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41.
Efficiencies of different genes and different tree-building methods in recovering a known vertebrate phylogeny 总被引:24,自引:6,他引:18
The relative efficiencies of different protein-coding genes of the
mitochondrial genome and different tree-building methods in recovering a
known vertebrate phylogeny (two whale species, cow, rat, mouse, opossum,
chicken, frog, and three bony fish species) was evaluated. The
tree-building methods examined were the neighbor joining (NJ), minimum
evolution (ME), maximum parsimony (MP), and maximum likelihood (ML), and
both nucleotide sequences and deduced amino acid sequences were analyzed.
Generally speaking, amino acid sequences were better than nucleotide
sequences in obtaining the true tree (topology) or trees close to the true
tree. However, when only first and second codon positions data were used,
nucleotide sequences produced reasonably good trees. Among the 13 genes
examined, Nd5 produced the true tree in all tree-building methods or
algorithms for both amino acid and nucleotide sequence data. Genes Cytb and
Nd4 also produced the correct tree in most tree-building algorithms when
amino acid sequence data were used. By contrast, Co2, Nd1, and Nd41 showed
a poor performance. In general, large genes produced better results, and
when the entire set of genes was used, all tree-building methods generated
the true tree. In each tree-building method, several distance measures or
algorithms were used, but all these distance measures or algorithms
produced essentially the same results. The ME method, in which many
different topologies are examined, was no better than the NJ method, which
generates a single final tree. Similarly, an ML method, in which many
topologies are examined, was no better than the ML star decomposition
algorithm that generates a single final tree. In ML the best substitution
model chosen by using the Akaike information criterion produced no better
results than simpler substitution models. These results question the
utility of the currently used optimization principles in phylogenetic
construction. Relatively simple methods such as the NJ and ML star
decomposition algorithms seem to produce as good results as those obtained
by more sophisticated methods. The efficiencies of the NJ, ME, MP, and ML
methods in obtaining the correct tree were nearly the same when amino acid
sequence data were used. The most important factor in constructing reliable
phylogenetic trees seems to be the number of amino acids or nucleotides
used.
相似文献
42.
Liapis E Sandiford S Wang Q Gaidosh G Motti D Levay K Slepak VZ 《Journal of neurochemistry》2012,122(3):568-581
The R7 family of regulators of G protein signaling (RGS) is involved in many functions of the nervous system. This family includes RGS6, RGS7, RGS9, and RGS11 gene products and is defined by the presence of the characteristic first found in Disheveled, Egl-10, Pleckstrin (DEP), DEP helical extension (DHEX), Gγ-like, and RGS domains. Herein, we examined the subcellular localization of RGS7, the most broadly expressed R7 member. Our immunofluorescence studies of retinal and dorsal root ganglion neurons showed that RGS7 concentrated at the plasma membrane of cell bodies, in structures resembling lamellipodia or filopodia along the processes, and at the dendritic tips. At the plasma membrane of dorsal root ganglia neurons, RGS7 co-localized with its known binding partners R7 RGS binding protein (R7BP), Gαo, and Gαq. More than 50% of total RGS7-specific immunofluorescence was present in the cytoplasm, primarily within numerous small puncta that did not co-localize with R7BP. No specific RGS7 or R7BP immunoreactivity was detected in the nuclei. In transfected cell lines, ectopic RGS7 had both diffuse cytosolic and punctate localization patterns. RGS7 also localized in centrosomes. Structure-function analysis showed that the punctate localization was mediated by the DEP/DHEX domains, and centrosomal localization was dependent on the DHEX domain. 相似文献
43.
角果碱蓬(Suaeda corniculata)是藜科一年生盐生植物, 在我国分布于北方盐碱滩涂和盐碱荒漠地区。角果碱蓬具有棕色和黑色两种异型体种子(简称棕色和黑色种子)。对采自内蒙古鄂托克前旗盐渍化生境的角果碱蓬二型种子的形态、休眠和萌发特性开展对比研究, 测定了二型种子休眠和萌发行为对温度、光照和盐分(NaCl)的响应, 以揭示盐生植物异型种子对温带盐漠生境的适应对策。结果表明: (1)二型性种子在大小、种皮特性和结实比例方面有显著差异。与黑色种子相比, 棕色种子个体较大, 种皮透水性强。黑色种子与棕色种子的结实比例约为5.6 : 1。(2)新成熟的棕色种子的萌发对各温度梯度和光照条件不敏感, 萌发率较高(84%-100%); 而新成熟的黑色种子萌发率较低(8%-78%), 萌发对光照敏感。(3)黑色种子具有浅度生理休眠, 种皮划破、赤霉素处理和低温层积均可有效地提高种子的萌发率。(4)二型种子萌发对土壤盐分的胁迫具有不同的响应。与黑色种子相比, 棕色种子对盐分胁迫不敏感, 在较高的盐分浓度下仍有较高的萌发率, 低温层积处理能够降低黑色种子对盐胁迫的敏感性, 有效地提高种子的初始萌发率、萌发恢复率和最终萌发率。角果碱蓬二型种子不同的形态、休眠和萌发特性, 提高了该物种在高度异质性生境中的适合度, 对种群成功地适应温带盐漠环境具有重要的意义。 相似文献
44.
Motti Hakim 《Journal of molecular biology》2009,391(4):758-768
Large double-stranded DNA viruses, including poxviruses and mimiviruses, encode enzymes to catalyze the formation of disulfide bonds in viral proteins produced in the cell cytosol, an atypical location for oxidative protein folding. These viral disulfide catalysts belong to a family of sulfhydryl oxidases that are dimers of a small five-helix fold containing a Cys-X-X-Cys motif juxtaposed to a flavin adenine dinucleotide cofactor. We report that the sulfhydryl oxidase pB119L from African swine fever virus (ASFV) uses for self-assembly surface different from that observed in homologs from mammals, plants, and fungi. Within a protein family, different packing interfaces for the same oligomerization state are extremely rare. We find that the alternate dimerization mode seen in ASFV pB119L is not characteristic of all viral sulfhydryl oxidases, as the flavin-binding domain from a mimivirus sulfhydryl oxidase assumes the same dimer structure as the known eukaryotic enzymes. ASFV pB119L demonstrates the potential of large double-stranded DNA viruses, which have faster mutation rates than their hosts and the tendency to incorporate host genes, to pioneer new protein folds and self-assembly modes. 相似文献
45.
Riccardo Motti Vincenzo Antignani Marisa Idolo 《Human ecology: an interdisciplinary journal》2009,37(6):775-782
The Phlegraean Fields Regional Park in southern Italy has an especially long history of human exploitation. For our ethnobotanical
studies we interviewed 39 people native to the area and recorded 962 use-reports. For each species, we provide scientific
and vernacular names, plant parts used, and preparation and administration processes. In all, 69 species belonging to 35 families
were classified. The species most frequently mentioned were Citrus limon, Chamomilla recutita, Malva sylvestris, Parietaria judaica, Ficus carica, Foeniculum vulgare and Laurus nobilis. The commonest plant use recorded is medicinal, followed by culinary and domestic; for 26% of the species inventoried, more
than one use was recorded. The present study confirms the persistence of traditional plant use in regions of central and southern
Italy. 相似文献
46.
采用红外气体分析仪,于2008年10月17-19日连续3个昼夜原位监测了荷木的树干CO_2释放通量、树干温度、木质部液流密度和CO_2浓度.结果表明:树干CO_2释放通量(EA)日变化呈S形曲线,不同径级间差异显著.EA与树干温度呈显著幂函数关系(0.24Abstract: By using a Li-820 infra-red CO_2 gas analyzer, an in situ measurement of Schima super-ba stem CO_2 efflux was conducted for three consecutive days from 17 to 19 October 2008. In the meantime, the stem temperature, xylem sap efflux density, and xylem CO_2 concentration were measured. The stem CO_2 efflux had a diurnal variation of "S" pattern, and differed significantly with stem diameter. There was a significant exponential relationship between stem CO_2 efflux and stem temperature (0. 24 < R~2 < 0. 78). The temperature coefficient (b) and regression coeffi-cient (R~2) were higher at nighttime than at daytime, and the Q_(10) value ranged from 2. 01 to 2. 79. The stem CO_2 efflux correlated significantly with the xylem CO_2 concentration, and the best regression curve was cubic (R~2= 0. 48). Excluding the effects of stem temperature, the stem CO_2 efflux showed a significant negative correlation with xylem sap flux density (r =-0.462). Therefore, only using simple temperature function to estimate stem CO_2 efflux would yield a significant error, and xylem sap flux should be taken into consideration in the stem CO_2 emux estimation. 相似文献
47.
High concentrations of acrylate, 542–683 μmol g−1 of the non-skeletal dry mass (DM), were measured in the Great Barrier Reef coral, Acropora millepora, using quantitative nuclear magnetic resonance spectroscopy (qNMR). As the amount of NaCl salt in the samples was substantial
but variable, the total carbon (TC) in the coral extracts was determined, and the carbon due to acrylate found to represent
13–15% of the TC present in the total organic extracts (TOE). Acrylate, a C3 compound, is thus a substantial carbon source in the coral holobiont and is known to be derived from dimethylsulfoniopropionate
(DMSP), which has previously been found in corals and other organisms that harbor Symbiodinium spp. The reason for such high levels of acrylate in the corals is unknown; possible functions include antimicrobial and/or
antioxidant roles, as well as playing a role in the structuring of the healthy resident coral bacteria. 相似文献
48.
Neuza M Alcantara-Neves Samuel J Badaró Mariese CA dos Santos Lain Pontes-de-Carvalho Maurício L Barreto 《Respiratory research》2010,11(1):114
Background
The elucidation of factors that trigger the development of transient wheezing in early childhood may be an important step toward understanding the pathogenesis of asthma and other allergic diseases later in life. Transient wheezing has been mainly attributed to viral infections, although sensitisation to aeroallergens and food allergens may occur at an early age. In developing countries, intestinal helminthic infections have also been associated with allergy or atopy-related disorders.Objective
The aim of this study was to explore the association of Trichuris trichiura and Ascaris lumbricoides infections with wheezing and atopy in early childhood.Study design
A cross-sectional study using a Portuguese-language ISAAC phase I questionnaire, adapted for preschool-aged children, nested in a cohort study of childhood diarrhoea, was conducted on 682 children. Two faecal samples per child were examined for the presence of intestinal helminthic infection. IgE antibodies against three allergenic preparations (Dermatophagoides pteronyssinus, Blomia tropicalis and common child food), as well as against A. lumbricoides antigens, were measured in a sub-sample of these children, whose parents allowed the procedure. Atopy was defined by the presence of levels of serum IgE antibodies ≥0.35 kU/L against at least one of the three tested allergenic preparations.Results
Active T. trichiura infection but not A. lumbricoides infection was positively associated with wheezing in the total studied children population [adjusted OR = 2.60; CI = 1.54;4.38] and in the atopic children sub-population [adjusted OR = 3.07; CI = 1.00;9.43]. The association with atopy was also positive and statistically significant only in the brute analysis [OR = 2.13; CI = 1.03;4.40]. Anti-A. lumbricoides IgE antibodies, but not current A. lumbricoides infection, were positively associated with wheezing in atopic children [adjusted OR = 2.01; CI = 1.00;4.50] and in non-atopic children [adjusted OR = 3.07; CI = 1.13;8.35] and it was also associated with atopy [adjusted OR = 7.29; CI = 3.90; 13.4]. On the other hands, reports of wheezing were not significantly associated with atopy.Conclusions
These data corroborate previous studies showing that wheezing is predominantly associated with infection in early childhood and shows that anti-A. lumbricoides IgE antibodies, but not active Ascaris infections, are associated with wheezing and atopy. Additionally, the data demonstrate that T. trichiura infection may play a role in the pathogenesis of atopic wheezing in early childhood. 相似文献49.
50.
Ubydul Haque Ricardo J Soares Magalhães Heidi L Reid Archie CA Clements Syed Masud Ahmed Akramul Islam Taro Yamamoto Rashidul Haque Gregory E Glass 《Malaria journal》2010,9(1):120