Exonic Re-Sequencing of the Chromosome 2q24.3 Parkinson’s Disease Locus

Genome-wide association studies (GWAS) in Parkinson’s disease (PD) have identified over 20 genomic regions associated with disease risk. Many of these loci include several candidate genes making it difficult to pinpoint the causal gene. The locus on chromosome 2q24.3 encompasses three genes: B3GALT1, STK39, and CERS6. In order to identify if the causal variants are simple missense changes, we sequenced all 31 exons of these three genes in 187 patients with PD. We identified 13 exonic variants including four non-synonymous and three insertion/deletion variants (indels). These non-synonymous variants and rs2102808, the GWAS tag SNP, were genotyped in three independent series consisting of a total of 1976 patients and 1596 controls. Our results show that the seven identified 2q24.3 coding variants are not independently responsible for the GWAS association signal at the locus; however, there is a haplotype, which contains both rs2102808 and a STK39 exon 1 6bp indel variant, that is significantly associated with PD risk (Odds Ratio [OR] = 1.35, 95% CI: 1.11–1.64, P = 0.003). This haplotype is more associated than each of the two variants independently (OR = 1.23, P = 0.005 and 1.10, P = 0.10, respectively). Our findings suggest that the risk variant is likely located in a non-coding region. Additional sequencing of the locus including promoter and regulatory regions will be needed to pinpoint the association at this locus that leads to an increased risk to PD.     

Random BAC FISH of monocot plants reveals differential distribution of repetitive DNA elements in small and large chromosome species

BAC FISH (fluorescence in situ hybridization using bacterial artificial chromosome probes) is a useful cytogenetic technique for physical mapping, chromosome marker screening, and comparative genomics. As a large genomic fragment with repetitive sequences is inserted in each BAC clone, random BAC FISH without adding competitive DNA can unveil complex chromosome organization of the repetitive elements in plants. Here we performed the comparative analysis of the random BAC FISH in monocot plants including species having small chromosomes (rice and asparagus) and those having large chromosomes (hexaploid wheat, onion, and spider lily) in order to understand a whole view of the repetitive element organization in Poales and Asparagales monocots. More unique and less dense dispersed signals of BAC FISH were observed in species with smaller chromosomes in both the Poales and Asparagales species. In the case of large-chromosome species, 75-85% of the BAC clones were detected as dispersed repetitive FISH signals along entire chromosomes. The BAC FISH of Lycoris did not even show localized repetitive patterns (e.g., centromeric localization) of signals.     

Diversity,ecology, and bioprospecting of culturable fungi in lakes impacted by anthropogenic activities in Maritime Antarctica

In this study, we accessed culturable fungal assemblages present in the sediments of three lakes potentially impacted anthropogenically in the Fildes Peninsula, King George Island, Antarctica and identified 63 taxa. Cladosporium sp. 2, Pseudeurotium hygrophilum, and Pseudogymnoascus verrucosus were recovered from the sampled sediments of all lakes. High concentrations of metals and the lowest fungal diversity indices were detected in the sediments of the Central Lake, which can be influenced by human activities due to their proximity to research stations to those of the other two lakes, which were far from the Antarctic stations. At least one type of biological activity was demonstrated by 40 fungal extracts. Among these, P. hygrophilum, P. verrucosus, Penicillium glabrum, and Penicillium solitum demonstrated strong trypanocidal, herbicidal, and antifungal activities. Our results suggest that an increase of the anthropogenic activities in the region might have affected the microbial diversity and composition. In addition, the fungal diversity in these lakes may be a useful model to study the effect of anthropogenic activities in Antarctica. We isolated a diverse group of fungal taxa from Antarctic lake sediments, which have the potential to produce novel compounds for the both the medical and agriculture sectors.

     

Occurrence of galactosamine-6-phosphate as a constituent of Bacillus megaterium spore coat

Galactosamine-6-phosphate was identified as a component of the coat of the Bacillus megaterium QM B1551 spore. It was one of the main constituents of the outermost layer of the spore coat, but it was absent from the other integuments including the cortex. These findings suggest that galactosamine-6-phosphate comprises the phosphorus-containing skeleton structure of the spore coat.     

Importance of co-cultivation medium pH for successful Agrobacterium-mediated transformation of Lilium × formolongi

An efficient system for Agrobacterium-mediated transformation of Lilium × formolongi was established by preventing the drastic drop of pH in the co-cultivation medium with MES. Meristematic nodular calli were inoculated with an overnight culture of A. tumefaciens strain EHA101 containing the plasmid pIG121-Hm which harbored intron-containing β-glucuronidase (GUS), hygromycin phosphotransferase (HPT), and neomycin phosphotransfease II (NPTII) genes. After three days of co-cultivation on 2 g/l gellan gum-solidified MS medium containing 100 μM acetosyringone, 30 g/l sucrose, 1 mg/l picloram and different concentrations of MES, they were cultured on the same medium containing 12.5 mg/l meropenem to eliminate Agrobacterium for 2 weeks and then transferred onto medium containing the same concentration of meropenem and 25 mg/l hygromycin for selecting putative transgenic calli. Transient GUS expression was only observed by adding MES to co-cultivation medium. Hygromycin-resistant transgenic calli were obtained only when MES was added to the co-cultivation medium especially at 10 mM. The hygromycin-resistant calli were successfully regenerated into plantlets after transferring onto picloram-free medium. Transformation of plants was confirmed by histochemical GUS assay, PCR analysis and Southern blot analysis.     

Does the regional oxygen uptake measured by near infrared spectroscopy reflect the phase II pulmonary oxygen uptake at the onset of exercise?

It has been hypothesized that the signals of near infrared spectroscopy (NIRS) would reflect muscle O(2) uptake (mVO(2)). Although it is not definite that NIRS signals accurately reflect mVO(2), there is every possibility that NIRS signals at least reflect regional O(2) uptake (rVO(2)). The phase II kinetics of pulmonary oxygen uptake (pVO(2)) is regarded as reflecting mVO(2) at the onset of exercise. To examine whether the rVO(2) on-kinetics measured by NIRS reflects the mVO(2) on-kinetics at the onset of exercise, we compared the rVO(2) as measured by NIRS with the phase II kinetics of pVO(2) at the onset of exercise. Twelve healthy male subjects cycled a Monark ergometer at three different intensities: below the ventilatory threshold (VT) level (below-VT), on the VT level (on-VT), and above the VT level (above-VT), for 6 minutes on three separate occasions. The rVO(2) was calculated from the concentration of oxyhemoglobin and deoxyhemoglobin, as measured by NIRS every 3 seconds. The pVO(2) was determined by the breath-by-breath method. A significant relationship between the amount of increases of pVO(2) and rVO(2) from rest to the end of exercise among all levels of exercise intensity was found (r=0.935, P<0.001). The time constants of rVO(2) (rVO(2)-Tc: below-VT: 6.514+/-2.159 s, on-VT: 7.760+/-2.035 s, above-VT: 9.532+/-2.342 s) were significantly faster than the time constants of pVO(2) (pVO(2)-Tc: below-VT: 23.8+/-4.4 s, on-VT: 25.9+/-5.1 s, above-VT: 26.3+/-5.7 s) (P<0.001). There was no significant relationship between rVO(2)-Tc and pVO(2)-Tc for each intensity (P>0.05). We conclude that the rVO(2) on-kinetics measured by NIRS does not necessarily reflect the mVO(2) kinetics at the onset of exercise.     

Relationship between cerebral activity and movement frequency of maximal finger tapping

To examine the cerebral activity of the motor cortex during maximum movement, we measured regional cerebral blood flow (rCBF) in twelve normal volunteers, using near infrared spectroscopy (NIRS). Repetitive tapping of the right index finger was performed at 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, and 4.5 Hz, and during maximum effort (ME). The relative increase rate of rCBF during movement beginning with a resting condition was calculated for each movement condition. The left primary sensorimotor cortex showed significant activation during ME compared to the other frequencies. The rapid increase of rCBF was seen immediately after the initiation of finger tapping at all the tested frequencies but showed no increase following that. However, the rCBF during ME continued to increase until the end of the task.Change of the integrated electromyogram (iEMG) for the frequency and change of rCBF for the frequency at all the tested frequencies showed similar tendencies.