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131.
The robustness of two phylogenetic methods: four-taxon simulations reveal a slight superiority of maximum likelihood over neighbor joining 总被引:6,自引:3,他引:3
The robustness (sensitivity to violation of assumptions) of the maximum-
likelihood and neighbor-joining methods was examined using simulation.
Maximum likelihood and neighbor joining were implemented with Jukes-
Cantor, Kimura, and gamma models of DNA substitution. Simulations were
performed in which the assumptions of the methods were violated to varying
degrees on three model four-taxon trees. The performance of the methods was
evaluated with respect to ability to correctly estimate the unrooted
four-taxon tree. Maximum likelihood outperformed neighbor joining in 29 of
the 36 cases in which the assumptions of both methods were satisfied. In
133 of 180 of the simulations in which the assumptions of the
maximum-likelihood and neighbor-joining methods were violated, maximum
likelihood outperformed neighbor joining. These results are consistent with
a general superiority of maximum likelihood over neighbor joining under
comparable conditions. They extend and clarify an earlier study that found
an advantage for neighbor joining over maximum likelihood for
gamma-distributed mutation rates.
相似文献
132.
Evolutionary transfer of ORF-containing group I introns between different subcellular compartments (chloroplast and mitochondrion) 总被引:10,自引:2,他引:8
Turmel M; Cote V; Otis C; Mercier JP; Gray MW; Lonergan KM; Lemieux C 《Molecular biology and evolution》1995,12(4):533-545
We describe here a case of homologous introns containing homologous open
reading frames (ORFs) that are inserted at the same site in the large
subunit (LSU) rRNA gene of different organelles in distantly related
organisms. We show that the chloroplast LSU rRNA gene of the green alga
Chlamydomonas pallidostigmatica contains a group I intron (CpLSU.2)
encoding a site-specific endonuclease (I-CpaI). This intron is inserted at
the identical site (corresponding to position 1931-1932 of the Escherichia
coli 23S rRNA sequence) as a group I intron (AcLSU.m1) in the mitochondrial
LSU rRNA gene of the amoeboid protozoon Acanthamoeba castellanii. The
CpLSU.2 intron displays a remarkable degree of nucleotide similarity in
both primary sequence and secondary structure to the AcLSU.m1 intron;
moreover, the Acanthamoeba intron contains an ORF in the same location
within its secondary structure as the CpLSU.2 ORF and shares with it a
strikingly high level of amino acid similarity (65%; 42% identity). A
comprehensive survey of intron distribution at site 1931 of the chloroplast
LSU rRNA gene reveals a rather restricted occurrence within the
polyphyletic genus Chlamydomonas, with no evidence of this intron among a
number of non- Chlamydomonad green algae surveyed, nor in land plants. A
parallel survey of homologues of a previously described and similar
intron/ORF pair (C. reinhardtii chloroplast CrLSU/A. castellanii
mitochondrial AcLSU.m3) also shows a restricted occurrence of this intron
(site 2593) among chloroplasts, although the intron distribution is
somewhat broader than that observed at site 1931, with site-2593 introns
appearing in several green algal branches outside of the Chlamydomonas
lineage. The available data, while not definitive, are most consistent with
a relatively recent horizontal transfer of both site-1931 and site- 2593
introns (and their contained ORFs) between the chloroplast of a
Chlamydomonas-type organism and the mitochondrion of an Acanthamoeba- like
organism, probably in the direction chloroplast to mitochondrion. The data
also suggest that both introns could have been acquired in a single event.
相似文献
133.
Rescue of Murine Sarcoma Virus from a Sarcoma-Positive Leukemia-Negative Cell Line: Requirement for Replicating Leukemia Virus 总被引:10,自引:6,他引:4
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P. T. Peebles R. H. Bassin D. K. Haapala L. A. Phillips S. Nomura P. J. Fischinger 《Journal of virology》1971,8(5):690-694
The nature of murine sarcoma virus (MSV) "defectiveness" was investigated by employing an MSV-transformed mouse 3T3 cell line which releases noninfectious virus-like particles. Rescue kinetics of MSV, observed after murine leukemia virus (MuLV) superinfection of these "sarcoma-positive leukemia-negative (S + L -)" mouse 3T3 cells, consisted of a 9- to 12-hr eclipse period followed by simultaneous release of both MSV and MuLV with no evidence for release of infectious MSV prior to the production of progeny MuLV. Addition of thymidine to the growth medium of MuLV-superinfected S + L - cells at a concentration suppressing deoxyribonucleic acid synthesis inhibited the replication of MuLV and the rescue of MSV. MSV production closely paralleled MuLV replication under a variety of experimental conditions. These results suggest that replication of MuLV is required for the rescue of infectious MSV from S + L - cells and that one (or more) factor, produced late in the MuLV replicative cycle, is utilized by both viruses during virion assembly. During the course of these experiments, virus stocks were recovered which contained infectious MSV in apparent excess over MuLV. These stocks were used for generating new S + L - cell lines by simple end point dilution procedures. 相似文献
134.
135.
Expression of N-linked sialyl Le(x) determinants and O-glycans in the carbohydrate moiety of human amniotic fluid transferrin during pregnancy 总被引:3,自引:0,他引:3
Transferrin, a glycoprotein involved in iron transport in body fluids, was
isolated from amniotic fluid of a hydramniospatient by sequential
anion-exchange chromatography and gel filtration. The N-glycans of human
amniotic fluid transferrin (hAFT) were enzymatically liberated by PNGase-F
digestion, isolated by gel filtration and fractionated by (high-pH)
anion-exchange chromatography. After alkaline borohydride treatment of
native hAFT, the released O-glycans were isolated by gel filtration and
fractionated by anion-exchange chroma-tography. Structure elucidation of 14
N- and 2 O-glycans was performed by 500 or 600 MHz1H-NMR spectroscopy.
Besides conventional N-glycans established earlier for human serum
transferrin (hST), new (alpha1-3)-fucosylated N- glycans were found,
representing sialyl Le(x) elements. Furthermore, as compared to hST, a
higher degree of (alpha1-6)-fucosylation and an increase in branching from
di- to triantennary compounds has been detected. The presence of O-glycans
is demonstrated for the first time in transferrin.
相似文献
136.
137.
C Tardif H Maamar M Balfin JP Belaich 《Journal of industrial microbiology & biotechnology》2001,27(5):271-274
Electropermeabilization of Clostridium cellulolyticum was optimized using ATP leakage assays. Electrotransformation was then performed under optimized conditions (6 to 7.5 kV
cm−1 field strength applied during 5 ms to a mixture containing methylated plasmids and late exponential phase cell suspensions
(10 molecules:1 cell) in a sucrose-containing buffer). Transformants were only obtained when 7 or 7.5 kV cm−1 pulses were applied. Transformation efficiencies evaluated from the growth curves of transformed cells were between 105 and 107 transformants per microgram of plasmid DNA for five different replicon-based plasmids. Restriction nuclease digestion patterns
of pJIR418 purified from transformed Clostridia and Escherichia coli were indistinguishable, indicating that heterologous DNA was structurally stable in the Clostridium strain. Copy numbers of 130, 70 and 10 were estimated from purification yield for pCTC1, pKNT19 and pJIR418, respectively.
Journal of Industrial Microbiology & Biotechnology (2001) 27, 271–274.
Received 12 September 2000/ Accepted in revised form 25 November 2000 相似文献
138.
Gill Furze Alun Roebuck Peter Bull Robert JP Lewin David R Thompson 《BMC cardiovascular disorders》2002,2(1):4
Background
What people believe about their illness may affect how they cope with it. It has been suggested that such beliefs stem from those commonly held within society . This study compared the beliefs held by people with angina, regarding causation and coping in angina, with the beliefs of their friends who do not suffer from angina. 相似文献139.
Publication of the complete diploid genome sequence of the yeast Candida albicans will accelerate research into the pathogenesis of Candida infections. Comparative genomic analysis highlights genes that may contribute to C. albicans survival and its fitness as a human commensal and pathogen. 相似文献
140.
Improved phosphate removal by selective sludge discharge in aerobic granular sludge reactors 总被引:1,自引:0,他引:1
Bassin JP Winkler MK Kleerebezem R Dezotti M van Loosdrecht MC 《Biotechnology and bioengineering》2012,109(8):1919-1928
Two lab-scale aerobic granular sludge sequencing batch reactors were operated at 20 and 30°C and compared for phosphorus (P) removal efficiency and microbial community composition. P-removal efficiency was higher at 20°C (>90%) than at 30°C (60%) when the sludge retention time (SRT) was controlled at 30 days by removing excess sludge equally throughout the sludge bed. Samples analyzed by fluorescent in situ hybridization (FISH) indicated a segregation of biomass over the sludge bed: in the upper part, Candidatus Competibacter phosphatis (glycogen-accumulating organisms--GAOs) were dominant while in the bottom, Candidatus Accumulibacter phosphatis (polyphosphate-accumulating organisms--PAOs) dominated. In order to favour PAOs over GAOs and hence improve P-removal at 30°C, the SRT was controlled by discharging biomass mainly from the top of the sludge bed (80% of the excess sludge), while bottom granules were removed in minor proportions (20% of the excess sludge). With the selective sludge removal proposed, 100% P-removal efficiency was obtained in the reactor operated at 30°C. In the meantime, the biomass in the 30°C reactor changed in color from brownish-black to white. Big white granules appeared in this system and were completely dominated by PAOs (more than 90% of the microbial population), showing relatively high ash content compared to other granules. In the reactor operated at 20°C, P-removal efficiency remained stable above 90% regardless of the sludge removal procedure for SRT control. The results obtained in this study stress the importance of sludge discharge mainly from the top as well as in minor proportions from the bottom of the sludge bed to control the SRT in order to prevent significant growth of GAOs and remove enough accumulated P from the system, particularly at high temperatures (e.g., 30°C). 相似文献