Research article Special Issues

Columnar structure of SV40 minichromosome

  • Received: 13 July 2015 Accepted: 20 July 2015 Published: 30 July 2015
  • Like the sequence of the strongest 601 clone nucleosome of Lowary and Widom, the SV40 genome sequence contains tracks of YR dinucleotides separated by small integers of the 10.4n base series (10, 11, 21 and 30 bases). The tracks, however, substantially exceed the nucleosome DNA size and, thus, correspond to more extended structure - columnar chromatin. The micrococcal nuclease digests of the SV40 chromatin do not show uniquely positioned individual nucleosomes. This confirms the columnar structure of the minichromosome, as well as earlier electron microscopy studies.

    Citation: Edward N Trifonov. Columnar structure of SV40 minichromosome[J]. AIMS Biophysics, 2015, 2(3): 274-283. doi: 10.3934/biophy.2015.3.274

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  • Like the sequence of the strongest 601 clone nucleosome of Lowary and Widom, the SV40 genome sequence contains tracks of YR dinucleotides separated by small integers of the 10.4n base series (10, 11, 21 and 30 bases). The tracks, however, substantially exceed the nucleosome DNA size and, thus, correspond to more extended structure - columnar chromatin. The micrococcal nuclease digests of the SV40 chromatin do not show uniquely positioned individual nucleosomes. This confirms the columnar structure of the minichromosome, as well as earlier electron microscopy studies.


    The classical beta function

    $ B(δ1,δ2)=0tδ11(1t)δ21dt,((δ1)>0,(δ2)>0)
    $
    (1.1)

    and its relation with well known gamma function is given by

    $ B(δ1,δ2)=Γ(δ1)Γ(δ2)Γ(δ1+δ2),(δ1)>0,(δ2)>0.
    $

    The Gauss hypergeometric, confluent hypergeometric and Appell's functions which are respectively defined by(see [27])

    $ 2F1(δ1,δ2;δ3;z)=n=0(δ1)n(δ2)n(δ3)nznn!,(|z|<1),    (δ1,δ2,δ3C  and  δ30,1,2,3,),
    $
    (1.2)

    and

    $ 1Φ1(δ2;δ3;z)=n=0(δ2)n(δ3)nznn!,(|z|<1),    (δ2,δ3C  and  δ30,1,2,3,).
    $
    (1.3)

    The Appell's series or bivariate hypergeometric series is defined by

    $ F1(δ1,δ2,δ3;δ4;x,y)=m,n=0(δ1)m+n(δ2)m(δ3)nxmyn(δ4)m+nm!n!;
    $
    (1.4)

    for all $ \delta_1, \delta_2, \delta_3, \delta_4\in \mathbb{C}, \delta_4\neq 0, -1, -2, -3, \cdots, \quad |x|, |y| < 1 < 1 $.

    The integral representation of hypergeometric, confluent hypergeometric and Appell's functions are respectively defined by

    $ 2F1(δ1,δ2;δ3;z)=Γ(δ3)Γ(δ2)Γ(δ3δ2)10tδ21(1t)δ3δ21(1zt)δ1dt,
    $
    (1.5)
    $ \Big(\Re(\delta_3) \gt \Re(\delta_2) \gt 0, |\arg(1-z)| \lt \pi\Big), $

    and

    $ 1Φ1(δ2;δ3;z)=Γ(δ3)Γ(δ2)Γ(δ3δ2)10tδ21(1t)δ3δ21eztdt,
    $
    (1.6)
    $ \Big(\Re(\delta_3) \gt \Re(\delta_2) \gt 0\Big). $
    $ F1(δ1,δ2,δ3;δ4;x,y)=Γ(δ4)Γ(δ1)Γ(δ4δ1)10tδ11(1t)δ4δ11(1xt)δ2(1yt)δ3dt.
    $
    (1.7)

    The $ \mathtt{k} $-gamma function, $ \mathtt{k} $-beta function and the $ \mathtt{k} $-Pochhammer symbol introduced and studied by Diaz and Pariguan [5]. The integral representation of $ \mathtt{k} $-gamma function and $ \mathtt{k} $-beta function respectively given by

    $ Γk(z)=kzk1Γ(zk)=0tz1ezkkdt,(z)>0,k>0
    $
    (1.8)
    $ Bk(x,y)=1k10txk1(1t)yk1dt,(x)>0,(y)>0.
    $
    (1.9)

    Here, we recall the following relations (see [5]).

    $ Bk(x,y)=Γk(x)Γk(y)Γk(x+y),
    $
    (1.10)
    $ (z)n,k=Γk(z+nk)Γk(z),
    $
    (1.11)

    where $ (z)_{n, \mathtt{k}} = (z)(z+\mathtt{k})(z+2\mathtt{k})\cdots(z+(n-1)\mathtt{k}); \quad (z)_{0, \mathtt{k}} = 1 $ and $ \mathtt{k} > 0 $

    and

    $ n=0(α)n,kznn!=(1kz)αk.
    $
    (1.12)

    These studies were followed by Mansour [16], Kokologiannaki [13], Krasniqi [14] and Merovci [17]. In 2012, Mubeen and Habibullah [18] defined the $ \mathtt{k} $-hypergeometric function as

    $ 2F1,k(δ1,δ2;δ3;z)=n=0(δ1)n,k(δ2)n,k(δ3)n,kznn!,
    $
    (1.13)

    where $ \delta_1, \delta_2, \delta_3\in\mathbb{C} $ and $ \delta_3\neq0, -1, -2, \cdots $ and its integral representation is given by

    $ 2F1,k(δ1,δ2;δ3;z)=1kBk(δ2,δ3δ2)×10tδ2k1(1t)δ3δ2k1(1ktz)δ1kdt.
    $
    (1.14)

    The $ \mathtt{k} $-Riemann-Liouville (R-L) fractional integral using $ \mathtt{k} $-gamma function introduced in [19]:

    $ (Iαkf(t))(x)=1kΓk(α)x0f(t)(xt)αk1dt,k,αR+.
    $
    (1.15)

    Later on Mubeen and Iqbal [11] established the improved version of Gruss type inequalities by utilizing $ k $-fractional integrals. In [1], Agarwal et al. presented certain Hermite-Hadamard type inequalities for generalized $ k $-fractional integrals. Set et al. [29] presented an integral identity and generalized Hermite–Hadamard type inequalities for Riemann–Liouville fractional integral. Mubeen et al. [24] established integral inequalities of Ostrowski type for $ k $-fractional Riemann–Liouville integrals. Recently, many researchers have introduced generalized version of $ k $-fractional integrals and investigated a large bulk of various inequalities via the said fractional integrals. The interesting readers are referred to see the work of [9,10,26,30]. Farid et al. [7] introduced Hadamard $ k $-fractional integrals. In [8] introduced Hadamard-type inequalities for $ k $-fractional Riemann-Liouville integrals. In [12,31], the authors established certain inequalities by utilizing Hadamard-type inequalities for $ k $-fractional Riemann-Liouville integrals. In [25], Nisar et al. established certain Gronwall type inequalities associated with Riemann-Liouville $ k $- and Hadamard $ k $-fractional derivatives and their applications. In [25], they presented dependence solutions of certain $ k $-fractional differential equations of arbitrary real order with initial conditions. Recently, Samraiz et al. [28] defined an extension of Hadamard $ k $-fractional derivative and proved its various properties.

    The solution of some integral equations involving confluent $ \mathtt{k} $-hypergeometric functions and $ \mathtt{k} $-analogue of Kummer's first formula are given in [22,23]. While the $ \mathtt{k} $-hypergeometric and confluent $ \mathtt{k} $-hypergeometric differential equations are introduced in [20]. In 2015, Mubeen et al. [21] introduced $ \mathtt{k} $-Appell hypergeometric function as

    $ F1,k(δ1,δ2,δ3;δ4;z1,z2)=m,n=0(δ1)m+n,k(δ2)m,k(δ3)m,k(δ4)m+n,kzm1zn2m!n!
    $
    (1.16)

    for all $ \delta_1, \delta_2, \delta_3, \delta_4\in \mathbb{C}, \delta_4\neq 0, -1, -2, -3, \cdots, \quad \max\{|z_{1}|, |z_{2}|\} < \frac{1}{\mathtt{k}} $ and $ \mathtt{k} > 0 $. Also, Mubeen et al. defined its integral representation as

    $ F1,k(δ1,δ2,δ3;δ4;z1,z2)=1kBk(δ1,δ4δ1)10tδ1k1(1t)δ4δ1k1(1kz1t)δ2k(1kz2t)δ3kdt,
    $
    (1.17)
    $ \left(\Re(\delta_4) \gt \Re(\delta_1) \gt 0\right) . $

    In this section, we recall the following definition of fractional derivatives from and give a new extension called Riemann-Liouville $ \mathtt{k} $-fractional derivative.

    Definition 2.1. The well-known R-L fractional derivative of order $ \mu $ is defined by

    $ Dμx{f(x)}=1Γ(μ)x0f(t)(xt)μ1dt,(μ)<0.
    $
    (2.1)

    For the case $ m-1 < \Re(\mu) < m $ where $ m = 1, 2, \cdots $, it follows

    $ Dμx{f(x)}=dmdxmDμmx{f(x)}=dmdxm{1Γ(μ+m)x0f(t)(xt)μ+m1dt}.
    $
    (2.2)

    For further study and applications, we refer the readers to the work of [2,3,4,15,32]. In the following, we define Riemann-Liouville $ \mathtt{k} $-fractional derivative of order $ \mu $ as

    Definition 2.2.

    $ kDμx{f(x)}=1kΓk(μ)x0f(t)(xt)μk1dt,(μ)<0,kR+.
    $
    (2.3)

    For the case $ m-1 < \Re(\mu) < m $ where $ m = 1, 2, \cdots $, it follows

    $ kDμx{f(x)}=dmdxmkDμmkx{f(x)}=dmdxm{1kΓk(μ+mk)x0f(t)(xt)μk+m1dt}.
    $
    (2.4)

    Note that for $ \mathtt{k} = 1 $, definition 2.2 reduces to the classical R-L fractional derivative operator given in definition 2.1.

    Now, we are ready to prove some theorems by using the new definition 2.2.

    Theorem 1. The following formula holds true,

    $ kDμz{zηk}=zημkΓk(μ)Bk(η+k,μ),(μ)<0.
    $
    (2.5)

    Proof. From (2.3), we have

    $ kDμz{zηk}=1kΓk(μ)z0tηk(zt)μk1dt.
    $
    (2.6)

    Substituting $ t = uz $ in (2.6), we get

    $ kDμz{zηk}=1kΓk(μ)10(uz)ηk(zuz)μk1zdu=zημkkΓk(μ)10uηk(1u)μk1du.
    $

    Applying definition (1.9) to the above equation, we get the desired result.

    Theorem 2. Let $ \Re(\mu) > 0 $ and suppose that the function $ f(z) $ is analytic at the origin with its Maclaurin expansion given by $ f(z) = \sum_{n = 0}^\infty a_n z^n $ where $ |z| < \rho $ for some $ \rho\in \mathbb{R^+} $. Then

    $ kDμz{f(z)}=n=0ankDμz{zn}.
    $
    (2.7)

    Proof. Using the series expansion of the function $ f(z) $ in (2.3) gives

    $ kDμz{f(z)}=1kΓk(μ)z0n=0antn(zt)μk1dt.
    $

    As the series is uniformly convergent on any closed disk centered at the origin with its radius smaller then $ \rho $, therefore the series so does on the line segment from $ 0 $ to a fixed $ z $ for $ |z| < \rho $. Thus it guarantee terms by terms integration as follows

    $ kDμz{f(z)}=n=0an{1kΓk(μ)z0tn(zt)μk1dt=n=0ankDμz{zn},
    $

    which is the required proof.

    Theorem 3. The following result holds true:

    $ kDημz{zηk1(1kz)βk}=Γk(η)Γk(μ)zμk12F1,k(β,η;μ;z),
    $
    (2.8)

    where $ \Re(\mu) > \Re(\eta) > 0 $ and $ |z| < 1 $.

    Proof. By direct calculation, we have

    $ kDημz{zηk1(1kz)βk}=1kΓk(μη)z0tηk1(1kt)βk(zt)μηk1dt=zμηk1kΓk(μη)z0tηk1(1kt)βk(1tz)μηk1dt.
    $

    Substituting $ t = zu $ in the above equation, we get

    $ kDημz{zηk1(1kz)βk}=zμk1kΓk(μη)10uηk1(1kuz)βk(1u)μηk1zdu.
    $

    Applying (1.14) and after simplification we get the required proof.

    Theorem 4. The following result holds true:

    $ kDημz{zηk1(1kaz)αk(1kbz)βk}=Γk(η)Γk(μ)zμk1F1,k(η,α,β;μ;az,bz),
    $
    (2.9)

    where $ \Re(\mu) > \Re(\eta) > 0 $, $ \Re(\alpha) > 0 $, $ \Re(\beta) > 0 $, $ \max\{|az|, |bz|\} < \frac{1}{\mathtt{k}} $.

    Proof. To prove (2.9), we use the power series expansion

    $ (1kaz)αk(1kbz)βk=m=0n=0(α)m,k(β)n,k(az)mm!(bz)nn!.
    $

    Now, applying Theorem 1, we obtain

    $ kDημz{zηk1(1kaz)αk(1kbz)βk}=m=0n=0(α)m,k(β)n,k(a)mm!(b)nn!kDημz{zηk+m+n1}=m=0n=0(α)m,k(β)n,k(a)mm!(b)nn!βk(η+mk+nk,μη)Γk(μη)zμk+m+n1=m=0n=0(α)m,k(β)n,k(a)mm!(b)nn!Γk(η+mk+nk)Γk(μ+mk+nk)zμk+m+n1.
    $

    In view of (1.16), we get

    $ kDημz{zηk1(1kaz)αk(1kbz)βk}=Γk(η)Γk(μ)zμk1F1,k(η,α,β;μ;az,bz).
    $

    Theorem 5. The following Mellin transform formula holds true:

    $ M{exkDμz(zηk);s}=Γ(s)Γk(μ)Bk(η+k,μ)zημk,
    $
    (2.10)

    where $ \Re(\eta) > -1 $, $ \Re(\mu) < 0 $, $ \Re(s) > 0 $.

    Proof. Applying the Mellin transform on definition (2.3), we have

    $ M{exkDμz(zηk);s}=0xs1exkDμz(zη);s}dx=1kΓk(μ)0xs1ex{z0tηk(zt)μk1dt}dx=zμk1kΓk(μ)0xs1ex{z0tηk(1tz)μk1dt}dx=zημkkΓk(μ)0xs1ex{10uηk(1u)μk1du}dx
    $

    Interchanging the order of integrations in above equation, we get

    $ M{exkDμz(zηk);s}=zημkkΓk(μ)10uηk(1u)μk1(0xs1exdx)du.=zημkkΓk(μ)Γ(s)10uηk(1u)μk1du=Γ(s)Γk(μ)Bk(η+k,μ)zημk,
    $

    which completes the proof.

    Theorem 6. The following Mellin transform formula holds true:

    $ M{exkDμz((1kz)αk);s}=zμkΓ(s)Γk(μ)Bk(k,μ)2F1,k(α,k;μ+k;z),
    $
    (2.11)

    where $ \Re(\alpha) > 0 $, $ \Re(\mu) < 0 $, $ \Re(s) > 0 $, and $ |z| < 1 $.

    Proof. Using the power series for $ (1-\mathtt{k}z)^{-\frac{\alpha}{\mathtt{k}}} $ and applying Theorem 5 with $ \eta = n\mathtt{k} $, we can write

    $ M{exkDμz((1kz)αk);s}=n=0(α)n,kn!M{exkDμz(zn);s}=Γ(s)kΓk(μ)n=0(α)n,kn!Bk(nk+k,μ)znμk=Γ(s)zμkΓk(μ)n=0Bk(nk+k,μ)(α)n,kznn!=Γ(s)zμkn=0Γk(k+nk)Γk(μ+k+nk)(α)n,kznn!=Γ(s)Γk(μ+k)zμkn=0(k)n,k(μ+k)n,k(α)n,kznn!=Γ(s)zμkΓk(μ)Bk(k,μ)2F1,k(α,k;μ+k;z),
    $

    which is the required proof.

    Theorem 7. The following result holds true:

    $ kDημz[zηk1Eμk,γ,δ(z)]=zμk1kΓk(μη)n=0(μ)n,kΓk(γn+δ)Bk(η+nk,μη)znn!,
    $
    (2.12)

    where $ \gamma, \delta, \mu\in\mathbb{C} $, $ \Re(p) > 0 $, $ \Re(q) > 0 $, $ \Re(\mu) > \Re(\eta) > 0 $ and $ E_{\mathtt{k}, \gamma, \delta}^{\mu}(z) $ is $ \mathtt{k} $-Mittag-Leffler function (see [6]) defined as:

    $ Eμk,γ,δ(z)=n=0(μ)n,kΓk(γn+δ)znn!.
    $
    (2.13)

    Proof. Using (2.13), the left-hand side of (2.12) can be written as

    $ kDημz[zηk1Eμk,γ,δ(z)]=kDημz[zηk1{n=0(μ)n,kΓk(γn+δ)znn!}].
    $

    By Theorem 2, we have

    $ kDημz[zηk1Eμk,γ,δ(z)]=n=0(μ)n,kΓk(γn+δ){kDμz[zηk+n1]}.
    $

    In view of Theorem 1, we get the required proof.

    Theorem 8. The following result holds true:

    $ kDημz{zηk1mΨn[(αi,Ai)1,m;|z(βj,Bj)1,n;]}=zμk1kΓk(μη)×n=0mi=1Γ(αi+Ain)nj=1Γ(βj+BjnBk(η+nk,μη)znn!,
    $
    (2.14)

    where $ \Re(p) > 0 $, $ \Re(q) > 0 $, $ \Re(\mu) > \Re(\eta) > 0 $ and $ _m\Psi_n(z) $ is the Fox-Wright function defined by (see [15], pages 56–58)

    $ mΨn(z)=mΨn[(αi,Ai)1,m;|z(βj,Bj)1,n;]=n=0mi=1Γ(αi+Ain)nj=1Γ(βj+Bjnznn!.
    $
    (2.15)

    Proof. Applying Theorem 1 and followed the same procedure used in Theorem 7, we get the desired result.

    Recently, many researchers have introduced various generalizations of fractional integrals and derivatives. In this line, we have established a $ k $-fractional derivative and its various properties. If we letting $ \mathtt{k}\rightarrow1 $ then all the results established in this paper will reduce to the results related to the classical Reimann-Liouville fractional derivative operator.

    The author K.S. Nisar thanks to Deanship of Scientific Research (DSR), Prince Sattam bin Abdulaziz University for providing facilities and support.

    The authors declare no conflict of interest.

    [1] Griffith JD (1975) Chromatin structure: deduced from a minichromosome. Science 187: 1202-1203. doi: 10.1126/science.187.4182.1202
    [2] Bellard M, Oudet P, Germond JE, et al. (1976) Subunit structure of simian-virus-40 minichromosome. Eur J Biochem 70: 543-553. doi: 10.1111/j.1432-1033.1976.tb11046.x
    [3] Mengeritsky G, Trifonov EN (1984) Nucleotide sequence-directed mapping of the nucleosomes of SV40 chromatin. Cell Bioph 6: 1-9. doi: 10.1007/BF02788576
    [4] Ambrose C, Lowman H, Rajadhyaksha A, et al. (1990) Location of nucleosomes in simian virus 40 chromatin. J Mol Biol 214: 875-884. doi: 10.1016/0022-2836(90)90342-J
    [5] Tatchell K, van Holde KE (1978) Compact oligomers and nucleosome phasing. Proc Natl Acad Sci USA 75: 3583-3587.
    [6] Fajkus J, Trifonov EN (2001) Columnar packing of telomeric nucleosomes. Biochem Biophys Res Comm 280: 961-963. doi: 10.1006/bbrc.2000.4208
    [7] Salih B, Trifonov EN (2015) Strong nucleosomes of A. thaliana concentrate in centromere regions. J Biomol Str Dyn 33: 10-13.
    [8] Salih B, Trifonov EN (2015). Strong nucleosomes reside in meiotic centromeres of C. elegans. J Biomol Str Dyn 33: 365-373. doi: 10.1080/07391102.2013.879263
    [9] Nibhani R, Trifonov EN (2015) Reading sequence-directed computational nucleosome maps. J Biomol Str Dyn 33:1558-1566. doi: 10.1080/07391102.2014.958877
    [10] Gu SG, Goszczynski B, McGhee JD, et al. (2013) Unusual DNA packaging characteristics in endoreduplicated Caenorhabditis elegans oocytes defined by in vivo accessibility to an endogenous nuclease activity. Epigenet Chromatin 6: 37. doi: 10.1186/1756-8935-6-37
    [11] Ponder BAJ, Crawford LV (1977) Arrangement of nucleosomes in nucleoprotein complexes from polyoma-virus and SV40. Cell 11: 35-49. doi: 10.1016/0092-8674(77)90315-4
    [12] Zhang T, Talbert PB, Zhang W, et al. (2013) The CentO satellite confers translational and rotational phasing on cenH3 nucleosomes in rice centromeres. Proc Natl Acad Sci U S A 110: E4875-4883.
    [13] Rattner JB, Hamkalo BA (1978) Higher-order structure in metaphase chromosomes Chromosoma 69: 373-379.
    [14] Dubochet J, Adrian M, Schultz P, et al. (1986) Cryo-electron microscopy of vitrified SV40 minichromosomes: the liquid drop model. EMBO J 5: 519-528.
    [15] Wanner G, Formanek H (2000) A new chromosome model. J Struct Biol 132: 147-161. doi: 10.1006/jsbi.2000.4310
    [16] Karpov VL, Bavykin SG, Preobrazhenskaya OV, et al. (1982) Alignment of nucleosomes along DNA and organization of spacer DNA in drosophila chromatin. Nucl Acids Res 10: 4321-4337. doi: 10.1093/nar/10.14.4321
    [17] Widom J (1992) A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells. Proc Natl Acad Sci U S A 89:1095-1099.
    [18] Rapoport AE, Frenkel ZM, Trifonov EN (2011) Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. J Biomol Str Dyn 28: 567-574. doi: 10.1080/07391102.2011.10531243
    [19] Frenkel ZM, Bettecken T, Trifonov EN (2011) Nucleosome DNA sequence structure of isochores. BMC Genomics 12: 203. doi: 10.1186/1471-2164-12-203
    [20] Tripathi V, Salih B, Trifonov EN (2015) Universal full-length nucleosome mapping sequence probe. J Biomol Str Dyn 33: 666-673. doi: 10.1080/07391102.2014.891262
    [21] Lowary PT, Widom J (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence directed nucleosome positioning. J Mol Biol 276: 19-42. doi: 10.1006/jmbi.1997.1494
    [22] Trifonov EN, Nibhani R (2015) Review fifteen years of search for strong nucleosomes. Biopolymers, 103: 432-437. doi: 10.1002/bip.22604
    [23] Nibhani R, Trifonov EN, TA-periodic (“601”-like) centromeric nucleosomes of A.thaliana. J Biomol Str Dyn [in press].
    [24] Vasudevan D, Chua EYD, Davey CA (2010) Crystal structures of nucleosome core particles containing the ‘601’ strong positioning sequence. J Mol Biol 403: 1-10. doi: 10.1016/j.jmb.2010.08.039
    [25] Zhurkin VB (1982) Periodicity in DNA primary structure and specific alignment of nucleosomes. Stud Biophys 87: 151-152.
    [26] Zhurkin VB (1983) Specific alignment of nucleosomes on DNA correlates with periodic distribution of purine pyrimidine and pyrimidine purine dimers. FEBS Lett 158: 293-297. doi: 10.1016/0014-5793(83)80598-5
    [27] Zhurkin VB, Lysov YP, Ivanov VI (1979) Anisotropic flexibility of DNA and the nucleosomal structure. Nucl Acids Res 6: 1081-1096. doi: 10.1093/nar/6.3.1081
    [28] Wang D, Ulyanov NB, Zhurkin VB (2010) Sequence-dependent kink-and-slide deformations of nucleosomal DNA facilitated by histone arginines bound in the minor groove. J Biomol Str Dyn 27: 843-859. doi: 10.1080/07391102.2010.10508586
    [29] McDowall AW, Smith JM, Dubochet J (1986) Cryo-electron microscopy of vitrified chromosomes in situ. EMBO J 5: 1395-1402.
    [30] Trifonov EN Nucleosome repeat lengths and columnar chromatin structure. J Biomol Str Dyn [in press].
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