Thermal stress accelerates Arabidopsis thaliana mutation rate.

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 Arabidopsis thaliana mutation, studying whole genome profiles of mutation accumulation (MA) lineages grown for 11 successive generations at 29°C. Whereas growth of A. thaliana at standard temperature (ST; 23°C) is associated with a mutation rate of 7 × 10-9 base substitutions per site per generation, growth at stressful high temperature (HT; 29°C) is highly mutagenic, increasing the mutation rate to 12 × 10-9 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.

Pediatric Pharmacy Services: Current Models and Justification for Expansion.

Despite recommendations from numerous health care bodies, some hospitals that care for children have struggled to establish or expand pediatric pharmacy services. The current state of dedicated pediatric operational and clinical pharmacy services was characterized by results from a survey of hospitals that provide care to pediatric patients. The discussion of quality of care, safety, and financial impact is meant to provide concepts for justification of pediatric pharmacy service expansion.

Patterns of homoeologous gene expression shown by RNA sequencing in hexaploid bread wheat.

BACKGROUND: Bread wheat (Triticum aestivum) has a large, complex and hexaploid genome consisting of A, B and D homoeologous chromosome sets. Therefore each wheat gene potentially exists as a trio of A, B and D homoeoloci, each of which may contribute differentially to wheat phenotypes. We describe a novel approach combining wheat cytogenetic resources (chromosome substitution 'nullisomic-tetrasomic' lines) with next generation deep sequencing of gene transcripts (RNA-Seq), to directly and accurately identify homoeologue-specific single nucleotide variants and quantify the relative contribution of individual homoeoloci to gene expression. RESULTS: We discover, based on a sample comprising ~5-10% of the total wheat gene content, that at least 45% of wheat genes are expressed from all three distinct homoeoloci. Most of these genes show strikingly biased expression patterns in which expression is dominated by a single homoeolocus. The remaining ~55% of wheat genes are expressed from either one or two homoeoloci only, through a combination of extensive transcriptional silencing and homoeolocus loss. CONCLUSIONS: We conclude that wheat is tending towards functional diploidy, through a variety of mechanisms causing single homoeoloci to become the predominant source of gene transcripts. This discovery has profound consequences for wheat breeding and our understanding of wheat evolution.

Microarray-based ultra-high resolution discovery of genomic deletion mutations.

BACKGROUND: 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. RESULTS: 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. CONCLUSIONS: 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.

Microarray-based optimization to detect genomic deletion mutations.

We performed array comparative genome hybridization (aCGH) analyses of five Arabidopsis thaliana mutants with genomic deletions ranging in size from 4 bp to > 5 kb. 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.

HANDS: a tool for genome-wide discovery of subgenome-specific base-identity in polyploids.

BACKGROUND: The analysis of polyploid genomes is problematic because homeologous subgenome sequences are closely related. This relatedness makes it difficult to assign individual sequences to the specific subgenome from which they are derived, and hinders the development of polyploid whole genome assemblies. RESULTS: We here present a next-generation sequencing (NGS)-based approach for assignment of subgenome-specific base-identity at sites containing homeolog-specific polymorphisms (HSPs): 'HSP base Assignment using NGS data through Diploid Similarity' (HANDS). We show that HANDS correctly predicts subgenome-specific base-identity at >90% of assayed HSPs in the hexaploid bread wheat (Triticum aestivum) transcriptome, thus providing a substantial increase in accuracy versus previous methods for homeolog-specific base assignment. CONCLUSION: We conclude that HANDS enables rapid and accurate genome-wide discovery of homeolog-specific base-identity, a capability having multiple applications in polyploid genomics.

Development and validation of a nurse-assessed patient comfort score for colonoscopy.

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.

Rape as a weapon of war in the Democratic Republic of the Congo.

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.

Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana.

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.

Autotrophic, sulfur-oxidizing actinobacteria in acidic environments.

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.

Effects of UV-B radiation on seed yield of Glycine max and an assessment of F1 generation progeny for carryover effects.

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.