Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing.

Chemical mutagenesis efficiently generates phenotypic variation in otherwise homogeneous genetic backgrounds, enabling functional analysis of genes. Advances in mutation detection have brought the utility of induced mutant populations on par with those produced by insertional mutagenesis, but systematic cataloguing of mutations would further increase their utility. We examined the suitability of multiplexed global exome capture and sequencing coupled with custom-developed bioinformatics tools to identify mutations in well-characterized mutant populations of rice (Oryza sativa) and wheat (Triticum aestivum). In rice, we identified ∼18,000 induced mutations from 72 independent M2 individuals. Functional evaluation indicated the recovery of potentially deleterious mutations for >2600 genes. We further observed that specific sequence and cytosine methylation patterns surrounding the targeted guanine residues strongly affect their probability to be alkylated by ethyl methanesulfonate. Application of these methods to six independent M2 lines of tetraploid wheat demonstrated that our bioinformatics pipeline is applicable to polyploids. In conclusion, we provide a method for developing large-scale induced mutation resources with relatively small investments that is applicable to resource-poor organisms. Furthermore, our results demonstrate that large libraries of sequenced mutations can be readily generated, providing enhanced opportunities to study gene function and assess the effect of sequence and chromatin context on mutations.

Oxidative stress status in congenital hypogonadism: an appraisal.

Patients with hypogonadism are at increased risk of cardiac and metabolic diseases. However, the pathogenesis of increased cardiometabolic risk in patients with hypogonadism is not clear. Oxidative stress plays an important role in the pathogenesis of cardiometabolic diseases. This study aimed to investigate possible differences in oxidative stress conditions between patients with hypogonadism and healthy controls. In this study, 38 male patients with congenital hypogonadotropic hypogonadism (CHH) (mean age: 21.7 ± 1.6 years) and 44 healthy male controls (mean age: 22.3 ± 1.4 years) with almost equal body mass index were enrolled. The demographic parameters, follicle-stimulating hormone (FSH), luteinizing hormone (LH), total and free testosterone, homeostatic model assessment of insulin resistance (HOMA-IR) and oxidative stress parameters, such as superoxide dismutase, catalase (CAT), glutathione peroxidase (GPx) and malondialdehyde (MDA), were compared between both groups. Compared to the healthy controls, triglycerides (p = .02), insulin levels, HOMA-IR values, CAT activities and MDA levels (p < .001 for all) were significantly higher and HDL cholesterol (p = .04), total and free testosterone, FSH, LH levels and GPx activity were significantly lower (p < .001 for all) in patients with CHH. There were significant correlations between total testosterone levels and CAT activity (r = -.33 p = .01), GPx activity (r = .36 p = .007) and MDA (r = -.47 p < .001) levels. The results of this study showed that young and treatment-naïve patients with congenital hypogonadism had an increased status of oxidative stress.

Osteoprotegerin, fibroblast growth factor 23, and vitamin D3 levels in male patients with hypogonadism.

Cardiometabolic disorders and osteoporosis are prevalent in patients with hypogonadism. Osteoprotegerin (OPG) and fibroblast growth factor-23 (FGF-23), are co-secreted from bones and vascular endothelium, regulating bone mineral metabolism and vascular functions. Vitamin D is another hormone with dual effects on bone and vascular metabolism. The aim of this study was to search for any difference between the serum levels of OPG, FGF-23, and vitamin D in patients with hypogonadism and the healthy controls. We also aimed to search for any relationship between these parameters and endothelial dysfunction or insulin resistance. Forty-nine male patients with congenital hypogonadotropic hypogonadism (CHH) (mean age 20.71 ± 1.75 years) and 43 BMI matched healthy male subjects (mean age 21.37 ± 1.04 years) were enrolled. OPG, FGF-23, vitamin D, and asymmetric dimethylarginine (ADMA) levels were measured from the fasting serum samples. The insulin sensitivity was estimated by homeostatic model assessment-insulin resistance (HOMA-IR) formula. Triglycerides, insulin, HOMA-IR, and ADMA levels in the patient group were significantly higher than the values of the control group (p = 0.014, p = 0.002, p = 0.003, p < 0.001, respectively). The OPG, FGF-23, and vitamin D levels of the patients were not significantly different from the healthy controls. In addition, these markers were not correlated to ADMA or HOMA-IR levels. The results show that young and treatment naive subjects with CHH have endothelial dysfunction and insulin resistance when compared to their healthy counterparts. However, the OPG, FGF-23, and vitamin D levels were similar in the 2 groups. In addition, these parameters are not significantly related to the endothelial functions or insulin resistance in these subjects.

A k-mer-based bulked segregant analysis approach to map seed traits in unphased heterozygous potato genomes.

High-throughput sequencing-based methods for bulked segregant analysis (BSA) allow for the rapid identification of genetic markers associated with traits of interest. BSA studies have successfully identified qualitative (binary) and quantitative trait loci (QTLs) using QTL mapping. However, most require population structures that fit the models available and a reference genome. Instead, high-throughput short-read sequencing can be combined with BSA of k-mers (BSA-k-mer) to map traits that appear refractory to standard approaches. This method can be applied to any organism and is particularly useful for species with genomes diverged from the closest sequenced genome. It is also instrumental when dealing with highly heterozygous and potentially polyploid genomes without phased haplotype assemblies and for which a single haplotype can control a trait. Finally, it is flexible in terms of population structure. Here, we apply the BSA-k-mer method for the rapid identification of candidate regions related to seed spot and seed size in diploid potato. Using a mixture of F1 and F2 individuals from a cross between 2 highly heterozygous parents, candidate sequences were identified for each trait using the BSA-k-mer approach. Using parental reads, we were able to determine the parental origin of the loci. Finally, we mapped the identified k-mers to a closely related potato genome to validate the method and determine the genomic loci underlying these sequences. The location identified for the seed spot matches with previously identified loci associated with pigmentation in potato. The loci associated with seed size are novel. Both loci are relevant in future breeding toward true seeds in potato.

HDL cholesterol subfractions and the effect of testosterone replacement in hypogonadism.

Metabolic disorders and cardiovascular events are increased in hypogonadism. Serum HDL composition is a better cardiovascular predictor than the HDL counts. However, there is no information about the HDL subfractions in patients with hypogonadism. We designed a prospective study to investigate the HDL subfractions in treatment naïve subjects with hypogonadism and the effects of 2 different testosterone replacement regimens on the HDL subfractions. Seventy young male patients with congenital hypogonadotropic hypogonadism (CHH) and 70 age and BMI-matched healthy males were enrolled in the present study. The patients were assigned to receive intramuscular injections of testosterone esters 250 mg every 3 weeks and transdermal testosterone applications 50 mg daily. Biochemical investigations including HDL subfractions and insulin resistance were done. Patients with CHH had higher levels of insulin, HOMA-IR, WC, triglyceride, and diastolic blood pressure. Although, the HDL cholesterol concentrations were similar in both groups, hypogonadal patients had lower HDL2 and higher HDL3 levels. The total testosterone levels were independent determinants of the HDL2 subfractions. During the follow-up, a significant increase in the BMI and WC values and a significant decrease in the levels of total cholesterol, HDL cholesterol, and HDL3 were observed. No difference was present between the 2 treatment arms. These results show that patients with hypogonadism have unfavorable HDL compositions in addition to the other dysmetabolic features. However, testosterone replacement for about six months neither improves the metabolic problems nor the HDL composition. Mechanistic studies are warranted to better understand the cardiovascular effects of unfavorable HDL compositions in hypogonadism.

Implication of gammadelta T cells in the human immune response to cytomegalovirus.

In normal individuals, gammadelta T cells account for less than 6% of total peripheral T lymphocytes and mainly express T-cell receptor (TCR) Vdelta2-Vgamma9 chains. We have previously observed a dramatic expansion of gammadelta T cells in the peripheral blood of renal allograft recipients only when they developed cytomegalovirus (CMV) infection. This increase was long lasting (more than 1 year), was associated with an activation of gammadelta T cells, and concerned only Vdelta1 or Vdelta3 T-cell subpopulations. Analysis of gammadelta TCR junctional diversity revealed that CMV infection in these patients was accompanied by (a) a marked restriction of CDR3 size distribution in Vdelta3 and, to a lesser extent, in Vdelta1 chains; and (b) a selective expansion of Vdelta1 cells bearing recurrent junctional amino acid motifs. These features are highly suggestive of an in vivo antigen-driven selection of gammadelta T-cell subsets during the course of CMV infection. Furthermore, Vdelta1 and Vdelta3 T cells from CMV-infected kidney recipients were able to proliferate in vitro in the presence of free CMV or CMV-infected fibroblast lysates but not uninfected or other herpes virus-infected fibroblast lysates. This in vitro expansion was inhibited by anti-gammadelta TCR mAb's. These findings suggest that a population of gammadelta T cells might play an important role in the immune response of immunosuppressed patients to CMV infection.

An unusual presentation of primary hyperparathyroidism: multiple brown tumors and coexisting thyroid carcinoma.

We present a patient with a complex clinical picture of primary hyperparathyroidism with multiple destructive skeletal lesions suspicious of bone metastases and concomitant multifocal papillary thyroid carcinoma with a metastatic central lymph node. He presented with progressively worsening right hip pain and restricted motion. Magnetic resonance imaging revealed multiple lytic lesions involving predominantly the right trochanter minor and the left inferior and posterior pubic rami. Biochemical tests were consistent with primary hyperparathyroidism. Neck ultrasound and parathyroid scintigraphy revealed a single parathyroid adenoma and a thyroid nodule, preoperative cytology of which confirmed papillary thyroid carcinoma, as did the final surgical specimen. Biochemical results, regarding hyperparathyroidism, declined to normal levels and his complaints gradually decreased after surgery. Postoperative whole body bone scintigraphy showed increased tracer uptakes at multiple sites, but they were proved to be metabolically inactive by fluorodeoxyglucose positron emission tomography/computed tomography.

Creation and Genomic Analysis of Irradiation Hybrids in Populus.

Establishing efficient functional genomic systems for creating and characterizing genetic variation in forest trees is challenging. Here we describe protocols for creating novel gene-dosage variation in Populus through gamma-irradiation of pollen, followed by genomic analysis to identify chromosomal regions that have been deleted or inserted in each F1 individual. Irradiated pollen is used in a controlled, interspecific cross to create F1 progeny that carry deletions and insertions of chromosomal regions. These insertions and deletions result in novel changes in gene dosage that in turn affect both qualitative and quantitative phenotypic traits. The protocols described here outline the processes involved in optimizing irradiation levels and performing controlled crosses, sowing seed and propagating seedlings, and genome-wide sequence-based analysis of deletions and insertions in the F1 progeny. The same approach could be applied to other vegetatively propagated species. © 2016 by John Wiley & Sons, Inc.

It is Rous sarcoma virus protein P12 and not P19 that binds tightly to Rous sarcoma virus RNA.

The interactions between Rous Sarcoma virus (RSV) RNA and the viral proteins in the virus have been analysed by Sen & Todaro (1977) using ultraviolet light irradiation; they showed that the major protein ultraviolet light cross-linked to the viral RNA was P19 as identified by polyacrylamide gel electrophoresis. We report here that it is not viral protein P19 but P12 that binds tightly to RSV RNA upon ultraviolet light irradiation of the virus. Therefore, the binding sites of the viral protein along RSV RNA that we have characterized previously should be correctly attributed now to P12 and not P19.

Determination of ploidy levels in Ipheion uniflorum (R. C. Graham) Rafin (Liliaceae).

In this study, chromosome number and ploidy levels of Ipheion uniflorum cv. "Wisley Blue" (spring starflower) were determined. In meristematic root tip cells, chromosome number was found as 2n = 12 and 4n = 24. The ratios of diploid and tetraploid cells were found as 80.74% and 19.26%, respectively. In differentiated root tissues and mature leaf tissues ploidy levels were analysed by flow cytometry and polysomaty were found in both organs. In differentiated root tissues, ploidy levels were found as 2C, 4C, 8C and 16C DNA. In root tissues percentages of 2C, 4C, 8C and 16C nuclear DNA content were observed as 57.2%, 33.1%, 2.47% and 7.23%, respectively. In mature leaf tissues, ploidy levels were determined 2C, 4C, 8C and 16C DNA. In this tissue the frequency of 4C DNA was found very higher (74.3%) and 2C DNA content was determined as 19.2%. In mature leaf tissue, 8C and 16C nuclear DNA contents were observed as 2.72% and 3.78%, respectively. When nuclear DNA contents in leaves and roots were compared, an apparent difference in 2C and 4C DNA contents was found.

High-Throughput Analysis of T-DNA Location and Structure Using Sequence Capture.

Agrobacterium-mediated transformation of plants with T-DNA is used both to introduce transgenes and for mutagenesis. Conventional approaches used to identify the genomic location and the structure of the inserted T-DNA are laborious and high-throughput methods using next-generation sequencing are being developed to address these problems. Here, we present a cost-effective approach that uses sequence capture targeted to the T-DNA borders to select genomic DNA fragments containing T-DNA-genome junctions, followed by Illumina sequencing to determine the location and junction structure of T-DNA insertions. Multiple probes can be mixed so that transgenic lines transformed with different T-DNA types can be processed simultaneously, using a simple, index-based pooling approach. We also developed a simple bioinformatic tool to find sequence read pairs that span the junction between the genome and T-DNA or any foreign DNA. We analyzed 29 transgenic lines of Arabidopsis thaliana, each containing inserts from 4 different T-DNA vectors. We determined the location of T-DNA insertions in 22 lines, 4 of which carried multiple insertion sites. Additionally, our analysis uncovered a high frequency of unconventional and complex T-DNA insertions, highlighting the needs for high-throughput methods for T-DNA localization and structural characterization. Transgene insertion events have to be fully characterized prior to use as commercial products. Our method greatly facilitates the first step of this characterization of transgenic plants by providing an efficient screen for the selection of promising lines.

Attention and otoacoustic emissions: a review.

The possible existence of an attention effect on the peripheral auditory system remains a controversial issue. The aim of the present study is to show the possible contribution of otoacoustic emissions towards demonstrating cognitive control of peripheral auditory processes via the auditory efferent fibers. This measurement technique allows investigation of a further part of the peripheral auditory pathways and of whether efferent fibers, presumably involved in cochlear neurosensory activity, could mediate an attention effect by the selection of auditory information.

Respiratory syncytial virus nucleocapsid protein (N) expressed in insect cells forms nucleocapsid-like structures.

The gene coding for the N protein of RSV strain Long has been cloned and sequenced. It was introduced behind the polyhedrin promoter of the shuttle vector pVL941 and baculoviruses containing the N gene were constructed by homologous recombination. Infection of Spodoptera frugiperda 9 cells resulted in the production of large amounts of a protein similar in size and antigenicity to the authentic N protein. The baculovirus expressed N protein was concentrated in the cytoplasm of the insect cells and could be extracted at low salt concentration. Nucleocapsid structures similar to those purified from RSV-infected cells could be observed by electron microscopy after negative staining of cellular extracts.

Attention and evoked otoacoustic emissions: attempts at characterization of intersubject variation.

The present study has two aims: to define the visual attention effect on evoked otoacoustic emissions (EOAEs) found in several previous studies: a first experiment sought to determine the conditions necessary to produce such an effect, and found that, neither the complexity nor the duration of the task modified results obtained under attention conditions. The second experiment sought to characterize the great intersubject variation found in most visual attention studies; two possible explanations are discussed: medial efferent system activity, assessed through the recording of otoacoustic emissions, or subject "attention profile" as drawn from a questionnaire.

Differential effects of visual attention on spontaneous and evoked otoacoustic emissions.

A visual task decreases evoked otoacoustic emissions (TEOAE) to an interindividually variable degree. The aim of these two studies was to assess whether the presence or absence of spontaneous otoacoustic emissions (SOAE) is involved in this variability. The first experiment investigated spontaneous otoacoustic emission (SOAE) frequency shifts during a visual attention task with a Fast Fourier Transform analysis, and found no attention effect on SOAEs. Using a larger subject pool, the second experiment concerned the attention effect on transiently evoked otoacoustic emissions and SOAE amplitude, using different measurement methods with the same visual task. The sample was composed of two groups of subjects: group A comprising subjects presenting SOAEs and group B subjects without SOAEs. A decrease in EOAE amplitude for group B during attention was observed and seems to confirm a possible influence of attention on the cochlea via the medial olivocochlear efferent system (MOES). The TEOAE amplitude of group A did not vary during attention, showing the peculiarity of this population of subjects and suggesting a different cochlear functioning.

Visual attention and evoked otoacoustic emissions: a slight but real effect.

The effect of auditory or visual attention tasks on the peripheral auditory system, studied by Brainstem Auditory Evoked Potentials (BAEPs), electrocochleography or Evoked Oto-Acoustic Emissions (EOAEs), has been a subject of controversy. To investigate the divergences in findings, a study using EOAE and visual and auditory attention was run on 12 subjects. A significant effect during visual attention was obtained. A general diminution of EOAEs of 0.35 dB (equivalent reduction) was found. This result seems to prove that BAEPs are not the best technique to reveal the effect of attention on cochlear mechanisms, because of the weakness of the effect.

Comparative influence of repeated measurement and of attention on evoked otoacoustic emissions.

This study compared the influence of an auditory attention task and of repetitive measures on the peripheral auditory system, using evoked otoacoustic emissions (EOAEs). The experimental task protocol comprised three sessions (pre-control, attention and post-control conditions) with, in each session, six measurements of EOAEs, at intervals of about 60 seconds, while the other ear was receiving two pure tones of 2,500 and 750 Hz, with a probability of appearance of 20% and 80%, respectively. In the contralateral attention condition, the subject had to count the number of the less frequent high pitched sounds. A long duration protocol (20 min for the total experiment) was used in order to examine a possible time-effect on EOAEs. An increase in EOAE amplitude during the second and third sessions, with linear saturation around the last measurements, was observed. While no attention effect could be identified, a time-effect seemed to be present. Possible explanations for the influence of repeated measurements on EOAEs are discussed. Moreover, EOAE amplitudes of subjects presenting spontaneous otoacoustic emissions were compared to those of subjects without SOAEs: significant differences were found, showing the particularity of cochleas emitting SOAEs.

Validation assessment of a French version of the tinnitus reaction questionnaire: a comparison between data from English and French versions.

The present study compares the results obtained on original and French versions of the TRQ (Tinnitus Reaction Questionnaire) initially published by Wilson, Henry, Bowen, and Haralambous (1991) in English to evaluate the psychological distress of tinnitus sufferers. Reliability and validity of the French translation were determined using data from 173 normal hearing or hearing-impaired patients with tinnitus lasting from 1 month to 41 years. They completed the translated questionnaire and a short version of the Minnesota Multiphasic Personality Inventory. The results indicated good internal consistency (Cronbach's alpha = .94), and the reliability of the French version of the TRQ was demonstrated, except for items 5 and 20. High statistically significant correlations were found between the TRQ and Depression, Psychaesthenia, and Anxiety Mini-Mult subscales. The validation demonstrates only minor effects of language. The French version of the TRQ thus is an equally valid tool as the original English version for evaluating tinnitus distress of a patient.

[Validation of French translation of the "Tinnitus Reaction Questionnaire", Wilson et al. 1991]. / Validation d'une traduction française du questionnaire "mesure de la détresse liée à l'acouphène (Tinnitus Reaction Questionnaire, Wilson et al. 1991).

The present study proposes a validation of a french translation of the TRQ initially published by Wilson et al., for evaluating the psychological distress of tinnitus sufferers. The 26 items translated into french were used on a sample of 173 tinnitus sufferers, who also filled out the Mini-Mult, a short version of the MMPI proposed by Kincannon. Internal validity was demonstrated by strong correlations (i) between each item (except items 5 and 20) and total TRQ score (0.33 < or = r < or = 0.87, p < or = 0.0001), (ii) between each internal TRQ factor (0.58 < r < 0.81, p < 0.0001) and the others. Cronbach's alpha test also showed the questionnaire to have a good internal validity (alpha = 0.94). The external factors used for testing concurrent validity were the scores on depression, psychaesthenia and anxiety Mini-Mult scales. The strong correlations (one factor ANOVA and simple linear regression tests) between scores on depression and psychaesthenia scales and (1) each TRQ item, (2) each TRQ factor, (3) total TRQ scores, confirmed concurrent validity. Scores obtained on anxiety index showed high correlations only with TRQ score, factor 3 score and some TRQ items (most of them included in factor 3). The internal and concurrent validities of the French version of the TRQ justify the use of this questionnaire, with the reserve that items 5 and 20 appeared irrelevant for the measuring of tinnitus distress in French-speaking countries. Such a questionnaire should improve our knowledge of tinnitus' life-impact and enable detection of patients whose psychological distress necessitates rapid intervention.

Women with polycystic ovary syndrome have increased plasma chitotriosidase activity: a pathophysiological link between inflammation and impaired insulin sensitivity?

Polycystic ovary syndrome (PCOS) is characterized by insulin resistance. Chronic low grade inflammation has been reported to participate in the pathogenesis of insulin resistance. Chitotriosidase (ChT), a protein secreted by activated macrophages, has been shown to be involved in chronic inflammatory responses. In the present study, serum chitotriosidase activity and its relationship with insulin resistance were determined in patients with PCOS.34 patients with PCOS and 44 age and body mass index (BMI) matched healthy controls were enrolled in the study. ChT activity was measured by the fluorescence method. High sensitivity C reactive protein (hs-CRP) and adiponectin levels were determined by enzyme immunoassay (EIA). Insulin resistance was calculated by the homeostasis model assessment of insulin resistance (HOMA-IR) formula.Plasma ChT activity, hs-CRP level and HOMA-IR score were significantly higher (p=0.024, p=0.002, p=0.001, respectively) while plasma adiponectin concentration was significantly lower (p=0.018) in women with PCOS compared to healthy controls. Blood ChT activity correlated positively with age, waist-to-hip ratio (WHR), BMI, hs-CRP, HOMA-IR and negatively with blood adiponectin level. After adjustment for age and BMI, ChT activity, total testosterone level and WHR remained as the independent predictors of HOMA-IR score in logistic regression analysis.ChT activity is increased in patients with PCOS in concordance with insulin resistance. These findings may reflect the pronounced risk for metabolic syndrome and atherosclerotic diseases in this particular patient group.