SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation.

Genetic diversity was studied in a collection of 61 accessions of Brassica rapa, which were mostly oil-type turnip rapes but also included two oil-type subsp. dichotoma and five subsp. trilocularis accessions, as well as three leaf-type subspecies (subsp. japonica, pekinensis, and chinensis) and five turnip cultivars (subsp. rapa). Two-hundred and nine SNP markers, which had been discovered by amplicon resequencing, were used to genotype 893 plants from the B. rapa collection using Illumina BeadXpress. There was great variation in the diversity indices between accessions. With STRUCTURE analysis, the plant collection could be divided into three groups that seemed to correspond to morphotype and flowering habit but not to geography. According to AMOVA analysis, 65% of the variation was due to variation within accessions, 25% among accessions, and 10% among groups. A smaller subset of the plant collection, 12 accessions, was also studied with 5727 GBS-SNPs. Diversity indices obtained with GBS-SNPs correlated well with those obtained with Illumina BeadXpress SNPs. The developed SNP markers have already been used and will be used in future plant breeding programs as well as in mapping and diversity studies.

High SSR diversity but little differentiation between accessions of Nordic timothy (Phleum pratense L.).

A large collection of genebank accessions of the hexaploid outcrossing forage grass species timothy (Phleum pratense L.) was for the first time analysed for SSR diversity on individual, population and regional level. Timothy is the most important forage grass species in the Nordic countries. Eighty-eight timothy accessions from Nordic countries and eight accessions around Europe were analysed with recently developed simple sequence repeat (SSR) markers. Timothy proved to be very polymorphic: the 13 selected SSRs amplified a total of 499 polymorphic alleles, the number of alleles per SSR locus varying from 15 to 74. Taking all SSR alleles together, the observed number in each accession ranged from 95 to 203. Levels of diversity were found to be significantly different between countries, vegetation zones and different cultivar types. However, the differentiation between accessions was low: most of the variation (94%) in the studied timothy material was due to variation within accessions and only 5% was between accessions and 1% between countries. Lack of geographical differentiation may reflect the outcrossing and hexaploid nature of timothy. Our results showed that neutral SSR markers are suitable for demonstrating levels of diversity but not alone adequate to resolve population structure in timothy. Nordic timothy material seems to be diverse enough for breeding purposes and no decline in the level of diversity was observed in varieties compared to wild timothy populations. Challenges in analysing SSR marker data in a hexaploid outcrosser were discussed.

Galactolipid deficiency in the early pathogenesis of neuronal ceroid lipofuscinosis model Cln8mnd : implications to delayed myelination and oligodendrocyte maturation.

AIMS: CLN8 deficiency underlies one of a group of devastating childhood neurodegenerative disorders, the neuronal ceroid lipofuscinoses. The function of the CLN8 protein is currently unknown, but a role in lipid metabolism has been proposed. In human CLN8 diseased brains, alterations in lipid composition have been detected. To further investigate the connection of CLN8 to lipid metabolism, we characterized the lipid composition of early symptomatic Cln8-deficient mouse (Cln8(mnd)) brains. METHODS: For lipid profiling, Cln8(mnd) cerebral cortical tissue was analysed by liquid chromatography/mass spectrometry. Galactolipid synthesis was measured through enzyme activity and real-time mRNA expression analyses. Based on the findings, myelination and white matter integrity were studied by immunohistochemistry, stereological methods, electron microscopy and magnetic resonance imaging. The development of myelin-forming oligodendrocytes was also studied in vitro. RESULTS: Sphingolipid profiling showed a selective reduction in myelin-enriched galactolipids. The mRNA expression and activity of UDP-galactose:ceramide galactosyltransferase (CGT), the key enzyme in the galactolipid synthesis, was reduced in the Cln8(mnd) brain. Expression of oligodendrocyte markers suggests a maturation defect. The amount of myelin was reduced in 1-month-old Cln8(mnd) mice, but reached normal levels by 5 months of age. The level of Cln8 gene expression followed the developmental pattern of myelin formation and was high in primary oligodendrocytes. CONCLUSIONS: Taken together, these observations suggest that galactolipid deficiency and delayed myelin maturation characterize the early CLN8 disease pathogenesis through a maturation defect of oligodendrocytes.

Mapping of major spot-type and net-type net-blotch resistance genes in the Ethiopian barley line CI 9819.

Net blotch of barley (Hordeum vulgare L.), caused by the fungal phytopathogen Pyrenophora teres Drechs. f. teres Smedeg., constitutes one of the most serious constraints to barley production worldwide. Two forms of the disease, the net form, caused by P. teres f. teres, and the spot form, caused by P. teres f. maculata, are differentiated by the type of symptoms on leaves. Several barley lines with major gene resistance to net blotch have been identified. Earlier, one of these was mapped in the Rolfi x CI 9819 cross to barley chromosome 6H, using a mixture of 4 Finnish isolates of P. teres f. teres. In this study, we used the same barley progeny to map resistance to 4 spot-type isolates and 4 net-type isolates of P. teres. With all net-type isolates, a major resistance gene was located on chromosome 6H, in the same position as described previously, explaining up to 88% of the phenotypic variation in infection response in the progeny. We designate this gene Rpt5. Several minor resistance genes were located on chromosomes 1H, 2H, 3H, 5H, and 7H. These minor genes were not genuinely isolate-specific, but their effect varied among isolates and experiments. When the spot-type isolates were used for infection, a major isolate-specific resistance gene was located on chromosome 5H, close to microsatellite marker HVLEU, explaining up to 84% of the phenotypic variation in infection response in the progeny. We designate this gene Rpt6. No minor gene effects were detected in spot-type isolates. The Ethiopian 2-rowed barley line CI 9819 thus carries at least 2 independent major genes for net-blotch resistance: Rpt5, active against net-type isolates; and Rpt6, active against specific spot-type isolates.

Microsatellite diversity associated with ecological factors in Hordeum spontaneum populations in Israel.

Microsatellite diversity at 18 loci was analysed in 94 individual plants of 10 wild barley, Hordeum spontaneum (C. Koch) Thell., populations sampled from Israel across a southward transect of increasing aridity. Allelic distribution in populations was not distributed randomly. Estimates of mean gene diversity were highest in stressful arid-hot environments. Sixty-four per cent of the genetic variation was partitioned within populations and 36% between populations. Associations between ecogeographical variables and gene diversity, H(e), were established in nine microsatellite loci. By employing principle component analysis we reduced the number of ecogeographical variables to three principal components including water factors, temperature and geography. At three loci, stepwise multiple regression analysis explained significantly the gene diversity by a single principal component (water factors). Based on these observations it is suggested that simple sequence repeats are not necessarily biologically neutral.

Application of BARE-1 retrotransposon markers to the mapping of a major resistance gene for net blotch in barley.

Net blotch, which is caused by the fungus Pyrenophoral teres Drechs. f. teres Smedeg., presents a serious problem for barley production worldwide, and the identification and deployment of sources of resistance to it are key objectives for many breeders. Here, we report the identification of a major resistance gene, accounting for 65% of the response variation, in a cross between the resistant line C19819 and the susceptible cv. Rolfi. The resistance gene was mapped to chromosome 6H with the aid of two recently developed systems of retrotransposon-based molecular markers, REMAP and IRAP. A total of 239 BARE-1 and Sukkula retrotransposon markers were mapped in the cross, and the 30-cM segment containing the locus with significant resistance effect contained 26 of the markers. The type and local density of the markers should facilitate future map-based cloning of the resistance gene as well as manipulation of the resistance through backcross breeding.

Changes in hearing, cardiovascular functions, haemodynamics, upright body sway, urinary catecholamines and their correlates after prolonged successive exposures to complex environmental conditions.

This study deals with changes in temporary threshold shifts of hearing (TTS2), cardiovascular functions (HR, SBP, DBP, PP, RWA), haemodynamic activity (HDI), upright body sway (VUBSA), ratios of urinary catecholamines (10A/DA, 10NA/DA, A/NA, NA/A) and correlations between these changes in complex exposure situations. The study was carried out in a special exposure chamber on 60 healthy male students. It was based on a factorial experimental design with a total of 12 exposure combinations. Each individual experiment took 6 h with a pause of 1 h at noon. There were 12 sequential exposure periods lasting 16 min each. A pause of 4 min followed each exposure period. The subjects were exposed to noise and whole body vibration at two different dry bulb temperatures. Noise classes were: (1) no noise, and (2) stable broad-band noise of 90 dBA. Vibration classes were: (1) no vibration, (2) a sinusoidal 5 Hz vibration, and (3) a stochastic vibration with a frequency range of 2.8 to 11.2 Hz along the Z-axis and with an acceleration of 2.12 m/s2. Temperature classes were: (1) 20 degrees C and (2) 35 degrees C. Changes in body functions were registered during the pauses. Urine samples were gathered for the morning and afternoon sessions and for the preceding and the following night of the test. The changes were dependent on the combinations of noise, vibration and temperature to which the subjects were exposed. The TTS2 values at 4 kHz were associated with the HDI-values when subjects were exposed simultaneously to noise and stochastic vibration at 35 degrees C. The TTS2 values at 6 kHz were associated most strongly with the HDI values after exposure to a combination of noise, stochastic or sinusoidal vibration and a temperature of 20 degrees C. The TTS2 values at 4 and 6 kHz correlated positively with the NA/A ratio when subjects were exposed to noise at 35 degrees C. The association between TTS2 values and the 10A/NA ratio and especially the A/NA ratio was very strong when subjects had been simultaneously exposed to noise and sinusoidal or stochastic vibration at 35 degrees C. Furthermore, the highest positive correlation coefficients were found between TTS2 values at 4 kHz and VUBSA values in the X-direction when subjects had been exposed to noise or simultaneously to noise and sinusoidal vibration at 20 degrees C.(ABSTRACT TRUNCATED AT 400 WORDS)

Bioresponses in men after repeated exposures to single and simultaneous sinusoidal or stochastic whole body vibrations of varying bandwidths and noise.

This study deals with the changes in temporary hearing threshold (TTS2), upright body posture sway amplitudes in the X and Y direction, heart rate (HR), R-wave amplitude (RWA), systolic (SBP) and diastolic (DBP) blood pressure, pulse pressure (PP) and the index characterizing haemodynamic activity (HDI), when the subjects were exposed to noise alone, to vibrations alone or to simultaneous noise and vibrations. The experiments were carried out in an exposure chamber and the number of exposure combinations was 12. Seven healthy, male students volunteered as subjects, making a total number of 84 experiments. For each person the experiment consisted of a 30-min control period, five consecutive 16-min exposures, between which there was a 4-min measuring interval, and a 15-min recovery period. The noise was broadband (bandwidth 0.2-16.0 kHz) A-weighted (white) noise. The noise categories were: (1) no noise and (2) noise with an intensity of 90 dBA. The categories of low-frequency whole body vibration in the direction of the Z-axis were: (1) vibration within the range 4.4-5.6 Hz, (2) vibration within the range 2.8-5.6 Hz, (3) vibration within the range 2.8-11.2 Hz, (4) vibration within the range 1.4-11.2 Hz and (5) sinusoidal vibration with a frequency of 5 Hz. The (rms) acceleration in all the vibration models was 2.12 m/s2. The results showed that the TTS2 values at 4 and 6 kHz increased as a result of simultaneous exposure to noise and vibration significantly more than as a result of exposure to noise alone. The TTS2 values increased more intensely during the first 16-min exposure. The means of the variances in the amplitudes of body upright posture sway changed not only after exposures to vibration alone, but also after exposure to noise alone. The means of the sway variances in the X and Y directions at 0.1 Hz and within the range 0.06 to 2.00 Hz increased only when the vibration in the noise-vibration combination was sinusoidal. The changes in the heart rate, R-wave amplitude and blood pressure values also depended on the bandwidth of the vibration, the number of consecutive exposures and on whether the subjects were simultaneously exposed to noise in addition to vibration. As a rule, the effects of sinusoidal vibration differed from those due to stochastic vibrations.

Cardiovascular changes and hearing threshold shifts in men under complex exposures to noise, whole body vibrations, temperatures and competition-type psychic load.

This study deals with changes in the temporary hearing threshold (TTS2), heart rate (HR), R-wave amplitude (RWA), diastolic blood pressure (DBP), systolic blood pressure (SBP), pulse pressure (PP) and reaction time (RT) in subjects (n = 108) who, while working on a choice reaction apparatus, were exposed in an exposure chamber to combinations of noise and vibration at dry bulb temperatures of 20 degrees and 30 degrees C. The study was carried out as a type 2-3-3 factorial experiment, the number of the exposure combinations thus being 18. To find out the effects of competition-type psychic stress, some of the subjects were placed in a competitive group and some in a non-competitive group. The members of the competitive group were given financial encouragement and information on their progress during the test, whereas those in the non-competitive group worked at the rate they considered best without any monetary rewards or interim information. The noise classes were: no noise, a stable broadband (bandwidth 0.2-16.0 kHz) A-weighted noise of 90 dB not related to competition, and a stable broadband A-weighted noise of 90 dB related to competition about the fastest reaction time. The vibration classes were: no vibration, sinusoidal whole body vibration (Z-axis) at a frequency of 5 Hz, and stochastic broadband (bandwidth 2.8-11.2 Hz) whole body vibration (Z-axis). The acceleration (rms) of both vibrations was 2.12 m/s2. One experiment consisted of a control period of 30 min, three consecutive exposure periods of 16 min with an interval of 4 min, and a 15-min recovery period. The variance analysis model best explained the variation in TTS2 values at 4 kHz and second best the variation in TTS2 values at 6 kHz; it explained the variation in HR values third best, the variation in SBP values fourth best and the variation in PP values fifth best. On the other hand, the model explained least well the variation in DBP and RWA values. In general, the explanatory power of the model increased together with the number of exposures. The psychic stress caused by competition accelerated the growth of the TTS2 values, HR values and SBP values, when the subjects were simultaneously exposed to noise or to a combination of noise and vibration. An interesting finding for the continuation of the research project was that sinusoidal and stochastic vibration affected the cardiovascular changes, temporary hearing threshold and reaction times in different ways.

Single and joint actions of noise and sinusoidal whole body vibration on TTS2 values and low frequency upright posture sway in men.

In the present study the changes in the TTS2 values and body upright posture sway were examined after exposure of subjects (n = 10) to stable broadband (white) noise (90 dB) alone, to sinusoidal vibration alone [directed vertically at the whole body (Z axis)], and to simultaneous exposure combinations of noise and vibrations of the same type. The frequency of the vibration was 5 Hz, but its acceleration was either 2.12 or 2.44 m/s2. There were six exposure combinations, and subsequently 60 tests were carried out in an exposure chamber. One test consisted of a control period of 30 min, of three consecutive exposure periods of 16 min each and of a recovery period of 15 min. After the three exposure combinations which included noise, half of the subjects were exposed to vibration during the recovery period. Apart from indicating an increase in the temporary hearing threshold, the results showed that simultaneous exposure to noise and vibration increases the instability of the body upright posture. The TTS2 values at the 4 and 6 kHz frequencies increased considerably more rapidly when the subjects were exposed simultaneously to noise and vibration than when exposed to noise alone. Without exception, the TTS2 values increased most during the first exposure period. It was noteworthy that exposure to vibration during the recovery period accelerated the recursion of the TTS2 values, especially in cases where the subjects had been exposed to noise alone. The variance of the body sway amplitudes and the standard deviation increased within the frequency range 0.063-2.000 Hz owing to noise alone and simultaneous noise and vibration. In the directions X and Y, within the frequency ranges 0.063-0.100 Hz and 0.100-0.600 Hz, the means of the maximum amplitudes of body sway increased especially in connection with those tests in which the subjects had been simultaneously exposed to noise and vibration.

Hearing threshold and heart rate in men after repeated exposure to dynamic muscle work, sinusoidal vs stochastic whole body vibration and stable broadband noise.

Changes in the temporary hearing threshold ( TTS2 ) and heart rate (HR) were examined in subjects exposed to stable noise, whole body vibration and dynamic muscular work at a dry-bulb temperature of 30 degrees C. The exposure combinations consisted of three categories of dynamic muscular work with varying loads ( 2W , 4W , 8W ), of two categories of noise and of three categories of vibration. The noise categories were: (1) no noise, and (2) stable, broadband (bandwidth 0.2-16.0 kHz) A-weighted noise with an intensity of 90 dB. The vibration categories were: (1) no vibration, (2) sinusoidal whole body vibration (Z-axis) with a frequency of 5 Hz, and (3) stochastic broadband (bandwidth 2.8-11.2 Hz) whole body vibration. A single test consisted of a control period of 30 min, three consecutive exposure periods of 16 min, each followed by a 4-min post-exposure interval and a recovery period of 15 min. The results of the variance analyses indicated that noise had the most notable effect on the TTS2 values at the hearing frequencies of both 4 and 6 kHz. Of the paired combinations, noise plus vibration and noise plus dynamic muscular work caused the most obvious combined effects. The combined effect of all three factors (noise, vibration and work) on the TTS2 values after three consecutive exposure periods was significant at the 2.5% level at the 4 kHz hearing frequency and at the 5% level at the 6 kHz hearing frequency. The added effect of vibration on enhanced TTS2 values was particularly clear when the vibration was stochastic and when the subjects had a low ( 2W ) working efficiency. Increasing the working efficiency, on the other hand, seemed to retard increases in the hearing threshold. Thus TTS2 values seemed to reflect the changes in HR values. It is as if the low rate of cardiovascular activity during light dynamic muscular work had enabled the manifestation of the cardiovascular effects of noise and vibration; during strenuous dynamic muscular work, however, the high rate of cardiovascular activity aimed in some way at compensating for the effects of noise and vibration on blood circulation.

Simultaneous effects of sinusoidal whole body vibration and broadband noise on TTS2's and R-wave amplitudes in men at two different dry bulb temperatures.

The aim of this study was to investigate the temporary hearing threshold shift (TTS2) and R-wave amplitudes in eleven healthy males when they were exposed to paired sinusoidal whole body (Z-axis) vibration (5 Hz--2.12 m/s2) and stable broadband A-weighted white noise at dry bulb temperatures of 20 degrees C and 30 degrees C. The intensity of noise in the exposure combinations was 75, 85 and 95 dB(A). The total number of tests was 66, and they were carried out in an exposure chamber. The subjects were dressed in standard clothing, and carried out simple tasks using a choice reaction time device during the test. According to the results, the means of the TTS2 values were usually higher at the dry bulb temperature of 30 degrees C than at 20 degrees C. Hearing threshold shifts were the greatest at frequencies of 4 and 6 kHz, and the smallest at 8 kHz. The more intense the noise in the paired combination of noise and vibration, the clearer the tendency for an increase in the ambient temperature to accelerate the increase in the hearing threshold. The effect of the ambient temperature on the temporary hearing threshold shifts also appeared to be slightly stronger during successive exposure cycles. Changes in the values for the R-wave amplitudes seemed to be connected with those in the hearing threshold. The decrease in the R-wave amplitude was connected to the increase in the TTS2 values, especially when the subjects were simultaneously exposed to a 95 dB(A) noise and whole body vibration at the dry bulb temperature of 30 degrees C. This implies that an increase in the ambient temperature intensifies cardiovascular disturbances in the body, which accelerate the development of functional disturbance in the inner ear.

Studies of combined effects of sinusoidal whole body vibrations and noise of varying bandwidths and intensities on TTS2 in men.

This study analyses the data from three laboratory experiments concerning the separate and combined effects on temporary threshold shifts in hearing (TTS2) of sinusoidal low-frequency (5 Hz--2.12 m/s2 and 10 Hz--2.65 m/s2), whole body vibration (along the Z-axis), and continuous (white) noise with eight different bandwidths and intensity levels of 85 dB(A), 90 dB(A) and 98 dB(A). Altogether 370 separate personal experiments were performed using a one-man exposure chamber system. A single experiment consisted of a 30-min pre-exposure period, three 16-min exposure periods, and a 15-min post-exposure period. The data suggested that the TTS2 induced by noise was increased by vibration. Actually, vibration at a frequency of 5 Hz and noise with bandwidths of 1-4 kHz, 1-8 kHz or 0.2-16 kHz comprised the most significant exposure combinations. After such exposures, the increase in TTS2 values was defined most clearly for 4 kHz and 6 kHz test frequencies. The increase of thresholds was most marked during the first 16-min exposure period, even though most TTS2 values determined after the third consecutive exposure period were higher than after the first and second exposures. Figures obtained after the third exposure period proved that exposure to simultaneous vibration and broad band noise (i.e. noise with a bandwidth of 0.2-16 kHz) increased TTS2 values 1.2-1.5 times more in the 4 kHz audio range than such a broad band noise alone. No single vibration condition induced the same amount of TTS2.