A heterochromatic satellite DNA is highly amplified in a single chromosome of Muscari (Hyacinthaceae)

We examined the composition and evolution of a large heterochromatic region present in the genomes of certain species of the genus Muscari (Hyacinthaceae). We found that in Muscari comosum this heterochromatic region is composed mainly of a satellite DNA family, which we named MCSAT. Molecular analyses and in situ hybridization revealed that, through the evolution of Muscari species, the MCSAT sequences have been progressively amplified in several species of the genus, such as M. matritensis and M. dionysicum, attaining enormous amplification in the genome of M. comosum. We discuss the characteristics of this satellite DNA family, which, being exclusively amplified in one chromosome pair of M. comosum, constitute the major exception to the equilocal model of satellite DNA and heterochromatin distribution. Also, we discuss the possibility that the amplification of these sequences in a single chromosome could have contributed to a progressive increase in the asymmetry of the karyotypes in Muscari species.     

A revision of the species of <Emphasis Type="Italic">Saturnius</Emphasis> Manter, 1969 (Digenea: Hemiuridae), parasites of mullets (Teleostei: Mugilidae)

The genus Saturnius Manter, 1969 is defined, its species re-examined and a key to the species presented. S. overstreeti n. sp. is described from Mugil soiuy Basilewsky and M. cephalus L. from the Russian coast of the Sea of Japan and distinguished from the morphologically related S. papernai Overstreet, 1977 and S. maurepasi Overstreet, 1977. S. segmentatus Manter, 1969 is redescribed on the basis of the type- and newly collected material from M. cephalus on the Russian coast of the Sea of Japan. The morphometric variation of S. papernai is studied based on newly collected material from Liza aurata (Risso) in the Ebro Delta and off Santa Pola, Spain. The comparisons reveal lower ranges of most metrical features than previously known. A principal component analysis, carried out after adding the new data to those of Blasco-Costa et al. (2006), confirms the species identification. Other valid species recognised are S. mugilis (Yamaguti, 1970), S. maurepasi, S. belizensis Fischthal, 1977, S. dimitrovi Blasco-Costa et al., 2006 and S. minutus Blasco-Costa et al., 2006. Forms considered species inquirendae are S. valamugilis Rekharani & Madhavi, 1984, Bunocotyle constrictus Domnich & Sarabeev, 1999 [=S. papernai of Domnich & Sarabeev (2000a, b, c, d)], B. mugilis Yamaguti, 1970 of Solonchenko (1976) and S. mugilis of Dmitrieva & Gaevskaya (2001). Host and locality information is given in detail for all species. Lisa ramado (Risso) and Chelon labrosus (Cuvier) are new host records for S. papernai (sensu stricto) and S. dimitrovi. L. aurata is a new host record for S. dimitrovi and S. minutus, and L. saliens (Risso) is a new host record for S. minutus.     

Muscari vuralii sp. nov. (Liliaceae/Hyacinthaceae) from south Anatolia, Turkey

Muscari vuralii Y. Bağcı & Doğu sp. nov. (Liliaceae/Hyacinthaceae) from the Karaman (C4 Karaman–Turkey) is described and illustrated. It is closely related to M. coeleste Fomin and M. macbeathianum Kit Tan. Diagnostic morphological characters are discussed and a key to related Muscari species in Turkey is given. The geographical distribution of the new species is mapped. Notes are also presented on its ecology, biogeography and conservation status.     

Saturnius minutus n. sp. and S. dimitrovi n. sp. (Digenea: Hemiuridae) from Mugil cephalus L. (Teleostei: Mugilidae), with a multivariate morphological analysis of the Mediterranean species of Saturnius Manter, 1969

Three species of the bunocotyline genus Saturnius Manter, 1969 are described from the stomach lining of mugilid fishes of the Mediterranean and Black Seas. Two of the species are new: S. minutus n. sp. occurs in Mugil cephalus off the Mediterranean coast of Spain; and S. dimitrovi n. sp., a parasite of M. cephalus off the Bulgarian Black Sea coast and the Spanish Mediterranean coast, was originally described as S. papernai by Dimitrov et al. (1998). In addition, S. papernai Overstreet, 1977 is redescribed from M. cephalus off the Spanish Mediterranean coast and from Liza aurata and L. saliens off the Bulgarian Black Sea coast. The three species are distinguished morphometrically using univariate and multivariate analyses. These results were verified using Linear Discriminant Analysis which correctly allocated all specimens to their species designations based on morphology (i.e. 100% successful classification rate) and assigned almost all specimens to the correct population (locality). The following variables were selected for optimal separation between samples: the length of the forebody, ventral sucker and posterior testis, the length and width of the posteriormost pseudosegment, and the width of the muscular flange at ventral sucker level.     

Crystal structure of a high-affinity variant of rat alpha-parvalbumin

In model peptide systems, Ca2+ affinity is maximized in EF-hand motifs containing four carboxylates positioned on the +x and -x and +z and -z axes; introduction of a fifth carboxylate ligand reduces the affinity. However, in rat beta-parvalbumin, replacement of Ser-55 with aspartate heightens divalent ion affinity [Henzl, M. T., et al. (1996) Biochemistry 35, 5856-5869]. The corresponding alpha-parvalbumin variant (S55D/E59D) likewise exhibits elevated affinity [Henzl, M. T., et al. (2003) Anal. Biochem. 319, 216-233]. To determine whether these mutations produce a variation on the archetypal EF-hand coordination scheme, we have obtained high-resolution X-ray crystallographic data for alpha S55D/E59D. As anticipated, the aspartyl carboxylate replaces the serine hydroxyl at the +z coordination position. Interestingly, the Asp-59 carboxylate abandons the role it plays as an outer sphere ligand in wild-type rat beta, rotating away from the Ca2+ and, instead, forming a hydrogen bond with the amide of Glu-62. Superficially, the coordination sphere in the CD site of alpha S55D/E59D resembles that in the EF site. However, the orientation of the Asp-59 side chain is predicted to stabilize the D-helix, which may contribute to the heightened divalent ion affinity. DSC data indicate that the alpha S55D/E59D variant retains the capacity to bind 1 equiv of Na+. Consistent with this finding, when binding measurements are conducted in K(+)-containing buffer, divalent ion affinity is markedly higher. In 0.15 M KCl and 0.025 M Hepes-KOH (pH 7.4) at 5 degrees C, the macroscopic Ca2+ binding constants are 1.8 x 10(10) and 2.0 x 10(9) M(-1). The corresponding Mg2+ binding constants are 2.7 x 10(6) and 1.2 x 10(5) M(-1).     

Intraindividual variability in Sinonamuropteridae forewing venation (Grylloblattida; Late Carboniferous): taxonomic and nomenclatural implications

The family Sinonamuropteridae has been erected for nine fossil insect species from the Late Carboniferous Tupo Formation (Ningxia, China), each represented by a single isolated forewing. The family has been assigned to the order Diaphanopterodea (extinct palaeopteran order). We investigated the forewing venation pattern and its variability in this family based on an abundant collection from the same locality. Based on new data on Chelopterum peregrinum Carpenter, 1950 (Grylloblattida; Lower Permian; Wellington Formation, U.S.A.) and the new material, we demonstrate that the nine sinonamuropteridaean species form a single one: Sinonamuropteris ningxiaensis Peng et al., 2005 . The following genera are considered as synonyms of Sinonamuropteris: Separatonerva Peng et al., 2005 syn.n. , Combonerva Peng et al., 2005 syn.n. and Tectonerva Peng et al., 2005 syn.n. The following species (all with Peng et al., 2005 , as their authority) are considered as synonyms of S. ningxiaensis: Separatonerva longa syn.n. , Separatonerva qilianshanensis syn.n. , Combonerva granulata syn.n. , Combonerva huangheensis syn.n. , Tectonerva longovata syn.n. , Sinonamuropsis zhongweiensis syn.n. , Sinonamuropsis rugoverrucosa syn.n. , Sinonamuropsis xiaheyanensis syn.n. The family must be assigned to the neopteran order Grylloblattida.     

三种东亚冷杉植物的核型研究

首次报道了急尖长苞冷杉ＡｂｉｅｓｇｅｏｒｇｅｉＯｒｒｖａｒ．ｓｍｉｔｈｉｉ（ＶｉｇｕｉｅｅｔＧａｕｓｓｅｎ）Ｃｈｅｎｇｅｔ．Ｌ．Ｋ．Ｆｕ,臭冷杉Ａ．ｎｅｐｈｒｏｌｅｐｉｓ（Ｔｒａｕｒｖ．）Ｍａｘｉｍ和杉松,Ａ．ｈｏｌｏｐｈｙｌｌａｍａｘｉｍ等３种东亚冷杉植物的核型,它们的核型公式分别是Ｋ（２ｎ）＝２４＝１８ｍ（２ＳＣ）＋６ｓｍ,１８ｍ（６ＳＣ）＋６ｓｍ和１４ｍ（６ＳＣ）＋１０ｓｍ,染色体相对长度组     

Chemical shift assignments of Ribosomal protein S1 from <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis>

RpsA, also known as ribosomal protein S1, is an essential protein required for translation initiation of mRNAs when their Shine-Dalgarno sequence is degenerated (Sorensen et al. 1998). In addition, RpsA of Mycobacterium tuberculosis (M. tb) is involved in trans-translation, which is an effective system mediated by tmRNA-SmpB to release stalled ribosomes from mRNA in the presence of rare codons (Keiler 2008). Shi et al. found that POA binds to RpsA of Mtb and disrupts the formation of RpsA–tmRNA complex (Shi et al. 2011) and mutations at the C-terminus of RpsA confer PZA resistance. The previous work reported the pyrazinoic acid-binding domain of RpsA (Yang et al. Mol Microbiol 95:791–803, 2015). However, the HSQC spectra of the isolated S1 domain does not overlap with that of MtRpsA280-438, suggesting that substantial interactions occur between the flexible C-terminus and the S1 domain in MtRpsA .To further study the PZA resistance and how substantial interactions influence/affect protein structure, using heteronuclear NMR spectroscopy, we have completed backbone and side-chain ¹H, ¹⁵N, ¹³C chemical shift assignments of MtRpsA280-438 which contains S1 domain and the flexible C-terminus. These NMR resonance assignments provide the framework for detailed characterization of the solution-state protein structure determination, dynamic studies of this domain, as well as NMR-based drug discovery efforts.     

The Friedreich ataxia gene is assigned to chromosome 9q13-q21 by mapping of tightly linked markers and shows linkage disequilibrium with D9S15.

Chamberlain et al. have assigned the gene for Friedreich ataxia (FA), a recessive neurodegenerative disorder, to chromosome 9, and have proposed a regional localization in the proximal short arm (9p22-cen), on the basis of linkage to D9S15 and to interferon-beta (IFNB), the latter being localized in 9p22. We confirmed more recently the close linkage to D9S15 in another set of families but found much looser linkage to IFNB. We also reported another closely linked marker, D9S5. Additional families have now been studied, and our updated lod scores are z = 14.30 at theta = .00 for D9S15-FA linkage and z = 6.30 at theta = .00 for D9S5-FA linkage. Together with the recent data of Chamberlain et al., this shows that D9S15 is very likely within 1 cM of the FA locus. We have found very significant linkage disequilibrium (delta Std = .28, chi 2 = 9.71, P less than .01) between FA and the D9S15 MspI RFLP in French families, which further supports the very close proximity of these two loci. No recombination between D9S5 and D9S15 was found in the FA families or Centre d'Etude du Polymorphisme Humain families (z = 9.30 at theta = .00). Thus D9S5, D9S15, and FA define a cluster of tightly linked loci. We have mapped D9S5 by in situ hybridization to 9q13-q21, and, accordingly, we assign the D9S5, D9S15, and FA cluster to the proximal part of chromosome 9 long arm, close to the heterochromatic region.     

Muscari turcicum (Liliaceae/Hyacinthaceae), a new species from south Anatolia, Turkey

Muscari turcicum Uysal, Ertugrul & Dural (Liliaceae/Hyacinthaceae) is described and illustrated from south Anatolia, Turkey. This species grows on alpine steppe in the Middle Taurus (C4 Konya Province). Muscari turcicum , an endemic confined to the Middle Taurus, is closely related to M. discolor Boiss. & Hausskn. and M. anatolicum Cowley & Özhatay. Diagnostic morphological characters are discussed and compared with those of closely related taxa.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 233–236.     

四种云杉的核型分析

首次报道了中国珍稀濒危保护植物长叶云杉 ( P. smithiana ( Wall.) Boiss.)和康定云杉 ( P. likian-gensis( Franch.) Pritz.var.montigena( Mast.) Cheng ex Chen)及我国特产的青海云杉 ( P.crassif oliaKom.)和林芝云杉 ( P.likiangensis( Franch.) Pritz.var.linzhiensis Cheng et L.K.Fu)的核型。它们的核型公式都是 K( 2 n) =2 4 =2 2 m+2 sm (林芝云杉有 1条 B染色体 ) ,染色体相对长度组成分别为 2 n=1 4 M2 +8M1 +2 S,2 L+1 2 M2 +6M1 +4S,2 L +1 0 M2 +1 0 M1 +2 S,和 2 L+1 2 M2 +6M1 +4S.均为 2 A (除青海云杉 1 A外 )核型类型。     

A novel role for Greatwall kinase in recovery from DNA damage

Activation of the DNA damage response (DDR) is critical for genomic integrity and tumor suppression. The occurrence of DNA damage quickly evokes the DDR through ATM/ATR-dependent signal transduction, which promotes DNA repair and activates the checkpoint to halt cell cycle progression (Halazonetis et al., 2008; Motoyama and Naka, 2004; Zhou and Elledge, 2000). The "turn off" process of the DDR upon satisfaction of DNA repair, also known as "checkpoint recovery", involves deactivation of DDR elements, but the mechanism is poorly understood. Greatwall kinase (Gwl) has been identified as a key element in the G2/M transition (Archambault et al., 2007; Jackson, 2006; Zhao et al., 2008; Yu et al., 2004; Yu et al., 2006; Zhao et al., 2006) and helps maintain M phase through inhibition of PP2A/B55δ (Burgess et al., 2010; Castilho et al., 2009; Goldberg, 2010; Lorca et al., 2010; Vigneron et al., 2009), the principal phosphatase for Cdk-phosphorylated substrates. Here we show that Gwl also promotes recovery from DNA damage and is itself directly inhibited by the DNA damage response (DDR). In Xenopus egg extracts, immunodepletion of Gwl increased the DDR to damaged DNA, whereas addition of wild type, but not kinase dead Gwl, inhibited the DDR. The removal of damaged DNA from egg extracts leads to recovery from checkpoint arrest and entry into mitosis, a process impaired by Gwl depletion and enhanced by Gwl over-expression. Moreover, activation of Cdk1 after the removal of damaged DNA is regulated by Gwl. Collectively, these results defines Gwl as a new regulator of the DDR, which plays an important role in recovery from DNA     

Thermodynamics of phospholipid bilayer assembly

Thermodynamic properties of bilayer assembly have been obtained from measurements of the solubility of the sodium salt of dimyristoylphosphatidylglycerol (DMPG) in water. The standard free energy of bilayer assembly delta G degree a is shown to be RT 1n Xs + zF psi 0 where Xs is the mole fraction of dissolved lipid, F is the Faraday constant, z is the valence of the counterion (Na+), and psi 0 is the electrical double-layer potential of the ionized bilayer. The function d 1n Xs/dT was found to be discontinuous at 24 degrees C, the gel-liquid-crystal transition temperature (Tm) for DMPG. This function was unaffected when solubilities were measured in 0.001 M NaCl solutions; thus, psi 0 is constant in the experimental temperature interval (4-40 degrees C). Using a value of psi 0 = -180 mV [Eisenberg et al. (1979) Biochemistry 18, 5213-5223], and the temperature dependence of delta G degrees a, values for delta H degrees a and delta S degree a at 24 degrees C were calculated for the gel and liquid-crystal states of DMPG. For the gel, delta H degrees a and T delta S a are -26.2 and 12.7 kcal/mol, respectively; for the liquid-crystal, delta H degrees a and T delta S degrees a are -19.2 and -5.7 kcal/mol, respectively. The calculated value for the latent heat of the gel-liquid-crystal transition is 7 kcal/mol, in agreement with calorimetric measurements.     

An integrative approach in the assessment of species delimitation and structure of the <Emphasis Type="Italic">Merodon nanus</Emphasis> species group (Diptera: Syrphidae)

The Merodon nanus group (Diptera, Syrphidae) is a small group of closely related species with high morphological similarity. Until now, based on morphological characters, this group consisted of five species: M. nanus Sack, 1931; M. telmateia Hurkmans, 1987; M. kopensis Vuji? et Hayat, 2015; M. neonanus Vuji? et Taylor, 2015; and M. rasicus Vuji? et Radenkovi?, 2015. Here, using an integrative approach based on molecular characters (sequences of the D2–3 region of the nuclear 28S rRNA gene and the mitochondrial COI gene) and data obtained from geometric morphometry of wing shape, we distinguish all five previously morphologically defined species of the group. Additionally, we identify one species as being new to science, M. vladimiri Vuji? et Ko?i? Tubi? sp. n. We emphasize the separation of this newly described species according to the sequences obtained from the slowly evolving 28S rRNA gene, which demonstrated four to five mutation positions between this species and morphologically the most similar M. neonanus species. Also, our results show a clear division of M. telmateia into at least three population groups that we designate as the subspecies: M. telmateia mediterraneus A?anski et Ko?i? Tubi? subsp. n. and M. telmateia samosensis A?anski et Ko?i? Tubi? subsp. n. exhibiting western distributions (western Anatolia and the Greek island of Samos, respectively) and the nominative subspecies M. telmateia telmateia with an eastern Anatolian distribution.     

Electron paramagnetic resonance spectroscopy with N-methyl-D-glucamine dithiocarbamate iron complexes distinguishes nitric oxide and nitroxyl anion in a redox-dependent manner: applications in identifying nitrogen monoxide products from nitric oxide synthase

Though a large number of studies indicate that nitric oxide synthase (NOS) is responsible for NO&z.rad; production in biological systems, controversy still remains concerning whether NOS directly produces NO&z.rad;. Schmidt et al. (PNAS 93:144492, 1996) proposed that NOS first synthesizes nitroxyl anion (NO(-)), which is then converted to NO&z.rad; by superoxide dismutase (SOD). With electron paramagnetic resonance spectroscopy using N-methyl-D-glucamine dithiocarbamate iron (Fe-MGD), we directly detected NO&z.rad; from purified NOS in the absence of SOD (Xia et al., PNAS 94:12705, 1997). We also showed that the requirement for SOD in the previous NO&z.rad; measurements appeared to be due to the high levels of exogenous superoxide production in their reaction system because of the presence of free FAD. However, it was recently questioned whether Fe-MGD can discriminate NO&z.rad; from NO(-) (Komarov et al., FRBM 28:739-742, 2000). In this study we examined the trapping specificity of different redox forms of Fe-MGD. With Fe(2+)-MGD, NO&z.rad; generated characteristic triplet NO&z.rad;-Fe(2+)-MGD signals (g = 2. 04, a(N) = 12.7 G), whereas NO(-) from Angeli's salt was EPR silent. Both NO&z.rad; and NO(-) gave rise to NO&z.rad;-Fe(2+)-MGD signals when Fe(3+)-MGD was used. Strong NO&z.rad; signals were measured from purified nNOS using the NO&z.rad; selective Fe(2+)-MGD and this was not affected by SOD. Thus, spin trapping with Fe-MGD can distinguish NO&z.rad; and NO(-) and this depends on the redox status of the iron. The detection of NO&z.rad; from purified NOS by Fe(2+)-MGD unambiguously reconfirms our previous report that NOS directly synthesizes NO&z.rad; but not NO(-).     

Diagnosis of infantile and juvenile forms of GM2 gangliosidosis variant 0. residual activities toward natural and different synthetic substrates

Summary p-Nitrophenyl-6-sulfo-2-acetamido-2-deoxy--d-glucopyranoside, which is known to be a specific substrate for human hexosaminidase A, has recently been used successfully for diagnosis of variants B and B¹ of G_M2-gangliosidosis (Fuchs et al. 1983; Kytzia et al. 1983; Li et al. 1983). However, it is hydrolyzed by hexosaminidase S as well and is therefore not suitable for detection of patients with variant 0, who reach the normal range of activity toward this substrats. Assay of ganglioside G_M2 cleaving activity in fibroblast extracts in the presence of the natural G_M2 activator protein reveals residual hexosaminidase A activities of less than 2% of normal controls in two infantile and up to 7.5% in two juvenile patients with variant 0.     

Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base-pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14).

Optical melting curves of seven DNA dumbbells with the 16 base-pair duplex sequence 5'G-C-A-T-A-G-A-T-G-A-G-A-A-T-G-C3' linked on both ends by Tn (n = 2, 3, 4, 6, 8, 10, and 14) loops measured in 30, 70, and 120 mM Na+ are analyzed in terms of the numerically exact statistical thermodynamic model of DNA melting. The construction and characterization of these molecules were described in the previous paper (Amaratunga et al., 1992). As was recently reported for hairpins (T. M. Paner, M. Amaratunga, M. J. Doktycz, and A. S. Benight, 1990, Biopolymers, Vol. 29, pp. 1715-1734) theoretically calculated melting curves were fitted to experimental curves by simultaneously adjusting the parameters representing loop and circle formation to optimize the fits. The systematically determined empirical parameters provide evaluations of the free energies of hairpin loop formation delta Gloop (n) and single-strand circles delta Gcircle (N), as a function of end loop size, n = 2-14, and circle size, N = 32 + 2n. The dependence of these quantities on solvent ionic strength over the range from 30 to 120 mM Na+ was evaluated. An approximately analytical expression for the partition function Q(T) of the dumbbells was formulated that allowed a means for determining the transition enthalpy delta H degrees and entropy delta S degrees for every dumbbell, revealing the dependence of these quantities on loop size. In this multistate approach a manifold of partially melted intermediate microstates are considered and therefore no assumptions regarding the nature of the melting transitions (that they are two-state) are required. The transition thermodynamic parameters were also determined from a van't Hoff analysis of the melting curves. Comparisons between the results of the multistate analysis and the two-state van't Hoff analysis revealed significant differences for the dumbbells with larger end loops, indicating that the melting transitions of the larger looped dumbbells deviate considerably from two-state behavior. Results are then compared with published melting studies of much larger DNA dumbbells (D. B. Naritsin and Y. L. Lyubchenko, 1990, Journal of Biomolecular Structure and Dynamics, Vol. 8, pp. 1-13), of small hairpins (Paner et al., 1990; M. J. Doktycz, T. M. Paner, M. Amaratunga and A. S. Benight, 1990, Biopolymers, Vol. 30, pp. 829-845) and another dumbbell (A. S. Benight, J. M. Schurr, P. F. Flynn, B. R. Reid, and D. E. Wemmer, 1988) Journal of Molecular Biology, Vol. 200, pp. 377-399).(ABSTRACT TRUNCATED AT 400 WORDS)     

Resonance Raman characterization of <Emphasis Type="Italic">Rhodobacter capsulatus</Emphasis> reaction centers with lysine mutations near the accessory bacteriochlorophylls

Lysine residues have been introduced into Rhodobacter capsulatus reaction centers at M-polypeptide position 201 and at L-polypeptide position 178. These positions are in the proximity of ring V of the accessory bacterochlorophylls B_A and B_B, respectively. Resonance Raman studies indicate that the introduction of a Lys residue at either position M201 or L178 results in structural perturbations to the BChl cofactors. Lys at L178 directly interacts with B_B, most likely via a hydrogen bond. The hydrogen bonding interaction is consistent with enhanced B branch electron transfer that is observed in RCs from the S(L178)K/G(M201)D/L(M212)H triple mutant versus the G(M201)D/L(M212)H double mutant (C. Kirmaier et al. (1999) Biochemistry 38 11516–11530). In contrast, the introduction of a Lys at M201 does not result in hydrogen bonding to the B_A cofactor, in contrast to the introduction of a His at M201 (L. Chen et al. (2004) J Phys Chem 3 108: 0457–10464). Accordingly, the alkyl ammonium head group of the side chain of the Lys at M201 residue appears to be distant from B_A.     

夏蜡梅核型的研究

本文首次报道我国特有重点保护植物夏蜡梅的核型为K(2n)=2x=22=18m+2m(SAT)+2sm,属Stebbins的“1A”类型,在演化上处于相当原始的地位。它的核型似比北美的光叶红对称和原始,因此至少夏蜡梅属可能起源于中国。