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11.
Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies 总被引:13,自引:8,他引:5
Estimation of evolutionary distances from coding sequences must take into
account protein-level selection to avoid relative underestimation of longer
evolutionary distances. Current modeling of selection via site-to-site rate
heterogeneity generally neglects another aspect of selection, namely
position-specific amino acid frequencies. These frequencies determine the
maximum dissimilarity expected for highly diverged but functionally and
structurally conserved sequences, and hence are crucial for estimating long
distances. We introduce a codon- level model of coding sequence evolution
in which position-specific amino acid frequencies are free parameters. In
our implementation, these are estimated from an alignment using methods
described previously. We use simulations to demonstrate the importance and
feasibility of modeling such behavior; our model produces linear distance
estimates over a wide range of distances, while several alternative models
underestimate long distances relative to short distances. Site-to-site
differences in rates, as well as synonymous/nonsynonymous and
first/second/third-codon-position differences, arise as a natural
consequence of the site-to-site differences in amino acid frequencies.
相似文献
12.
High-level expression of the Endo-beta-N-acetylglucosaminidase F2 gene in E.coli: one step purification to homogeneity 总被引:1,自引:0,他引:1
The Endo F2gene was overexpressed in E.coli as a fusion protein joined to
the maltose-binding protein. MBP-Endo F2was found in a highly enriched
state as insoluble, inactive inclusion bodies. Extraction of the inclusion
bodies with 20% acetic acid followed by exhaustive dialysis rendered the
fusion protein active and soluble. MBP-Endo F2was digested with Factor
Xaand purified on Q-Sepharose. The enzyme was homogeneous by SDS-PAGE, and
appeared as a single symmetrical peak on HPLC. Analysis of the
amino-terminus demonstrated conclusively that recombinant Endo F2was
homogeneous and identical to the native enzyme.
相似文献
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15.
BUALUANG FAIYUE MOHAMMED J. AL‐AZZAWI TIMOTHY J. FLOWERS 《Plant, cell & environment》2010,33(5):702-716
Although an apoplastic pathway (the so‐called bypass flow) is implicated in the uptake of Na+ by rice growing in saline conditions, the point of entry of this flow into roots remains to be elucidated. We investigated the role of lateral roots in bypass flow using the tracer trisodium‐8‐hydroxy‐1,3,6‐pyrenetrisulphonic acid (PTS) and the rice cv. IR36. PTS was identified in the vascular tissue of lateral roots using both epifluorescence microscopy and confocal laser scanning microscopy. Cryo‐scanning electron microscopy and epifluorescence microscopy of sections stained with berberine‐aniline blue revealed that the exodermis is absent in the lateral roots. We conclude that PTS can move freely through the cortical layers of lateral roots, enter the stele and be transported to the shoot via the transpiration stream. 相似文献
16.
17.
In a chemical investigation of the seeds of Annona cherimola, a natural cyclic heptapeptide, cherimolacyclopeptide D, were isolated and purified by HPLC with three known cyclic peptides, cherimolacyclopeptides A, B and C. The structure was established by various analyses including MS/MS fragmentation, spectroscopic and chemical evidences. 相似文献
18.
Babacar Diao Papa Ahmed Fall Ibrahima Bah Cyrille Ze Ondo Yoro Diallo Lamine Niang Alain Khassim Ndoye Sérigne Maguèye Gueye Mamadou Ba Bay Assane Diagne 《Andrologie》2006,16(2):131-134
Patients and Methods
This is a retrospective study of patients admitted with gunshot injuries to the external genital organs to the urology departments of Aristide Le Dantec Hospital, Grand Yoff General Hospital and Dakar Principal Hospital, between January 1998 and January 2003. The following parameters were studied: patients’ age and gender, interval between accident and admission, clinical features, complementary investigations and treatment, and early and late outcomes.Results
Only males were observed and the mean age of these patients was 37.7 years (range: 22–52 years). Lesions were accidental in five cases. Two cases of testicular wounds, two cases of corpus cavernosum injuries, two cases of urethral injury, and one case of perineal wound were observed. After excision of the lesions, complementary procedures consisted of: orchidectomy in two cases, corpus cavernosum — albuginea suture in two cases and end-to-end urethral suture in one case. Perineoscrotal wounds were sutured three days after debridement. All patients received antibiotics and antitetanus serum. No death was observed during the immediate follow-up. No case of urethral stricture or erectile dysfunction was observed with a follow-up of 18 months. Semen analysis was normal in the two cases of orchidectomy. 相似文献19.
A reference microsatellite kit to assess for genetic diversity of Sorghum bicolor (Poaceae) 总被引:1,自引:0,他引:1
Billot C Rivallan R Sall MN Fonceka D Deu M Glaszmann JC Noyer JL Rami JF Risterucci AM Wincker P Ramu P Hash CT 《American journal of botany》2012,99(6):e245-e250
? Premise of the study: Discrepancies in terms of genotyping data are frequently observed when comparing simple sequence repeat (SSR) data sets across genotyping technologies and laboratories. This technical concern introduces biases that hamper any synthetic studies or comparison of genetic diversity between collections. To prevent this for Sorghum bicolor, we developed a control kit of 48 SSR markers. ? Methods and Results: One hundred seventeen markers were selected along the genome to provide coverage across the length of all 10 sorghum linkage groups. They were tested for polymorphism and reproducibility across two laboratories (Centre de Cooperation Internationale en Recherche Agronomique pour le Developpement [CIRAD], France, and International Crops Research Institute for the Semi-Arid Tropics [ICRISAT], India) using two commonly used genotyping technologies (polyacrylamide gel-based technology with LI-COR sequencing machines and capillary systems with ABI sequencing apparatus) with DNA samples from a diverse set of 48 S. bicolor accessions. ? Conclusions: A kit for diversity analysis (http://sat.cirad.fr/sat/sorghum_SSR_kit/) was developed. It contains information on 48 technically robust sorghum microsatellite markers and 10 DNA controls. It can further be used to calibrate sorghum SSR genotyping data acquired with different technologies and compare those to genetic diversity references. 相似文献
20.
Daniel Fonceka Hodo-Abalo Tossim Ronan Rivallan Hélène Vignes Elodie Lacut Fabien de Bellis Issa Faye Ousmane Ndoye Soraya C. M. Leal-Bertioli José F. M. Valls David J. Bertioli Jean-Christophe Glaszmann Brigitte Courtois Jean-Fran?ois Rami 《PloS one》2012,7(11)
Chromosome segment substitution lines (CSSLs) are powerful QTL mapping populations that have been used to elucidate the molecular basis of interesting traits of wild species. Cultivated peanut is an allotetraploid with limited genetic diversity. Capturing the genetic diversity from peanut wild relatives is an important objective in many peanut breeding programs. In this study, we used a marker-assisted backcrossing strategy to produce a population of 122 CSSLs from the cross between the wild synthetic allotetraploid (A. ipaënsis×A. duranensis)4x and the cultivated Fleur11 variety. The 122 CSSLs offered a broad coverage of the peanut genome, with target wild chromosome segments averaging 39.2 cM in length. As a demonstration of the utility of these lines, four traits were evaluated in a subset of 80 CSSLs. A total of 28 lines showed significant differences from Fleur11. The line×trait significant associations were assigned to 42 QTLs: 14 for plant growth habit, 15 for height of the main stem, 12 for plant spread and one for flower color. Among the 42 QTLs, 37 were assigned to genomic regions and three QTL positions were considered putative. One important finding arising from this QTL analysis is that peanut growth habit is a complex trait that is governed by several QTLs with different effects. The CSSL population developed in this study has proved efficient for deciphering the molecular basis of trait variations and will be useful to the peanut scientific community for future QTL mapping studies. 相似文献