Mutations are the source of both genetic diversity and mutational load. However, the effects of increasing environmental temperature on plant mutation rates and relative impact on specific mutational ...classes (e.g., insertion/deletion indel vs. single nucleotide variant SNV) are unknown. This topic is important because of the poorly defined effects of anthropogenic global temperature rise on biological systems. Here, we show the impact of temperature increase on
mutation, studying whole genome profiles of mutation accumulation (MA) lineages grown for 11 successive generations at 29°C. Whereas growth of
at standard temperature (ST; 23°C) is associated with a mutation rate of 7 × 10
base substitutions per site per generation, growth at stressful high temperature (HT; 29°C) is highly mutagenic, increasing the mutation rate to 12 × 10
SNV frequency is approximately two- to threefold higher at HT than at ST, and HT-growth causes an ∼19- to 23-fold increase in indel frequency, resulting in a disproportionate increase in indels (vs. SNVs). Most HT-induced indels are 1-2 bp in size and particularly affect homopolymeric or dinucleotide A or T stretch regions of the genome. HT-induced indels occur disproportionately in nucleosome-free regions, suggesting that much HT-induced mutational damage occurs during cell-cycle phases when genomic DNA is packaged into nucleosomes. We conclude that stressful experimental temperature increases accelerate plant mutation rates and particularly accelerate the rate of indel mutation. Increasing environmental temperatures are thus likely to have significant mutagenic consequences for plants growing in the wild and may, in particular, add detrimentally to mutational load.
Ionizing radiation has long been known to induce heritable mutagenic change in DNA sequence. However, the genome-wide effect of radiation is not well understood. Here we report the molecular ...properties and frequency of mutations in phenotypically selected mutant lines isolated following exposure of the genetic model flowering plant Arabidopsis thaliana to fast neutrons (FNs). Previous studies suggested that FNs predominantly induce deletions longer than a kilobase in A. thaliana. However, we found a higher frequency of single base substitution than deletion mutations. While the overall frequency and molecular spectrum of fast-neutron (FN)-induced single base substitutions differed substantially from those of "background" mutations arising spontaneously in laboratory-grown plants, G:C>A:T transitions were favored in both. We found that FN-induced G:C>A:T transitions were concentrated at pyrimidine dinucleotide sites, suggesting that FNs promote the formation of mutational covalent linkages between adjacent pyrimidine residues. In addition, we found that FNs induced more single base than large deletions, and that these single base deletions were possibly caused by replication slippage. Our observations provide an initial picture of the genome-wide molecular profile of mutations induced in A. thaliana by FN irradiation and are particularly informative of the nature and extent of genome-wide mutation in lines selected on the basis of mutant phenotypes from FN-mutagenized A. thaliana populations.
Background Comfort during colonoscopy is a critical component of safety and quality. Objective To develop and validate the Nurse-Assessed Patient Comfort Score (NAPCOMS). Design Prospective scale ...validation. Setting Colorectal cancer screening centers in the United Kingdom and Canada. Patients A total of 300 consecutive patients undergoing colonoscopy at participating colorectal cancer screening centers. Intervention The NAPCOMS was developed by using a modified Delphi process. During colonoscopy, two endoscopy room nurses independently observed and rated patient comfort and tolerability by using NAPCOMS. In addition, endoscopists reported global comfort scores and patients' reported global comfort by using visual 4-point Likert and National Health Service-United Kingdom Global Rating Scales. Main Outcome Measurements Reliability and validity of NAPCOMS was measured by using intraclass correlations (ICC) between nurse ratings of colonoscopies and between NAPCOMS, endoscopist ratings, and patient ratings of global comfort. Results The ICC for the overall NAPCOMS was 0.84 (95% confidence interval CI, 0.80-0.87). There was high agreement between the NAPCOMS and endoscopist ratings of comfort (ICC = 0.77; 95% CI, 0.72-0.81), moderate agreement between the NAPCOMS and patient ratings (ICC = 0.61; 95% CI, 0.53-0.67), and moderate agreement between the endoscopist and patient ratings (ICC = 0.52; 95% CI, 0.43-0.60). Limitations NAPCOMS was validated in outpatients who received colonoscopy with minimal to moderate sedation as part of a screening and surveillance program, so performance among inpatients or those requiring deep sedation was not tested. Conclusion NAPCOMS is a reliable and valid tool for assessing patient comfort in the setting of outpatient colonoscopy performed with minimal to moderate sedation.
A polymetallic sulfide ore from which several metals are commercially extracted has a high pyrrhotite content that results in elevated temperatures in the ore leaching heaps. Laboratory ore columns ...were inoculated with moderately thermophilic bacteria and thermophilic archaea to assess the influence of microbial activity on leaching of metals from the ore at 47°C and 68°C. The populations of moderately thermophilic bacteria that became established on the ore were dominated by acidophilic Actinobacteria. Excessive precipitation of oxidized iron compounds in the presence of microbial activity hindered extensive leaching from small-scale ore columns (0.7kg ore). Copper extraction was generally delayed in comparison to that of the other target metals (principally nickel and zinc) when ore column effluent solutions remained above about pH 2.5.
► A polymetallic sulfide ore was bioleached in laboratory columns with thermophiles. ► Bacteria and archaea catalyzed ferrous iron oxidation to promote metal release. ► Iron oxyhydroxysulfate precipitation at high temperatures restricted metal release. ► Copper release required an effluent pH of about or below pH 2.5. ► Acidophilic Actinobacteria dominated microbial populations at 47°C.
Some novel actinobacteria from geothermal environments were shown to grow autotrophically with sulfur as an energy source. These bacteria have not been formally named and are referred to here as “
...Acidithiomicrobium
” species, as the first of the acidophilic actinobacteria observed to grow on sulfur. They are related to
Acidimicrobium ferrooxidans
with which they share a capacity for ferrous iron oxidation. Ribulose bisphosphate carboxylase/oxygenase (RuBisCO) is active in CO
2
fixation by
Acidimicrobium ferrooxidans
, which appears to have acquired its RuBisCO-encoding genes from the proteobacterium
Acidithiobacillus ferrooxidans
or its ancestor. This lateral transfer of RuBisCO genes between a proteobacterium and an actinobacterium would add to those noted previously among proteobacteria, between proteobacteria and cyanobacteria and between proteobacteria and plastids. “
Acidithiomicrobium
” has RuBisCO-encoding genes which are most closely related to those of
Acidimicrobium ferrooxidans
and
Acidithiobacillus ferrooxidans
, and has additional RuBisCO genes of a different lineage. 16S rRNA gene sequences from “
Acidithiomicrobium
” species dominated clone banks of the genes extracted from mixed cultures of moderate thermophiles growing on copper sulfide and polymetallic sulfide ores in ore leaching columns.
The concentrations of ferrous iron in ore column effluents and the pH of the effluents during the leaching of a copper sulfide ore were followed as an indication of the activity of the microbial ...populations that were established in the ore columns. The impact of this activity and the release of copper were influenced by addition of ferric iron to the irrigation solution, by imposed anoxic conditions and, particularly at higher temperatures, by precipitation of oxidised iron compounds. Moderately thermophilic, acidophilic actinobacteria appeared to dominate the microbial population at 47–57°C with a transition to ferrous iron oxidation by thermophilic archaea as the temperature was increased above 60°C.
► Ferrous iron-oxidizing thermophiles were established in ore columns at 47–65°C. ► Ferric iron promoted copper release from sulfide ore columns. ► Ferrous iron content and pH of ore column effluents reflected microbial activity. ► Actinobacteria dominated microbial populations at 47°C, archaea dominated above 60°C.
Oligonucleotide microarray-based comparative genomic hybridization (CGH) offers an attractive possible route for the rapid and cost-effective genome-wide discovery of deletion mutations. CGH ...typically involves comparison of the hybridization intensities of genomic DNA samples with microarray chip representations of entire genomes, and has widespread potential application in experimental research and medical diagnostics. However, the power to detect small deletions is low.
Here we use a graduated series of Arabidopsis thaliana genomic deletion mutations (of sizes ranging from 4 bp to ~5 kb) to optimize CGH-based genomic deletion detection. We show that the power to detect smaller deletions (4, 28 and 104 bp) depends upon oligonucleotide density (essentially the number of genome-representative oligonucleotides on the microarray chip), and determine the oligonucleotide spacings necessary to guarantee detection of deletions of specified size.
Our findings will enhance a wide range of research and clinical applications, and in particular will aid in the discovery of genomic deletions in the absence of a priori knowledge of their existence.
We performed array comparative genome hybridization (aCGH) analyses of five Arabidopsis thaliana mutants with genomic deletions ranging in size from 4bp to >5kb. We used the Roche NimbleGen ...Arabidopsis CGH 3×720 K whole genome custom tiling array to optimize deletion detection. Details of the microarray design and hybridization data have been deposited at the NCBI GEO repository with accession number GSE55327.
The Democratic Republic of the Congo has been appropriately acknowledged as "the rape capital of the world." While the country has been trapped in conflict, the use of rape as a weapon of war has ...been rampant and unyielding. The sexual violence inflicted upon women has been nothing less than brutal and destructive, physically, socially, and psychologically. This paper analyzes the use of rape as a weapon of war in the Congo, taking into context the ongoing war, cultural and social situations that facilitate its existence, and the many consequences the victims are forced to endure. Drawing information from various academic journals, articles, and field research from international organizations, this paper paints a concise picture of the sexual atrocities occurring in the Democratic Republic of the Congo.
Glycine max (L.) Merr plants were grown outdoors in potted sand exposed to elevated ultraviolet-B (UV-B) radiation provided by filtered fluorescent lamps to determine the effects of UV-B on seed ...yield and UV-B-induced carryover effects in the F1 generation. Increased UV-B radiation had no detectable effects on reproductive parameters except for a reduction on seed number per plant and an increase in the number of unseeded pods per plant and dry weight of unseeded pods per plant in the field supplemental UV-B experiment. Studies on carryover effects in the greenhouse progeny growth trial also showed no effect of parental treatment with UV-B on biomass production, and most symbiotic-N traits and plant metabolite measured. However, the concentrations of N in nodules and starch in roots were significantly increased in the F1 generation progeny from elevated UV-B radiation relative to their F1 counterparts from ambient radiation. Assessing the effects of seed size on plant growth and symbiotic function in the F1 progeny showed that total biomass, dry matter yield of individual organs (leaves, stems, roots and nodules), total plant N and fixed-N rose with increasing seed size. Seed concentration of flavonoids was also enhanced with increasing seed size. These findings suggest that subtle changes did occur in the F1 generation progeny of parental plants exposed to elevated UV-B with potential to accumulate with further exposure to elevated UV-B radiation.
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