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Sampling properties of DNA sequence data in phylogenetic analysis 总被引:26,自引:6,他引:20
We inferred phylogenetic trees from individual genes and random samples of
nucleotides from the mitochondrial genomes of 10 vertebrates and compared
the results to those obtained by analyzing the whole genomes. Individual
genes are poor samples in that they infrequently lead to the whole-genome
tree. A large number of nucleotide sites is needed to exactly determine the
whole-genome tree. A relatively small number of sites, however, often
results in a tree close to the whole-genome tree. We found that blocks of
contiguous sites were less likely to lead to the whole-genome tree than
samples composed of sites drawn individually from throughout the genome.
Samples of contiguous sites are not representative of the entire genome, a
condition that violates a basic assumption of the bootstrap method as it is
applied in phylogenetic studies.
相似文献
3.
Mesut Taskin Yagmur Unver Melike Yildiz Serkan Ortucu Hakan Askin 《Bioprocess and biosystems engineering》2016,39(11):1671-1678
The purpose of this study was to elucidate whether exogenous nitric oxide (NO) has a potential beneficial effect on lipase production capacity of some microorganisms. Sodium nitroprusside (SNP) was used as an exogenous NO donor in production medium. In comparison with the control (0 nM SNP), SNP concentrations from 10 to 100 nM induced lipase production in mesophilic bacterium Bacillus subtilis and cold-adapted yeast Yarrowia lipolytica. Especially, the maximum lipase activities for Y. lipolytica (81.2 U/L) and B. subtilis (74.5 U/L) were attained at 30 and 50 nM SNP concentrations, respectively. When compared to the control, the optimal SNP concentrations resulted in about 5.14 and 2.27-fold increases in lipase activities of B. subtilis and Y. lipolytica, respectively. Besides, it was found that the optimal SNP concentrations provided shorter incubation periods for lipase production. Conversely, no significant positive effect of exogenous NO on lipase production was determined for thermophilic bacterium Geobacillus stearothermophilus. This study showed for the first time that exogenous NO could be used as an inducer in the production of microbial lipases. 相似文献
4.
Baydar T Papp A Aydin A Nagymajtenyi L Schulz H Isimer A Sahin G 《Biological trace element research》2003,92(3):231-244
The present study was undertaken to examine possible aluminum (Al) accumulation in the brain of rats and to investigate whether
subchronic exposure to the metal leads to behavioral and neurophysiological changes in both treated and control groups. Each
of the groups consisted of 10 animals. Aluminum chloride (AlCl3) at a low (50 mg/kg/d) or high (200 mg/kg/d) dose was applied to male Wistar rats by gavage for 8 wk. Al-free water by gavage
was given to the control group throughout the experiment. Behavioral effects were evaluated by open-field (OF) motor activity
and by acoustic startle response (ASR). Electrophysiological examination was done by recording spontaneous activity and sensory-evoked
potentials from the visual, somatosensory, as well as auditory cortex. The Al content of each whole brain was determined by
electrothermal atomic absorption spectrophotometry. Subchronic Al exposure slightly caused some changes in the evoked potentials
and electrocorticograms and in the OF and ASR performance, but these results were not statistically significant. The brain
Al levels of the control and the low and high dose of Al-exposed groups were measured as 0.717±0.208 μg/g (wet weight), 0.963±0.491
μg/g (wet weight) and 1.816±1.157 μg/g (wet weight), respectively. 相似文献
5.
BACKGROUND: Morbidity management is a core component of the global programme for the elimination of lymphatic filariasis. In a double-blind clinical trial, the tolerability and efficacy of Daflon (500 mg) + DEC (25 mg) or DEC (25 mg) alone, twice daily for 90 days, was studied in 26 patients with bancroftian filarial lymphoedema. RESULTS: None of the patients in either drug group reported any adverse reaction throughout the treatment period (90 days). Haematological and biochemical parameters were within normal limits and there was no significant difference between the pre-treatment (day 0) and post-treatment (day 90) values. The group receiving Daflon showed significant reduction in oedema volume from day 90 (140.6 PlusMinus; 18.8 ml) to day 360 (71.8 PlusMinus; 20.7 ml) compared to the pre-treatment (day 0, 198.4 PlusMinus; 16.5 ml) value. This accounted for a 63.8% reduction in oedema volume by day 360 (considering the pre-treatment (day 0) as 100%). In the DEC group, the changes in oedema volume (between day 1 and day 360) were not significant when compared to the pre-treatment (day 0) value. The percentage reduction at day 360 was only 9%, which was not significant (P > 0.05). CONCLUSION: This study has shown that Daflon (500 mg, twice a day for 90 days) is both safe and efficacious in reducing oedema volume in bancroftian filarial lymphoedema. Further clinical trials are essential for strengthening the evidence base on the role of this drug in the morbidity management of lymphatic filariasis. 相似文献
6.
Ziver Sahin Muge Bıcakcıgil Kenan Aksu Sevil Kamali Servet Akar Fatos Onen Omer Karadag Zeynep Ozbalkan Askin Ates Huseyin TE Ozer Vuslat Yilmaz Emire Seyahi Mehmet A Ozturk Ayse Cefle Veli Cobankara A Mesut Onat Ercan Tunc Nursen Düzgün Sibel Z Aydin Neslihan Yilmaz İzzet Fresko Yasar Karaaslan Sedat Kiraz Nurullah Akkoc Murat Inanc Gokhan Keser F Aytul Uyar Haner Direskeneli Güher Saruhan-Direskeneli 《Arthritis research & therapy》2012,14(1):R27-5
Introduction
HLA-B*51 and HLA-B*52 are two close human leukocyte antigen (HLA) allele groups with minor amino acid differences. However, they are associated with two different vasculitides (HLA-B*51 in Behçet's disease and HLA-B*52 in Takayasu's arteritis (TAK)) and with major clinical and immunological differences. In this study, we aimed to screen a large cohort of TAK patients from Turkey for the presence of HLA-B*51 and HLA-B*52 as susceptibility and severity factors.Methods
TAK patients (n = 330) followed at a total of 15 centers were included in the study. The mean age of the patients was 37.8 years, and 86% were women. DNA samples from the patients and healthy controls (HC; n = 210) were isolated, and the presence of HLA-B*51 or HLA-B*52 was screened for by using PCR with sequence-specific primers.Results
We found a significant association of HLA-B*52 with TAK (20.9% vs HC = 6.7%, P = 0.000, OR = 3.7, 95% CI = 2.02 to 6.77). The distribution of HLA-B*51 did not differ between TAK patients and HCs (22.7% vs 24.8%, OR = 0.9, 95% CI = 0.60 to 1.34). The presence of HLA-B*52 decreased in late-onset patients (> 40 years of age; 12.0%, P = 0.024, OR = 0.43, 95% CI = 0.20 to 0.91). Patients with angiographic type I disease with limited aortic involvement also had a lower presence of HLA-B*52 compared to those with all other disease subtypes (13.1% vs 26%, P = 0.005, OR = 0.43, 95% CI = 0.23 to 0.78).Conclusions
In this study, the previously reported association of TAK with HLA-B*52 in other populations was confirmed in patients from Turkey. The functional relevance of HLA-B*52 in TAK pathogenesis needs to be explored further. 相似文献7.
8.
Manbir S. Sodhi Alessandro Agnetis Ronald G. Askin 《Flexible Services and Manufacturing Journal》1994,6(4):287-310
The allocation of tools to machines determines potential part routes in flexible manufacturing systems. Given production requirements and a minimum feasible set of tools, the decision of how to fill vacant slots in tool magazines to maximize routing flexibility is shown to be a minimum cost network flow problem for the cases when routing flexibility is a function of the average workload per tool aggregated over tool types, or of the number of possible routes through the system. A linear programming model is then used to plan a set of routes for each part type so as to minimize either the material handling requirement or the maximum workload on any machine. The impact of these tool addition strategies on the material handling and workload equalization is investigated and computational results presented. The advantage of the overall approach is computational simplicity at each step and the ability to react to dynamic changes. 相似文献
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10.
Proteases are implicated in various diseases and several have been identified as potential drug targets or biomarkers. As a result, protease activity assays that can be performed in high throughput are essential for the screening of inhibitors in drug discovery programs. Here we describe the development of a simple, general method for the characterization of protease activity and its use for inhibitor screening. GFP was genetically fused to a comparatively unstable Tus protein through an interdomain linker containing a specially designed protease site, which can be proteolyzed. When this Tus–GFP fusion protein substrate is proteolyzed it releases GFP, which remains in solution after a short heat denaturation and centrifugation step used to eliminate uncleaved Tus–GFP. Thus, the increase in GFP fluorescence is directly proportional to protease activity. We validated the protease activity assay with three different proteases, i.e., trypsin, caspase 3, and neutrophil elastase, and demonstrated that it can be used to determine protease activity and the effect of inhibitors with small sample volumes in just a few simple steps using a fluorescence plate reader. 相似文献