Mutation bias reflects natural selection in Arabidopsis thaliana.

Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome-mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.

[Sleep disorders in patients with chronic tinnitus]. / Schlafstörungen bei Patienten mit chronischem Tinnitus.

Tinnitus has a lifetime prevalence of 25% in Germany. A common comorbidity in chronic cases are sleep disorders. The aims of this study were to detect sleep disorders and to identify possible associations with tinnitus parameters.Fifty patients with chronic tinnitus were recruited. The patients underwent audiometry, polysomnography, and completed standardised questionnaires on tinnitus and sleep behaviour.Data were available in 30 men and 9 women (age 50.2 ± 11 y, BMI 28.8 ± 4.4 kg/m²). The median duration of tinnitus was 36 (9; 120) months with a severity score of 2.00 (1.00; 3.00). The mean Tinnitus Questionnaire (TF) score was 43.6 ± 17.1, the Epworth Sleepiness Scale (ESS) score was 8.41 ± 4.27, the Pittsburgh Sleep Quality Index (PSQI) score was 9.21 ± 4.32, and the Screening Scale for Chronic Stress (SSCS) score was 58.13 ± 9.58.Sleep diagnoses included 18 cases of insomnia, 4 cases of RLS, and 11 cases of OSA. Patients with sleep comorbidities showed higher tinnitus severity, PSQI scores, and body weight compared to those without sleep disorders.Worse sleep quality was associated with higher tinnitus severity (p=0.038) and more disruptive tinnitus (p=0.03). Patients with subjectively highly disruptive tinnitus reported higher chronic stress scores. Tinnitus duration was correlated with OSA-severity (p=0.026).More than two-thirds of tinnitus patients showed sleep disorders as comorbidity. A sleep screening appears useful in cases of increased tinnitus severity. Whether CPAP therapy is helpful in reducing tinnitus symptoms could not be conclusively determined but deserves further attention.

Pro-inflammatory activation changes intracellular transport of bevacizumab in the retinal pigment epithelium in vitro.

PURPOSE: Bevacizumab is taken up and transported through the retinal pigment epithelium. Inflammatory signaling may influence this interaction. In the present study, we have investigated the effect of pro-inflammatory stimuli on the uptake, intracellular localization, and transepithelial transport of bevacizumab. METHODS: ARPE-19 cell line or primary porcine RPE cells were treated with clinical relevant concentrations of bevacizumab (250 µg/ml). Pro-inflammatory signaling was induced by TLR-3 agonist polyinosinic:polycytidylic acid (Poly I:C). Viability was investigated with MTT and trypan-blue exclusion assay, and cell number, uptake, and intracellular localization were investigated with immunofluorescence, investigating also actin filaments, the motor protein myosin 7a and lysosomes. Immunofluorescence signals were quantified. Intracellular bevacizumab was additionally detected in Western blot. Barrier function was investigated with transepithelial resistant measurements (TER). The transepithelial transport of bevacizumab and its influence on cytokine (IL-6, IL-8, IL-1ß, TNFα) secretion was investigated with ELISA. RESULTS: Poly I:C in combination with bevacizumab reduced the viability of the cells. Treatment with Poly I:C reduced the uptake of bevacizumab, changed the intensity of the actin filaments, and reduced the colocalization with myosin 7a. In addition, Poly I:C reduced the capacity of RPE cells to transport bevacizumab over the barrier. In addition, bevacizumab reduced the secretion of IL-8 and TNFα after Poly I:C stimulation at selected time points. CONCLUSIONS: Pro-inflammatory activation of RPE cells with TLR-3 agonist Poly I:C changes the interaction of RPE cells with the anti-VEGF compound bevacizumab, reducing its uptake and transport. On the other hand, bevacizumab might influence pro-inflammatory cytokine release. Our data indicate that inflammation may influence the pharmacokinetic of bevacizumab in the retina.

Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus.

The selection pressure exerted by herbicides has led to the repeated evolution of herbicide resistance in weeds. The evolution of herbicide resistance on contemporary timescales in turn provides an outstanding opportunity to investigate key questions about the genetics of adaptation, in particular the relative importance of adaptation from new mutations, standing genetic variation, or geographic spread of adaptive alleles through gene flow. Glyphosate-resistant Amaranthus tuberculatus poses one of the most significant threats to crop yields in the Midwestern United States, with both agricultural populations and herbicide resistance only recently emerging in Canada. To understand the evolutionary mechanisms driving the spread of resistance, we sequenced and assembled the A. tuberculatus genome and investigated the origins and population genomics of 163 resequenced glyphosate-resistant and susceptible individuals from Canada and the United States. In Canada, we discovered multiple modes of convergent evolution: in one locality, resistance appears to have evolved through introductions of preadapted US genotypes, while in another, there is evidence for the independent evolution of resistance on genomic backgrounds that are historically nonagricultural. Moreover, resistance on these local, nonagricultural backgrounds appears to have occurred predominantly through the partial sweep of a single haplotype. In contrast, resistant haplotypes arising from the Midwestern United States show multiple amplification haplotypes segregating both between and within populations. Therefore, while the remarkable species-wide diversity of A. tuberculatus has facilitated geographic parallel adaptation of glyphosate resistance, more recently established agricultural populations are limited to adaptation in a more mutation-limited framework.

Effect of long-term inflammation on viability and function of RPE cells.

PURPOSE: Degenerative ocular disorders like age-related macular degeneration (AMD) are associated with long-term pro-inflammatory signals on retinal pigment epithelial (RPE) cells. In this study, we investigated the effect of long term treatment of RPE cells with agonists of toll-like receptor (TLR) -3 (Polyinosinic:polycytidylic acid, Poly I:C), TLR-4 (lipopolysaccharide, LPS) and the pro-inflammatory cytokine TNFα. METHODS: All tests were conducted with primary porcine RPE. Cells were stimulated with Poly I:C (1, 10, 100 µg/ml), LPS (0.1, 1, 10 µg/ml) or TNFα (12.5, 25 or 50 ng/ml) for 1 day, 7 days or 4 weeks. Cell viability tests (MTT) were additionally tested in ARPE-19 cells. Cytokine secretion (IL-6, IL-1ß, IL-8, TNFα, TGF-ß) was tested in ELISA, phagocytosis in a microscopic assay, and expression of RPE65 in Western blot. Barrier function was tested in transwell-cultured cells by measuring transepithelial resistance for up to 3 days. RESULTS: LPS and TNFα significantly reduce cell viability after 1 day and 7 days, Poly I:C after 7 days and 4 weeks. LPS, Poly I:C and TNFα significantly induce the secretion of IL-6 and IL-8 at all tested time points. IL-1ß is increased by LPS and Poly I:C after 1 day, but not by TNFα. TNFα secretion is increased by Poly I:C and LPS after 1 day but not at later time points. TGF-ß secretion is not influenced by any stimulus. Concerning RPE function, LPS decreased phagocytosis after 7 days, while Poly I:C and TNFα showed no effect. RPE65 expression was strongly reduced by TNFα and LPS after 4 weeks. Wound healing capacity was reduced by Poly I:C but induced by LPS after 7 d and 4 w. Barrier function was not affected by Poly I:C or LPS, while TNFα reduced barrier function after 1 h, 4 h and 3 days. CONCLUSION: Long term pro-inflammatory stimuli reduce RPE viability, barrier properties and cellular function and induce pro-inflammatory cytokines and therefore may contribute directly to atrophic changes in AMD.

Clinical, Neuroimaging, and Metabolic Footprint of the Neurodevelopmental Disorder Caused by Monoallelic HK1 Variants.

Background and Objectives: Hexokinase 1 (encoded by HK1) catalyzes the first step of glycolysis, the adenosine triphosphate-dependent phosphorylation of glucose to glucose-6-phosphate. Monoallelic HK1 variants causing a neurodevelopmental disorder (NDD) have been reported in 12 individuals. Methods: We investigated clinical phenotypes, brain MRIs, and the CSF of 15 previously unpublished individuals with monoallelic HK1 variants and an NDD phenotype. Results: All individuals had recurrent variants likely causing gain-of-function, representing mutational hot spots. Eight individuals (c.1370C>T) had a developmental and epileptic encephalopathy with infantile onset and virtually no development. Of the other 7 individuals (n = 6: c.1334C>T; n = 1: c.1240G>A), 3 adults showed a biphasic course of disease with a mild static encephalopathy since early childhood and an unanticipated progressive deterioration with, e.g., movement disorder, psychiatric disease, and stroke-like episodes, epilepsy, starting in adulthood. Individuals who clinically presented in the first months of life had (near)-normal initial neuroimaging and severe cerebral atrophy during follow-up. In older children and adults, we noted progressive involvement of basal ganglia including Leigh-like MRI patterns and cerebellar atrophy, with remarkable intraindividual variability. The CSF glucose and the CSF/blood glucose ratio were below the 5th percentile of normal in almost all CSF samples, while blood glucose was unremarkable. This biomarker profile resembles glucose transporter type 1 deficiency syndrome; however, in HK1-related NDD, CSF lactate was significantly increased in all patients resulting in a substantially different biomarker profile. Discussion: Genotype-phenotype correlations appear to exist for HK1 variants and can aid in counseling. A CSF biomarker profile with low glucose, low CSF/blood glucose, and high CSF lactate may point toward monoallelic HK1 variants causing an NDD. This can help in variant interpretation and may aid in understanding the pathomechanism. We hypothesize that progressive intoxication and/or ongoing energy deficiency lead to the clinical phenotypes and progressive neuroimaging findings.

Single worm genotyping demonstrates that Onchocerca ochengi females simultaneously produce progeny sired by different males.

Onchocerca ochengi is a filarial nematode parasite of African cattle and most closely related to Onchocerca volvulus, the causing agent of river blindness. O. ochengi females induce the formation of a nodule in the dermis of the host, in which they remain sedentary in very close association with the host's tissue. Males, which do not adhere to the host's tissue, are also found within the nodules at an average number of about one male per nodule. Young O. ochengi females tend to avoid the immediate proximity of existing nodules. Therefore, O. ochengi nodules are dispersed in the ventral inguinal skin at considerable distances from each other. It has been speculated that males avoid the risk of leaving a female once they have found one and remain in the nodule as territorial males rendering the reproductive strategy of O. ochengi essentially monogamous. We developed a protocol that allows reliable PCR amplification of single copy loci from different developmental stages of O. ochengi including embryos and microfilariae. From 32 O. ochengi nodules, we genotyped the female worms and the 67 adult male worms, found in these nodules, together with a fraction of the progeny from within the uteri of females. In 18 of 32 gravid females progeny derived from multiple males were found. In five nodules, the males isolated from the same nodule as the female were not sufficient to explain the genotypes of the entire progeny. We conclude that frequently O. ochengi females simultaneously produce progeny sired by different males and that most but not all males are still present in the nodule when their offspring is ready to hatch.

Lung clearance index and diffusion capacity for CO to detect early functional pulmonary impairment in children with rheumatic diseases.

BACKGROUND: In adults with rheumatic diseases pulmonary complications are relevant contributors to morbidity and mortality. In these patients diffusion capacity for CO (DLCO) is an established method to detect early pulmonary impairment. Pilot studies using DLCO indicate that early functional pulmonary impairment is present even in children with rheumatic disease albeit not detectable by spirometry and without clinical signs of pulmonary disease. Since the lung clearance index (LCI) is also a non-invasive, feasible and established method to detect early functional pulmonary impairment especially in children and because it requires less cooperation (tidal breathing), we compared LCI versus DLCO (forced breathing and breath-holding manoeuvre) in children with rheumatic diseases. FINDINGS: Nineteen patients (age 9-17 years) with rheumatic disease and no clinical signs of pulmonary disease successfully completed LCI and DLCO during annual check-up. In 2 patients LCI and DLCO were within physiological limits. By contrast, elevated LCI combined with physiological results for DLCO were seen in 8 patients and in 9 patients both, the LCI and DLCO indicate early functional pulmonary changes. Overall, LCI was more sensitive than DLCO to detect early functional pulmonary impairment (p = 0.0128). CONCLUSIONS: Our findings suggest that early functional pulmonary impairment is already present in children with rheumatic diseases. LCI is a very feasible and non-invasive alternative for detection of early functional pulmonary impairment in children. It is more sensitive and less cooperation dependent than DLCO. Therefore, we suggest to integrate LCI in routine follow-up of rheumatic diseases in children.

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana.

Mutations are the ultimate source of all genetic variation. However, few direct estimates of the contribution of mutation to molecular genetic variation are available. To address this issue, we first analyzed the rate and spectrum of mutations in the Arabidopsis thaliana reference accession after 25 generations of single-seed descent. We then compared the mutation profile in these mutation accumulation (MA) lines against genetic variation observed in the 1001 Genomes Project. The estimated haploid single nucleotide mutation (SNM) rate for A. thaliana is 6.95 × 10-9 (SE ± 2.68 × 10-10) per site per generation, with SNMs having higher frequency in transposable elements (TEs) and centromeric regions. The estimated indel mutation rate is 1.30 × 10-9 (±1.07 × 10-10) per site per generation, with deletions being more frequent and larger than insertions. Among the 1694 unique SNMs identified in the MA lines, the positions of 389 SNMs (23%) coincide with biallelic SNPs from the 1001 Genomes population, and in 289 (17%) cases the changes are identical. Of the 329 unique indels identified in the MA lines, 96 (29%) overlap with indels from the 1001 Genomes dataset, and 16 indels (5% of the total) are identical. These overlap frequencies are significantly higher than expected, suggesting that de novo mutations are not uniformly distributed and arise at polymorphic sites more frequently than assumed. These results suggest that high mutation rate potentially contributes to high polymorphism and low mutation rate to reduced polymorphism in natural populations providing insights of mutational inputs in generating natural genetic diversity.

Browning Potential of C6-α-Dicarbonyl Compounds under Maillard Conditions.

In this work, the three major C6-α-dicarbonyl compounds glucosone (GLUC), 1-deoxyglucosone (1-DG), and 3-deoxyglucosone (3-DG) were synthesized and examined under Maillard conditions (aqueous solutions with the addition of l-alanine at 130 °C and pH 5/8). For the first time, the resulting color formation, antioxidant activity, and generation of short-chained α-dicarbonyls were investigated and compared to incubations of d-glucose and d-fructose. An additive effect on the formation of color, an antagonistic effect on the generation of α-dicarbonyl compounds, and a synergistic effect on the antioxidant activity could be observed for the 1-DG/GLUC combination. Despite their common degradation products, different extinctions could be measured, with 3-DG showing the strongest color formation, followed by GLUC and 1-DG. The analyzed α-dicarbonyl compounds have no direct impact on the formation of color but are precursors for most of the colored compounds. The main difference between the three substances is their ability to form different heterocyclic degradation products, such as pyranones (1-DG), furanones (1-DG), furans (GLUC and 3-DG), and the corresponding N-heterocycles in the presence of amino components. This seems to be the main reason for their varying browning potential and antioxidant activity.

[Guideline for the Development of Evidence-based Patient Information: insights into the methods and implementation of evidence-based health information]. / Leitlinie evidenzbasierte Gesundheitsinformation: Einblick in die Methodik der Entwicklung und Implementierung.

The "Guideline for the Development of Evidence-based Patient Information" project is a novelty. The aim of this project is to enhance the quality of health information. The development and implementation process is guided by national and international standards. Involvement of health information developers plays an essential role. This article provides an insight into the guideline's underlying methodology, using graphics as an example. In addition, the results of a qualitative study exploring the competencies of health information developers are presented. These results will guide the implementation of the guideline. We conducted systematic literature searches (until June 2014), critical appraisal and descriptive analyses applying GRADE for two selected guideline questions. Out of 3,287 hits 11 RCTs were included in the analysis. The evidence has been rated to be of low to moderate quality. Additional graphics may have a positive effect on cognitive outcomes. However, the relevance of the results is questionable. For graphics, we found some indication that especially pictograms but also bar graphs have a positive effect on cognitive outcomes and meet patients' preferences. In order to prepare for the implementation of the guideline, we conducted a qualitative study to explore the competencies of health information developers using expert interviews. Four telephone interviews were conducted, audio recorded, transcribed and analysed according to Grounded Theory. Six categories were identified: literature search, development of health information, participation of target groups, continuing education and further training of health information developers, cooperation with different institutions, essential competencies. Levels of competencies regarding the methods of evidence-based medicine and evidence-based health information vary considerably and indicate a need for training. These results have informed the development of a training programme that will support the implementation.

Reproductive biology of Onchocerca ochengi, a nodule forming filarial nematode in zebu cattle.

Onchocerca ochengi is a nodule-forming filarial nematode parasite of cattle in tropical Africa and closely related to the human pathogen Onchocerca volvulus. The adult worms reside in intradermal nodules. While females are sedentary, males may move between nodules. The first stage larvae (microfilariae) disperse in the skin of the host waiting to be taken up by the intermediate host. The density of microfilariae in the skin is largely independent of the number of adult worms present indicating some form of density dependent control. Recently, Onchocerca sp. Siisa, a form of Onchocerca distinguishable from O. ochengi by mitochondrial DNA sequences but not by morphology, was described to occur in cattle. This raised the question if Onchocerca sp. Siisa represents a different mitochondrial clade of O. ochengi or a new species. In order to study the reproductive biology and to understand this self-control of the off-spring population we systematically analyzed all Onchocerca nodules from the skin of one zebu cow and we examined a sample of microfilariae from a skin biopsy. We identified 87 O. ochengi females and 146 males. 56 (64.4%) of the females contained developing embryos. In order to assign the progeny to their respective parents we determined the genotypes at six nuclear and two mitochondrial molecular genetic markers in the adult worms, in a fraction of the progeny present in the uteri of the females and in the skin microfilariae. The 121 skin microfilariae we analyzed originated from at least 17 different mothers, which contributed rather differently to the total. Forty-five larvae (37.2%) were the progeny of a single female. Of the adult worms 16.7% were of the type Onchocerca sp. Siisa. These worms appeared to interbreed freely with the rest of the O. ochengi population and therefore belong to the same species.

Molecular evidence of 'Siisa form', a new genotype related to Onchocerca ochengi in cattle from North Cameroon.

Onchocerca ochengi, a filarial nematode parasite from African Zebu cattle is considered to be the closest relative of Onchocerca volvulus, the causative agent of river blindness. Both Onchocerca species share the vector, black flies of the Simulium damnosum complex. Correct identification of their infective third-stage larvae in man-biting vectors is crucial to distinguish the transmission of human or animal parasites. In order to identify different closely related Onchocerca species we surveyed the sequences from the three mitochondrial loci 12S rRNA, 16S rRNA and coxI in both adult worms isolated from Onchocerca-induced nodules in cattle and infective third stage larvae isolated from vector flies from North Cameroon. Two distinct groups of mitochondrial haplotypes were found in cattle as well as in flies. One of them has been formerly mentioned in the literature as Onchocerca sp. 'Siisa', a filaria isolated from the vector S. damnosum sensu lato in Uganda with hitherto unknown host. Both variants are found sympatric, also in the same nodule of the animal host and in the vector. In the flies we also found the mitochondrial haplotype that had been described for O. volvulus which is about equally different from the two previously mentioned ones as they are from each other. These results suggest a higher genetic diversification of Onchocerca ochengi than previously reported.