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  • 1
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    Identification of a sex-linked SCAR marker for Plecoglossus altivelis and its application for identifying gender in cultivated and wild populations (2018)
    Details
    Publication Date: 2021-05-19
    Description: Ayu (Plecoglossus altivelis), one kinds of valuable cultured fish species, show almost no morphological difference between male and female until sexual maturity. Here, we report the identification of sex-linked markers for the ayu, based on Amplified Fragment Length Polymorphism (AFLP) generated from cultured fish (15 males and 15 females) by using 63 different primer combinations. Genomic fragments (n = 3733) were produced with a mean frequency of 59 bands per primer pair. A male-specific of 139 base pair band was amplified and converted to a sequence-characterized amplified region (SCAR marker) designated as Ayu102. Six distinct genomic fragments were produced in 12 wild samples (6 males and 6 females). The fragments designated a, b, c, d, and e were detected only in males, and one fragment (f) was detected in both genders. Nucleotide sequence analysis showed that fragments e and f were 96.67% identical. Ayu102 marker was detected in 45-d-old larvae, in both cultured and wild fish populations, and in offsprings generated by gynogenesis. Fragment e was detected in all males, and in only 6.7% of females in cultured fish. Data suggest that Ayu102 marker is a male-specific marker linked to the sex-determining locus of the male ayu and can be used for gender identification.
    Description: Published
    Keywords: Biology ; Physiology ; AFLP ; Plecoglossus altivelis ; Sex-linked marker ; Identification ; Populations ; Genomics
    Repository Name: AquaDocs
    Type: Journal Contribution , Refereed
    Format: pp.895-906
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  • 2
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    Identification of a sex-linked SCAR marker for Plecoglossus altivelis and its application for identifying gender in cultivated and wild populations (2021)
    In:  http://aquaticcommons.org/id/eprint/22737 | 18721 | 2018-05-18 22:38:13 | 22737 | Iranian Fisheries Science Research Institute
    Details
    Publication Date: 2021-07-09
    Description: Ayu (Plecoglossus altivelis), one kinds of valuable cultured fish species, show almost no morphological difference between male and female until sexual maturity. Here, we report the identification of sex-linked markers for the ayu, based on Amplified Fragment Length Polymorphism (AFLP) generated from cultured fish (15 males and 15 females) by using 63 different primer combinations. Genomic fragments (n = 3733) were produced with a mean frequency of 59 bands per primer pair. A male-specific of 139 base pair band was amplified and converted to a sequence-characterized amplified region (SCAR marker) designated as Ayu102. Six distinct genomic fragments were produced in 12 wild samples (6 males and 6 females). The fragments designated a, b, c, d, and e were detected only in males, and one fragment (f) was detected in both genders. Nucleotide sequence analysis showed that fragments e and f were 96.67% identical. Ayu102 marker was detected in 45-d-old larvae, in both cultured and wild fish populations, and in offsprings generated by gynogenesis. Fragment e was detected in all males, and in only 6.7% of females in cultured fish. Data suggest that Ayu102 marker is a male-specific marker linked to the sex-determining locus of the male ayu and can be used for gender identification.
    Keywords: Aquaculture ; Biology ; Fisheries ; AFLP ; Plecoglossus altivelis ; Sex-linked marker ; Biology ; Physiology ; China ; Identification ; population ; fish species ; sexual maturity
    Repository Name: AquaDocs
    Type: article , TRUE
    Format: application/pdf
    Format: application/pdf
    Format: 895-906
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  • 3
    Electronic Resource
    Electronic Resource
    Use of Single Isomorphous Replacement Data of Proteins – Resolving the Phase Ambiguity and a New Procedure for Phase Extension (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 49-55 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A procedure combining direct methods and solvent flattening to break the phase ambiguity intrinsic to the single isomorphous replacement (SIR) technique has been tested with the experimental SIR data of the known protein RNase Sa at 2.5 Å resolution. The use of direct methods provided better initial phases for the solvent-flattening procedure, while the solvent-flattening procedure greatly improved direct-method phases leading to a traceable Fourier map. A small subset of known phases at low resolution makes direct phasing of SIR data much easier. Accordingly a method for extending low-resolution phases to high-resolution ones is proposed making use of additional SIR information. This reduces the problem of finding a value in the range of 0–2π for each unknown phase to that of just making a choice between two possible values. Tests with the known protein RNase Sa showed that the method is able to extend phases from a resolution of 6 to 2.5 Å leading to an easily traceable Fourier map. The solvent-flattening technique and the combination of which with direct methods were used for the phase extension. Either procedure yielded reasonably good results, but on the whole, the result from the combination of direct methods with solvent flattening is better. Results of the latter procedure were further compared with that from direct phasing of the 2.5 Å SIR data and with that from phase extension by solvent flattening without SIR information. An improvement gained by the use of SIR information is evident.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996009365
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  • 4
    Electronic Resource
    Electronic Resource
    Direct methods in superspace. I. Preliminary theory and test on the determination of incommensurate modulated structures (1987)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 43 (1987), S. 820-824 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The validity of the Sayre equation [Sayre (1952). Acta Cryst. 5, 60-65] for (3 + n)-dimensional periodic structures is examined. A practical procedure is proposed for the determination of incommensurate modulated structures; this is an extension of the direct method previously proposed for solving superstructures [Fan Hai-fu, He Lao, Qian Jin-zi & Liu Shi- xiang (1978). Acta Phys. Sin. 27, 554-558]. With the newly proposed method, the phase problem for the main as well as the satellite reflections can be solved directly without making particular assumptions about the modulation. A known incommensurate modulated structure, γ-Na2CO3, was used in the test. Satisfactory results were obtained.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767387098465
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  • 5
    Electronic Resource
    Electronic Resource
    Combining direct methods with isomorphous replacement or anomalous scattering data. VI. Incorporation of heavy-atom information into Hauptman's distributions (1988)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 44 (1988), S. 379-383 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Heavy-atom information has been incorporated into Hauptman's distributions of three-phase structure invariants for both isomorphous replacement and anomalous scattering cases. Reliable estimates of individual phases can be obtained by introducing the phase doublet expression φH = φ′H ± |ΔφH|. A test calculation with error-free data of insulin showed results better than previous methods.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767388000637
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  • 6
    Electronic Resource
    Electronic Resource
    A new iterative procedure for combining direct methods with solvent flattening – dealing with the phase ambiguity in protein crystallography (1997)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 53 (1997), S. 792-794 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new procedure for combining direct methods with the solvent-flattening technique is proposed for phasing single isomorphous replacement (SIR) or one-wavelength anomalous scattering (OAS) data of proteins. The new procedure differs from the previous one [Zheng, Zheng, Gu, Mo, Fan & Hao (1997). Acta Cryst. D53, 49–55] in that the direct method not only provides input phases to but also accepts feedback phases from solvent flattening, thus forming an iterative process for breaking the ambiguities and refining the values of phases. The new procedure was tested with the experimental SIR data of the known structure ribonuclease Sa. For the strongest 1000 of the total 7264 refelctions, the mean Fobs-weighted phase error is 7.5 and 9.4° lower than that of the previous procedure and that of solvent flattening alone, respectively.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744499700680X
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  • 7
    Electronic Resource
    Electronic Resource
    The program SAPI and its applications. III. Determination of structures having pseudo-translational symmetry (1990)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 46 (1990), S. 99-103 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Optimization has been made of the program SAPI for automatic solution of structures having pseudo-translational symmetry. This includes: (1) floating default cutoff of E's; (2) automatic and user-adjustable balance between the number of systematically strong reflections and that of the systematically weak ones; (3) R factors for reflection subsets corresponding to the 'strong' group and the 'weak' groups. Examples on solving structures with pseudo-translational symmetry are discussed in detail. They include known as well as unknown structures and centrosymmetric as well as non-centrosymmetric structures, all of which can be solved starting from a default run of SAPI.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767389010147
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  • 8
    Electronic Resource
    Electronic Resource
    On the determination of quasicrystal structures (1990)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 46 (1990), S. 473-478 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A possible approach to direct phasing of quasicrystal diffraction data is described. The data are first converted to a set of structure-factor amplitudes of a multidimensional crystal. The Patterson function of the quasicrystal is used to derive the converting factor. A direct method is then used to solve the phase problem in multi-dimensional space. The method has been tested with a hypothetical one-dimensional quasicrystal yielding a satisfactory result.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767390000289
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  • 9
    Electronic Resource
    Electronic Resource
    Direct-method-aided phasing of MAD data (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 250-253 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct methods of breaking the phase ambiguity intrinsic in one-wavelength anomalous scattering (OAS) data and MAD phasing are powerful methods in their own rights. In a different context, in addition to their success in phasing OAS data, direct methods can also be useful in the treatment of MAD data. The idea has been tested with the MAD data at 2.5 Å resolution from the protein human adenosine kinase [Mathews et al. (1998), Biochemistry, 37, 15607–15620]. The results showed that the incorporation of direct methods in MAD phasing led to a significant improvement of phases over those obtained from the conventional MAD phasing method alone, as indicated by improved map correlation coefficients (with the existing model), reduced phase errors by 4.5° and improved map connectivity.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444900018606
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  • 10
    Electronic Resource
    Electronic Resource
    Electron crystallographic image-processing investigation and superstructure determination for (Pb0.5Sr0.3Cu0.2)Sr2(Ca0.6Sr0.4)Cu2Oy (2001)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 540-547 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An electron crystallographic image-processing technique based on the combination of high-resolution electron microscopy and electron diffraction has been developed to investigate the commensurate structural modulation in the high-Tc superconductor (Pb0.5Sr0.3Cu0.2)Sr2(Ca0.6Sr0.4)Cu2Oy. After symmetry averaging, a structure image was obtained by image deconvolution at the resolution limited by that of the electron microscope. Then phase extension was employed to enhance the image resolution up to about 1.25 Å by means of the electron diffraction data corrected with an empirical method. In the final projected potential map, the occupational and/or positional modulation is clearly observed for all atoms, including oxygen. The key points of determining superstructures by the technique are studied and discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767301007632
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