGANS

10.31016/978-5-9902341-5-4.2020.21.383-387 ◽

2020 ◽

pp. 383-387

Author(s):

Sidor ◽

Andreyanov

Keyword(s):

Caenorhabditis Elegans ◽

Spectrophotometric Method ◽

Cell Biology ◽

Metabolic Regulation ◽

Enzyme Analysis ◽

Nematode Caenorhabditis Elegans ◽

E Coli ◽

C Elegans ◽

Energy Maintenance

The model nematode Caenorhabditis elegans is widely used in studies on metabolic regulation and aging processes, in developmental and cell biology, neurobiology and genetics. Recent studies have shown the crucial role of glycogen, the glucose polymer, in stress resistance, energy maintenance and aging of organisms. Currently, the main methods for determining glycogen in the C. elegans nematode are iodine staining, enzyme analysis, and Raman microspectroscopy, described in 2019 by A. Cherkas. The proposed spectrophotometric method allows us to quantify glycogen levels, in contrast to those used in modern practice. The nematode was grown on NGM agar seeded with E. coli as a food source for 7 days in a thermostat at 20±20 C. Then, it was washed with M9 buffer and separated from bacteria by centrifugation for 10 min at 9 000 g. The samples were placed in an ice bath and nematodes were counted in each sample at x 10 microscope magnification. The glycogen concentration was determined spectrophotometrically. This value is average for different stages of the nematode development and amounts to 0.001821 ± 0.000009 μg.

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Analysis of the constancy of DNA sequences during development and evolution of the nematode Caenorhabditis elegans.

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.76.3.1333 ◽

1979 ◽

Vol 76 (3) ◽

pp. 1333-1337 ◽

Cited By ~ 181

Author(s):

S. W. Emmons ◽

M. R. Klass ◽

D. Hirsh

Keyword(s):

Caenorhabditis Elegans ◽

Dna Sequences ◽

Nematode Caenorhabditis Elegans ◽

Development And Evolution

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Caenorhabditis elegans processes sensory information to choose between freeloading and self-defense strategies

eLife ◽

10.7554/elife.56186 ◽

2020 ◽

Vol 9 ◽

Cited By ~ 3

Author(s):

Jodie A Schiffer ◽

Francesco A Servello ◽

William R Heath ◽

Francis Raj Gandhi Amrit ◽

Stephanie V Stumbur ◽

...

Keyword(s):

Hydrogen Peroxide ◽

Caenorhabditis Elegans ◽

Sensory Information ◽

Local Environment ◽

Adaptive Strategy ◽

Chemical Weapon ◽

Nematode Caenorhabditis Elegans ◽

Defense Strategies ◽

E Coli ◽

Self Defense

Hydrogen peroxide is the preeminent chemical weapon that organisms use for combat. Individual cells rely on conserved defenses to prevent and repair peroxide-induced damage, but whether similar defenses might be coordinated across cells in animals remains poorly understood. Here, we identify a neuronal circuit in the nematode Caenorhabditis elegans that processes information perceived by two sensory neurons to control the induction of hydrogen peroxide defenses in the organism. We found that catalases produced by Escherichia coli, the nematode’s food source, can deplete hydrogen peroxide from the local environment and thereby protect the nematodes. In the presence of E. coli, the nematode’s neurons signal via TGFβ-insulin/IGF1 relay to target tissues to repress expression of catalases and other hydrogen peroxide defenses. This adaptive strategy is the first example of a multicellular organism modulating its defenses when it expects to freeload from the protection provided by molecularly orthologous defenses from another species.

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Microdissection of and microcloning from the short arm of human chromosome 2

Molecular and Cellular Biology ◽

10.1128/mcb.6.11.3826-3830.1986 ◽

1986 ◽

Vol 6 (11) ◽

pp. 3826-3830

Author(s):

G P Bates ◽

B J Wainwright ◽

R Williamson ◽

S D Brown

Keyword(s):

Human Chromosome ◽

Dna Sequences ◽

Chromosomal Location ◽

Genetic Diseases ◽

Repetitive Sequences ◽

Single Copy ◽

Chromosome 2 ◽

Insert Size ◽

Base Pairs ◽

The Mean

A bank of cloned DNA sequences from the distal half of the short arm of human chromosome 2 was generated by using microdissection and microcloning techniques. DNA was purified from 106 chromosomal fragments, manually dissected from peripheral lymphocytes in metaphase, and cloned into the EcoRI site of lambda gt10. A total of 257 putative recombinants were recovered, of which 41% were found to contain human inserts. The mean insert size was 380 base pairs (median size, 83 base pairs), and fewer than 10% of the clones contained highly repetitive sequences. All single-copy sequences examined were shown to map to the short arm of chromosome 2 by using hybrid panels. This technique provides a rapid method of isolating probes specific to a human subchromosomal region to generate linked markers to genetic diseases for which the chromosomal location is known.

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Effectiveness of Cleaners and Sanitizers in Killing Salmonella Newport in the Gut of a Free-Living Nematode, Caenorhabditis elegans

Journal of Food Protection ◽

10.4315/0362-028x-67.10.2151 ◽

2004 ◽

Vol 67 (10) ◽

pp. 2151-2157 ◽

Cited By ~ 14

Author(s):

STEPHEN J. KENNEY ◽

GARY L. ANDERSON ◽

PHILLIP L. WILLIAMS ◽

PATRICIA D. MILLNER ◽

LARRY R. BEUCHAT

Keyword(s):

Caenorhabditis Elegans ◽

Relative Humidity ◽

Nalidixic Acid ◽

Fruits And Vegetables ◽

Nematode Caenorhabditis Elegans ◽

Free Living ◽

E Coli ◽

C Elegans ◽

Salmonella Newport ◽

Free Living Nematode

Caenorhabditis elegans, a free-living nematode found in soil, has been shown to ingest human enteric pathogens, thereby potentially serving as a vector for preharvest contamination of fruits and vegetables. A study was undertaken to evaluate the efficacy of cleaners and sanitizers in killing Salmonella enterica serotype Newport in the gut of C. elegans. Adult worms were fed nalidixic acid–adapted cells of Escherichia coli OP50 (control) or Salmonella Newport for 24 h, washed, placed on paper discs, and incubated at temperatures of 4 or 20°C and relative humidities of 33 or 98% for 24 h. Two commercial cleaners (Enforce and K Foam Lo) and four sanitizers (2% acetic acid, 2% lactic acid, Sanova, and chlorine [50 and 200 μg/ml]) were applied to worms for 0, 2, or 10 min. Populations of E. coli and Salmonella Newport (CFU per worm) in untreated and treated worms were determined by sonicating worms in 0.1% peptone and surface plating suspensions of released cells on tryptic soy agar containing nalidixic acid. Populations of Salmonella Newport in worms exposed to 33 or 98% relative humidity at 4°C or 33% relative humidity at 20°C were significantly (P ≤ 0.05) lower than the number surviving exposure to 98% relative humidity at 20°C. In general, treatment of desiccated worms with cleaners and sanitizers was effective in significantly (P ≤ 0.05) reducing the number of ingested Salmonella Newport. Results indicate that temperature and relative humidity influence the survival of Salmonella Newport in the gut of C. elegans, and cleaners and sanitizers may not eliminate the pathogen.

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