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31.
Robert HS Kraus Hindrik HD Kerstens Pim Van Hooft Richard PMA Crooijmans Jan J Van Der Poel Johan Elmberg Alain Vignal Yinhua Huang Ning Li Herbert HT Prins Martien AM Groenen 《BMC genomics》2011,12(1):150
Background
Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl.Results
More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72.Conclusion
We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.32.
Robert HS Kraus Anne Zeddeman Pim van Hooft Dmitry Sartakov Sergei A Soloviev Ronald C Ydenberg Herbert HT Prins 《BMC genetics》2011,12(1):1-15
Background
Yami and Ivatan islanders are Austronesian speakers from Orchid Island and the Batanes archipelago that are located between Taiwan and the Philippines. The paternal genealogies of the Yami tribe from 1962 monograph of Wei and Liu were compared with our dataset of non-recombining Y (NRY) chromosomes from the corresponding families. Then mitochondrial DNA polymorphism was also analyzed to determine the matrilineal relationships between Yami, Ivatan, and other East Asian populations.Results
The family relationships inferred from the NRY Phylogeny suggested a low number of paternal founders and agreed with the genealogy of Wei and Liu (P < 0.01). Except for one Y short tandem repeat lineage (Y-STR), seen in two unrelated Yami families, no other Y-STR lineages were shared between villages, whereas mtDNA haplotypes were indiscriminately distributed throughout Orchid Island. The genetic affinity seen between Yami and Taiwanese aborigines or between Ivatan and the Philippine people was closer than that between Yami and Ivatan, suggesting that the Orchid islanders were colonized separately by their nearest neighbors and bred in isolation. However a northward gene flow to Orchid Island from the Philippines was suspected as Yami and Ivatan peoples both speak Western Malayo-Polynesian languages which are not spoken in Taiwan. Actually, only very little gene flow was observed between Yami and Ivatan or between Yami and the Philippines as indicated by the sharing of mtDNA haplogroup B4a1a4 and one O1a1* Y-STR lineage.Conclusions
The NRY and mtDNA genetic information among Yami tribe peoples fitted well the patrilocal society model proposed by Wei and Liu. In this proposal, there were likely few genetic exchanges among Yami and the Philippine people. Trading activities may have contributed to the diffusion of Malayo-Polynesian languages among them. Finally, artifacts dating 4,000 YBP, found on Orchid Island and indicating association with the Out of Taiwan hypothesis might be related to a pioneering stage of settlement, as most dating estimates inferred from DNA variation in our data set ranged between 100-3,000 YBP. 相似文献33.
Luisa?Pastò Emilio?Portaccio Angelo?Ghezzi Bahia?Hakiki Marta?Giannini Lorenzo?Razzolini Elisa?Piscolla Laura?De Giglio Carlo?Pozzilli Damiano?Paolicelli Maria?Trojano Maria?Giovanna?Marrosu Francesco?Patti Loredana?La Mantia Gian?Luigi?Mancardi Claudio?Solaro Rocco?Totaro Maria?Rosaria?Tola Valeria?Di Tommaso Alessandra?Lugaresi Lucia?Moiola Vittorio?Martinelli Giancarlo?Comi Maria?Pia?AmatoEmail author and for the MS Study Group of the Italian Neurological Society 《BMC neurology》2012,12(1):165
Background
Few studies have systematically addressed the role of epidural analgesia and caesarean delivery in predicting the post-partum disease activity in women with Multiple Sclerosis (MS).The objective of this study was to assess the impact of epidural analgesia (EA) and caesarean delivery (CD) on the risk of post-partum relapses and disability in women with MS.Methods
In the context of an Italian prospective study on the safety of immunomodulators in pregnancy, we included pregnancies occurred between 2002 and 2008 in women with MS regularly followed-up in 21 Italian MS centers. Data were gathered through a standardized, semi-structured interview, dealing with pregnancy outcomes, breastfeeding, type of delivery (vaginal or caesarean) and EA. The risk of post-partum relapses and disability progression (1 point on the Expanded Disability Status Sclae, EDSS, point, confirmed after six months) was assessed through a logistic multivariate regression analysis.Results
We collected data on 423 pregnancies in 415 women. Among these, 349 pregnancies resulted in full term deliveries, with a post-partum follow-up of at least one year (mean follow-up period 5.5±3.1 years). One hundred and fifty-five patients (44.4%) underwent CD and 65 (18.5%) EA. In the multivariate analysis neither CD, nor EA were associated with a higher risk of post-partum relapses. Post-partum relapses were related to a higher EDSS score at conception (OR=1.42; 95% CI 1.11-1.82; p=0.005), a higher number of relapses in the year before pregnancy (OR=1.62; 95% CI 1.15-2.29; p=0.006) and during pregnancy (OR=3.07; 95% CI 1.40-6.72; p=0.005). Likewise, CD and EA were not associated with disability progression on the EDSS after delivery. The only significant predictor of disability progression was the occurrence of relapses in the year after delivery (disability progression in the year after delivery: OR= 4.00; 95% CI 2.0-8.2; p<0.001; disability progression over the whole follow-up period: OR= 2.0; 95% CI 1.2-3.3; p=0.005).Conclusions
Our findings, show no correlation between EA, CD and postpartum relapses and disability. Therefore these procedures can safely be applied in MS patients. On the other hand, post-partum relapses are significantly associated with increased disability, which calls for the need of preventive therapies after delivery.34.
Monocrotaline (MCT) is a hepatotoxic pyrrolizidine alkaloid that is derived from plants; exposure may occur by consumption of contaminated grains, herbal teas and medicines. MCT can cause liver damage. We investigated the antioxidant effects of selenium (Se) and vitamin E against the toxic effects of MCT. Female Wistar albino rats were divided into four groups: a control group, an MCT group, an MCT + Se group, and an MCT + vitamin E group. Liver tissues were harvested, fixed, processed to paraffin and sections were cut. Anti-von Willebrand factor (vWF) immunohistochemistry, terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL), and hematoxylin and eosin staining were performed. Serum and liver tissue glutathione (GSH), catalase (CAT), and glutathione peroxidase (GPx) levels were measured. Histopathological and TUNEL data showed significantly increased liver damage in the MCT group compared to controls. Histopathological and TUNEL staining indicated significant improvements in the MCT + vitamin E and MCT + Se groups compared to the MCT group. MCT significantly reduced the serum GSH level and GPx activity, and liver GPx activity. Biochemical data indicated a significant improvement in serum GSH level in the MCT + vitamin E group compared to the MCT group. We suggest that vitamin E and Se afford limited protection against MCT hepatotoxicity. 相似文献
35.
Margot ME Gosman Dirkje S Postma Judith M Vonk Bea Rutgers Monique Lodewijk Mieke Smith Marjan A Luinge Nick HT ten Hacken Wim Timens 《Respiratory research》2008,9(1):1-9
Background
Surfactant protein D (SP-D), an innate immune molecule, plays an important protective role during airway inflammation. Deficiency of this molecule induces emphysematous changes in murine lungs, but its significance in human COPD remains unclear.Methods
We collected bronchoalveolar lavage fluid from 20 subjects with varying degrees of COPD (8 former smokers and 12 current smokers) and 15 asymptomatic healthy control subjects (5 never smokers, 3 remote former smokers, and 7 current smokers). All subjects underwent a complete medical history and pulmonary function testing. SP-D was measured by Enzyme-Linked ImmunoSorbent Assay. Statistical analysis was performed using nonparametric methods and multivariable linear regression for control of confounding. The effect of corticosteroid treatment on SP-D synthesis was studied in vitro using an established model of isolated type II alveolar epithelial cell culture.Results
Among former smokers, those with COPD had significantly lower SP-D levels than healthy subjects (median 502 and 1067 ng/mL, respectively, p = 0.01). In a multivariable linear regression model controlling for age, sex, race, and pack-years of tobacco, COPD was independently associated with lower SP-D levels (model coefficient -539, p = 0.04) and inhaled corticosteroid use was independently associated with higher SP-D levels (398, p = 0.046). To support the hypothesis that corticosteroids increase SP-D production we used type II alveolar epithelial cells isolated from adult rat lungs. These cells responded to dexamethasone treatment by a significant increase of SP-D mRNA (p = 0.041) and protein (p = 0.037) production after 4 days of culture.Conclusion
Among former smokers, COPD is associated with lower levels of SP-D and inhaled corticosteroid use is associated with higher levels of SP-D in the lung. Dexamethasone induced SP-D mRNA and protein expression in isolated epithelial cells in vitro. Given the importance of this molecule as a modulator of innate immunity and inflammation in the lung, low levels may play a role in the pathogenesis and/or progression of COPD. Further, we speculate that inhaled steroids may induce SP-D expression and that this mechanism may contribute to their beneficial effects in COPD. Larger, prospective studies are warranted to further elucidate the role of surfactant protein D in modulating pulmonary inflammation and COPD pathogenesis. 相似文献36.
Murgia R Tola G Archer SN Vallerga S Hirano J 《Marine biotechnology (New York, N.Y.)》2002,4(2):119-126
Mitochondrial DNA sequencing was used to identify and distinguish four species of commercially important Mediterranean grey
mullets. Partial cytochrome b and D-loop sequences were obtained from the four fish species, and these were used to perform phylogenetic analysis and to
determine species-specific DNA fingerprints. Species-specific amplification primers were designed from these fingerprints,
and these were used to characterize the species origin of several samples of commercial, processed mullet ovary products.
In addition to differentiating between food products from different species, this method is also sensitive enough to distinguish
food products from mullets of the same species from different regions. 相似文献
37.
38.
Geoffroy Berthelot Muriel Tafflet Nour El Helou Stéphane Len Sylvie Escolano Marion Guillaume Hala Nassif Julien Tola?ni Valérie Thibault Fran?ois Denis Desgorces Olivier Hermine Jean-Fran?ois Toussaint 《PloS one》2010,5(1)
The growth law for the development of top athletes performances remains unknown in quantifiable sport events. Here we present a growth model for 41351 best performers from 70 track and field (T&F) and swimming events and detail their characteristics over the modern Olympic era. We show that 64% of T&F events no longer improved since 1993, while 47% of swimming events stagnated after 1990, prior to a second progression step starting in 2000. Since then, 100% of swimming events continued to progress.We also provide a measurement of the atypicity for the 3919 best performances (BP) of each year in every event. The secular evolution of this parameter for T&F reveals four peaks; the most recent (1988) followed by a major stagnation. This last peak may correspond to the most recent successful attempt to push forward human physiological limits. No atypicity trend is detected in swimming. The upcoming rarefaction of new records in sport may be delayed by technological innovations, themselves depending upon economical constraints. 相似文献
39.
HT Thong & F Liebert Prof. Dr 《Archives of animal nutrition》2013,67(1):69-87
In this study we investigated the influence of harvest date and genotype on the ruminai degradability of the organic matter of ensiled maize grains. Grains of the varieties Avenir, Byzance, CGS 5104 and CGS 5107 from six different harvest dates were available; they are classified as intermediate types between flint and dent com. The six harvest dates, during which time the dry matter content of the ensiled grains rose from 52% to 66%, extended from 1st September to 19th October. Assuming a passage rate of k=0.08, the effective ruminai degradability declined in this period on average from 93% to just under 79%; variety‐specific deviations also increased markedly during this period. The dry matter content (x, DM in %) of the ensiled grains had a profound influence on ruminai degradation: a highly significant curvilinear decline in ruminai degradability (y) was calculated at increasing DM levels (k = 0.08), which can be described by the equation y = ?0.072x2 (±0.010)+7.417x(±1.186)?98.71(±34.58)(B=0.96;sy,x[%]=1.36). The ruminai degradability of ensiled maize grains is about 5–10% higher than that of fresh maize grains. 相似文献
40.
Kim de Jong H Marike Boezen Nick HT ten Hacken Dirkje S Postma Judith M Vonk 《Respiratory research》2013,14(1):83