bluuebunny/crossref_metadata_2025 huggingface dataset:
Epstein-Barr Virus SM Protein Functions as an Alternative Splicing Factor
Authors: Verma Dinesh , Swaminathan Sankar
Published: May 2008

Alternative splicing of RNA increases the coding potential of the genome and allows for additional regulatory control over gene expression. The full extent of alternative splicing remains to be defined but is likely to significantly expand the size of the human transcriptome. There are several examples of mammalian viruses regulating viral splicing or inhibiting cellular splicing in order to facilitate viral replication. Here, we describe a viral protein that induces alternative splicing of a cellular RNA transcript. Epstein-Barr virus (EBV) SM protein is a viral protein essential for replication that enhances EBV gene expression by enhancing RNA stability and export. SM also increases cellular STAT1 expression, a central mediator of interferon signal transduction, but disproportionately increases the abundance of the STAT1β splicing isoform, which can act as a dominant-negative suppressor of STAT1α. SM induces splicing of STAT1 at a novel 5′ splice site, resulting in a STAT1 mRNA incapable of producing STAT1α. SM-induced alternative splicing is dependent on the presence of an RNA sequence to which SM binds directly and which can confer SM-dependent splicing on heterologous RNA. The cellular splicing factor ASF/SF2 also binds to this region and inhibits SM-RNA binding and SM-induced alternative splicing. These results suggest that viruses may regulate cellular gene expression at the level of alternative mRNA splicing in order to facilitate virus replication or persistence in vivo.
Recombinant Adeno-Associated Viral Vectors Are Deficient in Provoking a DNA Damage Response
Authors: Fragkos Michalis , Breuleux Madlaina , Clément Nathalie , Beard Peter
Published: May 2008

Adeno-associated virus type 2 (AAV2) provokes a DNA damage response that mimics a stalled replication fork. We have previously shown that this response is dependent on ataxia telangiectasia-mutated and Rad3-related kinase and involves recruitment of DNA repair proteins into foci associated with AAV2 DNA. Here, we investigated whether recombinant AAV2 (rAAV2) vectors are able to produce a similar response. Surprisingly, the results show that both single-stranded and double-stranded green fluorescent protein-expressing rAAV2 vectors are defective in producing such a response. We show that the DNA damage signaling initiated by AAV2 was not due to the virus-encoded Rep or viral capsid proteins. UV-inactivated AAV2 induced a response similar to that of untreated AAV2. This type of DNA damage response was not provoked by other DNA molecules, such as single-stranded bacteriophage M13 or plasmid DNAs. Rather, the results indicate that the ability of AAV2 to produce a DNA damage response can be attributed to the presence of
cis
-acting AAV2 DNA sequences, which are absent in rAAV2 vectors and could function as origins of replication creating stalled replication complexes. This hypothesis was tested by using a single-stranded rAAV2 vector containing the p5 AAV2 sequence that has previously been shown to enhance AAV2 replication. This vector was indeed able to trigger DNA damage signaling. These findings support the conclusion that efficient formation of AAV2 replication complexes is required for this AAV2-induced DNA damage response and provide an explanation for the poor response in rAAV2-infected cells.
Identification of the Myelin Protein Plasmolipin as the Cell Entry Receptor forMus caroliEndogenous Retrovirus
Authors: Miller A. Dusty , Bergholz Ulla , Ziegler Marion , Stocking Carol
Published: May 2008

The Asian wild mouse speciesMus caroliharbors an endogenous retrovirus (McERV) that is closely related to but distinct from the endogenous retrovirus family defined by theMus dunniendogenous virus and theMus musculusendogenous retrovirus. McERV could infect some cell types from humans, dogs, and rats, but not all, and did not infect any mouse cell line tested. Because of its interesting host range and proposed ancestral relationship to primate retroviruses and because none of the entry receptors for this family of retroviruses had been identified, we began a search for the McERV receptor. We determined the chromosomal location of the receptor gene in the human genome by phenotypic screening of the G3 human-hamster radiation hybrid cell line panel and confirmed the localization by assaying for receptor activity conferred by bacterial artificial chromosome (BAC) clones spanning the region. We next localized the gene more precisely in one positive BAC by assaying for receptor activity following BAC digestion with several restriction enzymes that cleaved different sets of genes, and we confirmed that the final candidate gene, plasmolipin (PLLP; TM4SF11), is the novel receptor by showing that the expression of the human PLLP cDNA renders hamster and mouse cells susceptible to McERV infection. PLLP functions as a voltage-dependent potassium ion channel and is expressed primarily in kidney and brain, helping to explain the limited range of cell types that McERV can infect. Interestingly, mouse PLLP also functioned well as a receptor for McERV but was simply not expressed in the mouse cell types that we originally tested.
Small Capsid Protein pORF65 Is Essential for Assembly of Kaposi's Sarcoma-Associated Herpesvirus Capsids
Authors: Perkins Edward M. , Anacker Daniel , Davis Aaron , Sankar Vishwam , Ambinder Richard F. , Desai Prashant
Published: May 2008

Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiologic agent for KS tumors, multicentric Castleman's disease, and primary effusion lymphomas. Like other herpesvirus capsids, the KSHV capsid is an icosahedral structure composed of six proteins. The capsid shell is made up of the major capsid protein, two triplex proteins, and the small capsid protein. The scaffold protein and the protease occupy the internal space. The assembly of KSHV capsids is thought to occur in a manner similar to that determined for herpes simplex virus type 1 (HSV-1). Our goal was to assemble KSHV capsids in insect cells using the baculovirus expression vector system. Six KSHV capsid open reading frames were cloned and the proteins expressed in Sf9 cells: pORF25 (major capsid protein), pORF62 (triplex 1), pORF26 (triplex 2), pORF17 (protease), pORF17.5 (scaffold protein), and also pORF65 (small capsid protein). When insect cells were coinfected with these baculoviruses, angular capsids that contained internal core structures were readily observed by conventional electron microscopy of the infected cells. Capsids were also readily isolated from infected cells by using rate velocity sedimentation. With immuno-electron microscopy methods, these capsids were seen to be reactive to antisera to pORF65 as well as to KSHV-positive human sera, indicating the correct conformation of pORF65 in these capsids. When either virus expressing the triplex proteins was omitted from the coinfection, capsids did not assemble; similar to observations made in HSV-1-infected cells. If the virus expressing the scaffold protein was excluded, large open shells that did not attain icosahedral structure were seen in the nuclei of infected cells. The presence of pORF65 was required for capsid assembly, in that capsids did not form if this protein was absent as judged by both by ultrastructural analysis of infected cells and rate velocity sedimentation experiments. Thus, a novel outcome of this study is the finding that the small capsid protein of KSHV, like the major capsid and triplex proteins, is essential for capsid shell assembly.
Expected gain and status number following restricted individual and combined-index selection
Authors: Wei R.-P. , Yeh F. C. , Lindgren D.
Published: May 2008

Imposition of restrictions on number of individuals selected from a family and number of families from which superior individuals are selected could markedly alter the consequences of individual and combined-index selection. Predicted genetic gain and diversity measured as status number following selection were studied to draw general conclusions. Selection and its prediction were applied to two sets of real-life data. Theoretical prediction gave results close to those from factual selection. Gain and status number varied with initial family number and size, sib type, heritability, selection proportion, restriction type and intensity, and selection criteria. Proper restriction on the number of individuals selected can control the reduction of status number to an acceptable level, particularly when breeding values are used as the selection criterion. Restriction on the number of families selected would effectively improve the gain efficiency of selection based on phenotypic values. Choosing combinations of both restrictions might produce higher gain without the loss of status number. Given constant population size, family number should be large enough to ensure that restricted selection will yield higher gain and status number.Key words: restricted selection, phenotype, breeding value, genetic gain, effective size.
Survey of microsatellite DNA in pine
Authors: Echt C. S. , May-Marquardt P.
Published: May 2008

A large insert genomic library from eastern white pine (Pinus strobus) was probed for the microsatellite motifs (AC)nand (AG)n, all 10 trinucleotide motifs, and 22 of the 33 possible tetranucleotide motifs. For comparison with a species from a different subgenus, a loblolly pine (Pinus taeda) genomic library was also probed with the same set of di- and tri-nucleotide repeats and 11 of the tetranucleotide repeats. The four most abundant microsatellite motifs in both species were (AC)n, (AG)n, (AAT)n, and (ATC)n, which as a group accounted for over half the microsatellite sites investigated. The two dinucleotide repeats were the most abundant microsatellite motifs tested in both species, each at 2–4.5 sites/megabase pair (Mbp), but the two trinucleotide motifs were nearly as abundant and are considered good candidates for pine microsatellite marker development efforts. Eastern white pine had more than twice as many (AC)nas (AG)nloci, in contrast with loblolly pine and most other plant species in which (AG)nis more abundant. In both pine species the minimum estimated genome density for all microsatellites, excluding (AT)nrepeats, was 16 sites/Mbp.Key words: Pinus strobus, Pinus taeda, eastern white pine, loblolly pine, simple sequence repeats.
Robertsonian chromosomal variation in the house musk shrew (Suncus murinus, Insectivora: Soricidae) and the colonization history of the species
Authors: Rogatcheva M. B. , Borodin P. M. , Oda S.-I. , Searle J. B.
Published: May 2008

A high-resolution G-banding technique was used to identify five metacentrics that characterize Suncus murinus from Sri Lanka. These metacentrics were shown to be the product of Robertsonian fusion of acrocentric chromosomes identical to those in the standard karyotype defined by M.B. Rogatcheva et al. Two of the metacentrics in the Sri Lankan shrews (Rb(10.12) and Rb(14.15)) were the same as those reported by C.H. Sam et al. in Malayan populations of S. murinus. This finding provides strong support for the suggestion of T.H. Yosida that metacentric-carrying shrews colonized Malaya from Sri Lanka and hybridized with individuals of standard karyotype, generating the Robertsonian polymorphism now observed. In addition to the Robertsonian variation in S. murinus, we have used our high resolution technique (G- and C-banding) to characterize variants on chromosome 7, the X chromosome, and the Y chromosome.Key words: chromosome variation, Robertsonian fusions, colonization history, shrew, Suncus murinus.
Use of meiotic FISH for identification of a new monosome inGossypium hirsutumL.
Authors: Ji Yuanfu , Raska Dwaine A. , Islam-Faridi M. Nurul , Crane Charles F. , Zwick Michael S. , Hanson Robert E. , Price H. James , Stelly David M. , McKnight Thomas D.
Published: May 2008

The extensive use of molecular cytogenetics in human genetics and clinical diagnostics indicates that analogous applications in plants are highly feasible. One sort of application would be the identification of new aneuploids, which traditionally involves either direct karyotypic identification, which is feasible in only a few plant species, or tests with markers (cytogenetic, genetic, or molecular), which require sexual hybridization and at least one subsequent seed or plant generation. We have used meiotic fluorescence in situ hybridization (FISH) to analyze a new monosome of cotton (Gossypium hirsutum L., 2n = 4x = 52, 2(AD)1) that had a phenotype which seemed to be distinct from monosomes in the Cotton Cytogenetic Collection. Painting with A2-genome DNA revealed the monosome's D-subgenome origin. DAPI–PI staining showed that the monosome carries a major NOR, delimiting it to the major NOR-bearing chromosomes of the D-subgenome, i.e., 16 or 23. Dual-color FISH with 5S and 18S–28S rDNAs indicated that the monosome contains separate major clusters of each of these two tandemly repeated rDNA elements, thus delimiting the monosome to chromosome 23, for which the Cotton Cytogenetic Collection has previously been devoid of any sort of deficiency. Of the 26 chromosomes in the cotton genome, the Collection now provides coverage for 16 (70%) in the form of monosomy, and 20 (77%) in the form of monosomy and (or) telosomy. Use of molecular cytogenetic methods to identify a new plant aneuploid in cotton exemplifies the fact that a physicochemical karyotypic chromosome identification system is not required a priori for application of new molecular cytogenetic methods, thus indicating their potential applicability to nearly all plant species.Key words: fluorescence in situ hybridization, monosome, aneuploid, Gossypium hirsutum.
Indistinguishable patterns of recombination resulting from male and female meioses inBrassica napus(oilseed rape)
Authors: Kelly A. L. , Sharpe A. G. , Nixon J. H. , Lydiate D. J. , Evans E. J.
Published: May 2008

An F1individual derived from a cross between two distinct lines of spring oilseed rape (Brassica napus) was used to produce a pair of complementary backcross populations, each consisting of 90 individuals. The F1donated male gametes to the Male population and female gametes to the Female population. Genetic maps were generated from both populations and aligned using 117 common loci to form an integrated genome map of B. napus with 243 RFLP-defined loci. A comparison of the frequency and distribution of crossovers in the two populations of F1gametes (assayed in the Male and Female populations) detected no differences. The genetic maps derived from the Male and Female populations each consisted of 19 linkage groups spanning 1544 and 1577 cM, respectively. The maps were aligned with other B. napus maps, and all 19 equivalent linkage groups were unambiguously assigned. The genetic size and general organisation of the new maps were comparable with those of pre-existing B. napus maps in most respects, except that the levels of polymorphism in the constituent A and C genomes were unusually similar in the new cross.Key words: genetic linkage map, sex differences, recombination frequency, segregation distortion.
Phylogenetic and genomic relationships in the genus Glycine Willd. based on sequences from the ITS region of nuclear rDNA
Authors: Kollipara Krishna P. , Singh Ram J. , Hymowitz Theodore
Published: May 2008

Phylogenetic relationships among all 18 species of the genus Glycine were inferred from nucleotide sequence variation in the internal transcribed spacer (ITS) region of nuclear ribosomal DNA. Pairwise sequence divergence values ranged from 0.2% (a single nucleotide) between Glycine max and Glycine soja to 8.6% between Glycine hirticaulis and Glycine falcata. The length of the ITS1 and ITS2 sequences ranged from 215 to 238 nucleotides and from 205 to 222 nucleotides, respectively, and that of 5.8S was 168 nucleotides across all the species. Phylogenetic analyses of the ITS region clearly resolved all the genomic groups that were established previously based on cytogenetic and biochemical studies. Based on this study, we assign new genome symbols: HH to Glycine arenaria, H1H1 to Glycine hirticaulis, H2H2 to Glycine pindanica, II to Glycine albicans, and I1I1 to Glycine lactovirens. Parsimony analysis of the entire ITS region, using subgenus Soja as outgroup, resulted in a trichotomy consisting of the clades: G. falcata (F genome), Glycine cyrtoloba and Glycine curvata (C genome), and all other species (A, B, D, E, H, and I genomes) of the subgenus Glycine.Key words: Glycine spp., soybean, genomes, ITS region, rDNA.
A 2.8 megabase YAC contig spanning D8S339, which is tightly linked to the Werner syndrome locus
Authors: Bruskiewich R. , Schertzer M. , Wood S.
Published: May 2008

A number of gene loci, including the locus for Werner syndrome (WRN), map to proximal human chromosome 8p near the genetic marker D8S339. In this report, we present a long range physical map of an approximately 2.8 megabase yeast artificial chromosome contig centred on D8S339. In this map, we localize the WRN-linked polymorphic sequence-tagged sites (STS) D8S339 and D8S1055, as well as a novel polymorphic STS, D8S2297. We also refine the positions of three known gene loci, GTF2E2, GSR, and PPP2CB, relative to the location of WRN within the map.Key words: WRN, GTF2E2, GSR, PPP2CB, physical map, human chromosome 8p.
Chromosomal rearrangements in rock wallabies,Petrogale(Marsupialia: Macropodidae). IX. Further G-banding studies of thePetrogale lateraliscomplex:P.lateralis pearsoni, the West Kimberley race, and a population heterozygous for a centric fusion
Authors: Eldridge M. D. B. , Pearson D. J.
Published: May 2008

G-banded metaphase preparations from cultured fibroblasts were used to examine the karyotypes of Petrogale lateralis pearsoni and the West Kimberley (WK) race of P. lateralis. Petrogale lateralis pearsoni was found to retain the ancestral 2n = 22 Petrogale karyotype, while the WK race (2n = 20) was found to be characterized by a 9–10 centric fusion. This taxon had been reported to have an 8–10 fusion. Karyotypic analysis was also used to identify Petrogale populations in the Erskine Range, Western Australia (W.A.) as the WK race and in the Walter James Range, W.A. as the MacDonnell Ranges (MDR) race of P. lateralis. These findings represent significant range extensions for both taxa. A third P. lateralis population, from the Townsend Ridges, W.A., could not be definitively identified to subspecies or race and appears intermediate between the WK and MDR races. Four animals were examined from this population and all possessed an identical 2n = 21 karyotype characterized by homozygosity for a derived acrocentric chromosome 3 (3a) and heterozygosity for a 9–10 fusion. Rearrangement 3a is typical of the MDR race, while the 9–10 fusion is characteristic of the WK race. The polymorphic Townsend Ridges population could result from the de novo creation of a 9–10 fusion (similar in morphology to the 9–10 fusion of the WK race) or it may represent evidence of hybridization between the MDR race and either the WK race or a currently unknown taxon. Additional data will be required to distinguish between these hypotheses.Key words: rock wallabies, Petrogale, chromosome rearrangements, G-banding.
Construction of a RFLP genetic linkage map for oil palm (Elaeis guineensisJacq.)
Authors: Mayes S. , Jack P. L. , Corley R. H. V. , Marshall D. F.
Published: May 2008

We have developed a restriction fragment length polymorphism (RFLP) genetic map in oil palm (Elaeis guineensis Jacq.) for use in breeding programmes. A segregating population of 98 individuals was probed with 84 informative low copy clones (mainly PstI genomics). This yielded 103 scorable loci, of which 97 could be linked into 24 groups of two or more markers (n = 16 for oil palm), encompassing a total of 860 cM. The high level of linkage between markers (95%) suggests good genome coverage and very little segregation distortion of markers was observed. The mapping population, which was generated by the selfing of an important breeding palm (A 137/30), also segregated for the shell thickness character (Sh), enabling mapping of the gene conferring this major commercial trait. The nearest RFLP marker (pOPgSP1282) was located 9.8 cM from Sh in the mapping population and 6.6 cM away in a related (A137/30 × E80/29) smaller population (45 palms). Strategies for conversion of RFLP markers to a PCR format were explored and two important markers were shown to generate allelic variants following PCR amplification and restriction digestion of PCR products. The application of this map to oil palm breeding programmes is discussed.Key words: oil palm, Elaeis guineensis Jacq., RFLP, linkage map, shell thickness.
Analysis of a 103 kbp cluster homology region from the left end ofSaccharomyces cerevisiaechromosome I
Authors: Storms Reg K. , Wang Ying , Fortin Natalie , Hall John , Vo Danh H. , Zhong Wu-Wei , Bussey Howard , Downing Tom , Barton Arnold B. , Kaback David B. , Su Yuping
Published: May 2008

The DNA sequence and preliminary functional analysis of a 103-kbp section of the left arm of yeast chromosome I is presented. This region, from the left telomere to the LTE1 gene, can be divided into two distinct portions. One portion, the telomeric 29 kbp, has a very low gene density (only five potential genes and 21 kbp of noncoding sequence), does not encode any "functionally important" genes, and is rich in sequences repeated several times within the yeast genome. The other portion, with 37 genes and only 14.5 kbp of noncoding sequence, is gene rich and codes for at least 16 "functionally important" genes. The entire gene-rich portion is apparently duplicated on chromosome XV as an extensive region of partial gene synteney called a cluster homology region. A function can be assigned with varying degrees of precision to 23 of the 42 potential genes in this region; however, the precise function is know for only eight genes. Nineteen genes encode products presently novel to yeast, although five of these have homologs elsewhere in the yeast genome.Key words: Saccharomyces cerevisiae, chromosome I, cluster homology region, DNA sequence.
Genetic and chromosomal localization of the 5S rDNA locus in sugar beet (Beta vulgarisL.)
Authors: Schondelmaier J. , Schmidt T. , Jung C. , Heslop-Harrison J. S.
Published: May 2008

A digoxigenin-labelled 5S rDNA probe containing the 5S rRNA gene and the adjacent intergenic spacer was used for in situ hybridization to metaphase and interphase chromosomes of a trisomic stock from sugar beet (Beta vulgaris L.). Three chromosomes of primary trisomic line IV (T. Butterfass. Z. Bot. 52: 46–77. 1964) revealed signals close to the centromeres. Polymorphisms of 5S rDNA repeats in a segregating population were used to map genetically the 5S rRNA genes within a cluster of markers in linkage group II of sugar beet. The concentration of genetic markers around the centromere presumably reflects the suppressed recombination frequency in centromeric regions. The correlation of physical and genetic data allowed the assignment of a linkage group to sugar beet chromosome IV according to line IV of the primary trisomics.Key words: Beta vulgaris, sugar beet, 5S rRNA, in situ hybridization, RFLPs, trisomics.
DNA markers linked to a T10 loose smut resistance gene in wheat (Triticum aestivum L.)
Authors: Procunier J. D. , Gray M. A. , Howes N. K. , Knox R. E. , Bernier A. M.
Published: May 2008

Screening for loose smut resistance in wheat is difficult. Selecting lines with DNA markers linked to loose smut resistance would be more reliable and less costly. Molecular markers linked to a race T10 loose smut resistance gene were identified using a F6 single seed descent segregating population. A RAPD marker and a RFLP marker were located on opposite flanks of the resistance gene and were shown to be loosely linked. The RAPD marker was converted to a user friendly polymorphic SCAR marker that represented a single genetically defined locus in hexaploid wheat. Using these two bracketing markers simultaneously, the error rate for T10 resistance selection due to crossing-over was reduced to 4%. These markers can be used for a faster and more reliable selection of T10 resistant plants than previous conventional loose smut ratings.Key words: wheat, marker, loose smut, SCAR.
Molecular mapping of a thermosensitive genetic male sterility gene in rice using bulked segregant analysis
Authors: Subudhi P. K. , Borkakati R. P. , Virmani S. S. , Huang N.
Published: May 2008

The thermosensitive genetic male sterility (TGMS) system is considered to be a more efficient alternative to the cytoplasmic male sterility (CMS) system for hybrid rice. An F2population from a cross between a TGMS mutant line (IR32364TGMS) and IR68 was used to map the TGMS gene tms3(t). Fertile and sterile bulks were constructed following the classification of F2plants into true breeding sterile, fertile, and segregating fertile plants based on F3family studies. From the survey of 389 arbitrary primers in bulked segregant analysis, four RAPD markers were identified in which three, OPF182600, OPB19750, and OPAA7550, were linked to tms3(t) in repulsion phase and one, OPAC3640, was linked to tms3(t) in coupling phase. The tms3(t) gene was flanked by OPF182600and OPAC3640on one side and by OPAA7550and OPB19750on the other side. All four markers were low-copy sequences and two of them (OPF182600and OPAC3640) detected polymorphism when the markers were used to probe the genomic blots. Subsequently, OPAC3640was mapped to the short arm of chromosome 6 using a mapping population available at IRRI. However, no RFLP markers from this region showed linkage to tms3(t) owing to the lack of polymorphism between the parents. All RAPD fragments were cloned and partially sequenced from both ends. Thus, PCR primers can be designed to develop PCR markers for marker-assisted breeding to facilitate the transfer of tms3(t) from one genetic background to another.Key words: bulked segregant analysis, gene tagging, marker-assisted selection, RAPD, TGMS.
Characterization by RFLP analysis and genomic in situ hybridization of a recombinant and a monosomic substitution plant derived fromHordeum vulgareL. ×Hordeum bulbosumL. crosses
Authors: Pickering R. A. , Hill A. M. , Kynast R. G.
Published: May 2008

Interspecific crosses in Hordeum have been made with the aim of transferring desirable traits, such as disease resistance, from a wild species, Hordeum bulbosum, into cultivated barley (Hordeum vulgare). Interspecific recombinants have previously been identified using several methods, but there are limitations with all the techniques. We improved our ability to characterize progeny from H. vulgare × H. bulbosum crosses by using genomic in situ hybridization (GISH). The plant material comprised a recombinant and a monosomic alien substitution plant derived from H. vulgare × H. bulbosum crosses. The recombinant possesses a pubescent leaf sheath conferred by a gene transferred from H. bulbosum into barley cultivar Golden Promise. The use of GISH on a plant homozygous for the pubescence gene confirmed the presence of H. bulbosum DNA located distally on two barley chromosomes and we mapped the introgression to barley chromosome 4HL using RFLP analysis. Furthermore, by means of an allelism test we found that the transferred gene for pubescence is allelic or closely linked to a gene for pubescence (Hs) located on barley chromosome 4HL. The presence of a single H. bulbosum chromosome in the monosomic substitution plant was confirmed by GISH. A distal introgression of H. bulbosum DNA was also observed on one barley chromosome, which was located on chromosome 3HL by RFLP analysis.Key words: Hordeum vulgare, Hordeum bulbosum, interspecific hybrid, gene introgression, genomic in situ hybridization.
RAPD markers linked to the nuclear gene from Triticum timopheevii that confers compatibility with Aegilops squarrosa cytoplasm on alloplasmic durum wheat
Authors: Asakura Nobuaki , Nakamura Chiharu , Ohtsuka Ichiro
Published: May 2008

Alien cytoplasms cause a wide range of phenotypic alterations in the nucleus–cytoplasm (NC) hybrids in the Triticeae. Nuclear genomes of timopheevii wheat (Triticum timopheevii and Triticum araraticum) are fully compatible with the cytoplasm of Aegilops squarrosa, while those of a majority of emmer or durum wheat cultivars and more than half the wild emmer wheats are incompatible, and a maternal 1D chromosome is required to restore seed viability and male fertility in the NC hybrids. A euploid NC hybrid of Triticum durum cv. Langdon with Ae. squarrosa cytoplasm produced by introgressing the NC compatibility (Ncc) gene from T. timopheevii was used to identify random amplified polymorphic DNA (RAPD) markers linked to it. After a survey of 200 random decamer primers, four markers were selected, all of which were completely linked in 64 individuals of a SB8 mapping population. One marker was derived from a single locus, while three others were from interspersed repetitive sequences. Also, the hybrid chromosomes and those of the parental T. durum had identical C-banding patterns. RAPD-PCR analysis of 65 accessions from wild and cultivated tetraploid wheat species showed the exclusive presence of the markers in timopheevii wheat. In conclusion, the chromosomal region flanking Ncc of T. timopheevii is highly conserved in the genome of this group of tetraploid wheats.Key words: nucleus–cytoplasm compatibility, Ncc gene, Aegilops squarrosa, Triticum timopheevii, tetraploid wheat, RAPD marker.
Expression of the sex determining cascade genesSex-lethalanddoublesexin the phorid flyMegaselia scalaris
Authors: Sievert Volker , Kuhn Sylvia , Traut Walther
Published: May 2008

Sex-lethal (Sxl) and doublesex (dsx) are known to represent parts of the sex-determining cascade in Drosophila melanogaster. We generated cDNA probes of the homologous genes from Megaselia scalaris, a fly species with an epistatic maleness factor as the primary sex determining signal. In Northern blot hybridization of poly(A)+RNA, the M. scalaris dsx probe detected two bands, one of which had a sex-specific size difference, while the Sxl probe bound to RNAs of equal size in females and males. RT-PCR showed Sxl to be transcribed in gonads of adult females and males but not in somatic tissues. Thus, while dsx appears to have a similar function in M. scalaris and D. melanogaster, Sxl does not. The results suggest that the sex-determining pathway of M. scalaris joins that of D. melanogaster between the Sxl and dsx steps.Key words: RNA-binding domain, zinc finger, differential splicing, Drosophila.
Sex and death in the mouse: genetically delayed reproduction and senescence
Authors: Biddle F. G. , Eden S. A. , Rossler J. S. , Eales B. A.
Published: May 2008

A mammalian model of genetically postponed aging would be an important tool to test not only different mechanisms of aging but also the predictive value of various biomarkers of the aging process. Under conventional conditions, the historical strains of the laboratory mouse produce their first litter between 9 and 13 weeks of age and have a median time of death in their 2nd year. Our POSCH-2 strain, which was derived from wild-caught Mus musculus domesticus, produces its first litter in the current breeding generations at approximately 47 weeks of age and continues to breed throughout its 2nd and into its 3rd year of life. The aging curve of POSCH-2 has not yet been determined for economic reasons. Late onset of breeding is a characteristic of both females and males, but sexual maturity is more reliably assessed in females. The later breeding phenotype of POSCH-2 is genetically recessive to early breeding of the C57BL/6J historical laboratory strain and, since POSCH-2 females can be induced to ovulate at 8 weeks of age (but pregnancy does not result), the signal rather than the ovarian receptor to ovulate may be delayed. The genetically delayed reproduction and potentially longer life of the POSCH-2 strain appears to be a new trait in the mouse. The strain may be a useful mammalian model for aging studies and for the evaluation of antagonistic pleiotropy as a genetic model for the evolution of aging.Key words: delayed reproduction, senescence, aging, genetics, mouse.
Identification and mapping of a leaf rust resistance gene in barley line Q21861
Authors: Borovkova I. G. , Steffenson B. J. , Jin Y. , Kilian A. , Kleinhofs A. , Blake T. K.
Published: May 2008

Barley line Q21861 possesses an incompletely dominant gene (RphQ) for resistance to leaf rust caused by Puccinia hordei. To investigate the allelic and linkage relations between RphQ and other known Rph genes, F2 populations from crosses between Q21861 and donors of Rph1 to Rph14 (except for Rph8) were evaluated for leaf rust reaction at the seedling stage. Results indicate that RphQ is either allelic with or closely linked to the Rph2 locus. A doubled haploid population derived from a cross between Q21861 and SM89010 (a leaf rust susceptible line) was used for molecular mapping of the resistance locus. Bulked segregant analysis was used to identify markers linked to RphQ, using random amplified polymorphic DNAs (RAPDs), restriction fragment length polymorphisms (RFLPs), and sequence tagged sites (STSs). Of 600 decamer primers screened, amplified fragments generated by 9 primers were found to be linked to the RphQ locus; however, only 4 of them were within 10 cM of the target. The RphQ locus was mapped to the centromeric region of chromosome 7, with a linkage distance of 3.5 cM from the RFLP marker CDO749. Rrn2, an RFLP clone from the ribosomal RNA intergenic spacer region, was found to be very closely linked with RphQ, based on bulked segregant analysis. An STS marker, ITS1, derived from Rrn2, was also closely linked (1.6 cM) to RphQ.Key words: Hordeum vulgare, Puccinia hordei, allelism testing, linkage, molecular markers.
QTL analysis of morphological traits in a tomato recombinant inbred line population
Authors: Paran I. , Goldman I. , Zamir D.
Published: May 2008

Quantitative trait loci (QTLs) influencing morphological traits were identified by restriction fragment length polymorphism (RFLP) analysis in a population of recombinant inbred lines (RILs) derived from a cross of the cultivated tomato Lycopersicon esculentum with a related wild species, Lycopersicon cheesmanii. One hundred and thirty-two RFLP loci spaced throughout the tomato genome were used as DNA probes on genomic DNA from 97 RIL families. Morphological traits, including plant height, plant fresh mass, number of branches, number of nodes, first flower-bearing node, and leaf length, were evaluated in two controlled environment trials in 1992 and 1993. QTLs were detected via regression analyses at multiple marker loci for each morphological trait. A total of 41 markers were significantly associated with the traits examined. Large additive effects were measured at many of these loci. QTLs for multiple traits were detected on chromosomes 3 (TG74) and 4 (CT188), suggesting the possible association of these chromosome segments with genes controlling growth and development in tomato. These chromosomal regions were also associated with multiple morphological traits in a L. esculentum × Lycopersicon pennellii cross. A total of 13% of the QTLs identified for traits common to both studies occupied similar map positions.Key words: Lycopersicon, quantitative trait, restriction fragment length polymorphism.
Chromosomal and NOR patterns in the polyclonal stick insect Bacillus atticus atticus (Insecta; Phasmatodea)
Authors: Marescalchi Ombretta , Scali Valerio
Published: May 2008

Bacillus atticus atticus is a complex of thelytokous parthenogens, related to the bisexual Bacillus grandii, that ranges from Sardinia to Near Eastern countries. Karyotypic and cytogenetic differentiation of the B. atticus atticus diploid unisexual "isolates" is really higher than expected. Its standard karyotype has 2n = 34 chromosomes, but several instances of repatterned or even aneuploid complements have been found. The number and location of silver-stained NORs are particularly intriguing, since in addition to homozygous NOR patterns, simple or double hemizygous strains are found spread over specific and wide regions. The odd patterns are not due to Ag-NOR staining technique artifacts, since the FISH method, using rDNA probes, apparently labels the same ribosomal clusters. Transpositions and translocations have been suggested to account for some NOR patterns, but hybridizations between different NOR-bearing races are also a possible cause. This chromosomal survey clearly contributes to a better understanding of B. atticus phylogeny.Key words: aneuploidy, interracial hybrids, karyotype repatterning, NOR techniques, unisexuals.
Comparison of British populations of potato cyst nematodes with populations from continental Europe and South America using RAPDs
Authors: Blok V. C. , Phillips M. S. , Harrower B. E.
Published: May 2008

Genetic variation between populations of Globodera pallida, primarily from Britain but including populations from continental Europe and South America and two Globodera rostochiensis populations, was examined using random amplified polymorphic DNA (RAPD). Fourteen primers were used and 250 amplification products observed. A comparison was made of the similarities between the species and, within G. pallida, between populations from Britain, The Netherlands, Germany, and Switzerland, of the pathotypes Pa2 and Pa3. In addition, one Pa1 population and two others from South America were included. On the basis of the RAPD analysis, all the Pa2–Pa3 populations, except one from Scotland (Luffness), constituted a single group with no clear distinction based on pathotype designation. The Luffness population is known to be distinct in its virulence. The data indicated that the main Pa2–Pa3 group could be subdivided based on geographic origin, but this is not well supported by bootstrap analysis. The Pa1 population and the two populations from South America all formed distinct groups.Key words: genetic variation, Globodera pallida, introductions, RAPDs.
Distribution of highly repeated DNA sequences in species of the genusSecale
Authors: Cuadrado Angeles , Jouve Nicolás
Published: May 2008

The presence and distribution of the most important highly repetitive DNA sequences of rye in cultivated and wild species of the genus Secale were investigated using fluorescence in situ hybridization. Accurate identification of individual chromosomes in the most commonly recognized species or subspecies of the genus Secale (S. cereale, S. ancestrale, S. segetale, S. afghanicum, S. dighoricum, S. montanum, S. montanum ssp. kuprijanovii, S. africanum, S. anatolicum, S. vavilovii, and S. silvestre) was achieved using three highly repetitive rye DNA sequences (probes pSc119.2, pSc74, and pSc34) and the 5S ribosomal DNA sequence pTa794. It is difficult to superimpose trends in the complexity of repetitive DNA during the evolution of the genus on conclusions from other cytogenetic and morphological assays. However, there are two clear groups. The first comprises the self-pollinated annuals S. silvestre and S. vavilovii that have few repeated nucleotide sequences of the main families of 120 and 480 bp. The second group presents amplification and interstitialization of the repeated nucleotide sequences and includes the perennials S. montanum, S. anatolicum, S. africanum, and S. kuprijanovii, as well as the annual and open-pollinated species S. cereale and its related weedy forms. The appearance of a new locus for 5S rRNA in S. cereale and S. ancestrale suggests that cultivated ryes evolved from this wild weedy species.Key words: rye, repeated nucleotide sequence, 5S rDNA, fluorescence in situ hybridization, FISH.
Chromosomal localization of the human liver form cytochromecoxidase subunit VIIa gene
Authors: Merante Frank , Duncan Alessandra M. V. , Mitchell Grant , Duff Catherine , Rommens Joanna , Robinson Brian H.
Published: May 2008

The chromosomal loci corresponding to human cytochrome c oxidase (COX) subunit VIIa Liver (VIIa-L) isoform genes were determined utilizing a combined approach of genomic cloning, in situ hybridization, and somatic cell hybrid genetics. In contrast to the proposal of E. Arnaudo et al. (Gene (Amst.), 119: 299–305. 1992) that COX VIIa-L sequences are located on chromosomes 4 and 14, we found that COX VIIa-L related sequences reside on chromosome 6, while an additional COX VIIa-L cross-reacting sequence (ψ-gene) was located on chromosome 4.Key words: human, cytochrome c oxidase, gene mapping, pseudogenes.
Cloning, characterization, and chromosomal localization of human liver form cytochrome c oxidase subunit VIa related genes
Authors: Merante Frank , Ling Mingfu , Duff Catherine , Robinson Brian H. , Duncan Alessandra M. V.
Published: May 2008

The chromosomal location of human cytochrome c oxidase (COX) subunit VIa Liver (VIa-L) isoform related sequences has been determined by a combination of in situ hybridization and analysis of human–hamster somatic cell hybrid panels. COX VIa-L related sequences were present on chromosomes 6 and 12. It has been verified that at least two COX VIa-L genes are on chromosome 6, one of which is a pseudogene. In total, four COX VIa-L related sequences have been cloned and their nucleotide sequences analyzed. At least three of these sequences represent pseudogenes; their relatedness to the COX VIa-L cDNA is discussed.Key words: human, cytochrome c oxidase, chromosomal localization, COX VIa, cloning.
AFLP variation in wild barley (Hordeum spontaneum C. Koch) with reference to salt tolerance and associated ecogeography
Authors: Pakniyat H. , Powell W. , Baird E. , Handley L. L. , Robinson D. , Scrimgeour C. M. , Hackett C. A. , Forster B. P. , Nevo E. , Caligari P. D. S.
Published: May 2008

Thirty-nine genotypes of Hordeum spontaneum were selected from three geographically separated areas (southwestern, northern, and southeastern) of the Fertile Crescent. The lines were subject to AFLP (amplified fragment length polymorphism) analysis from which a similarity matrix was produced. A dendrogram of the data showed, with two exceptions, that the genotypes grouped together according to area of origin. This was confirmed by principal coordinate analysis in which the first principal coordinate separated the genotypes of the southwestern area from the other two areas, which in turn could be separated by the second principal coordinate. While genotypes from the same site of origin can exhibit very similar AFLP profiles, sharp genetic differences were detected between genotypes separated by relatively short distances. Thirty of the 39 genotypes were subjected to hydroculture salt tolerance tests. These were analysed for shoot Na+ content and carbon isotope composition (δ13C) after 4 weeks of treatment (100 mol∙m−3 NaCl). Shoot Na+ content and δ13C were highly correlated. Twelve AFLP markers were found to be associated with both shoot Na+ content and shoot δ13C and were also associated with site of origin ecogeographic data, particularly longitude. The most salt tolerant genotype came from Ilam in the southeastern area and the most salt sensitive genotype originated in the southwestern area. The 12 markers were partitioned into groups that showed significant associations within groups but no significant association between groups. In a multiple regression analysis, three AFLP markers, from separate groups, accounted for more than 60% of the variation for shoot Na+ content and δ13C. The results demonstrate the effectiveness of AFLP fingerprinting in genetic studies of complex traits at the wild species and (or) population level.Key words: wild barley, Hordeum spontaneum, AFLP, salt tolerance.
The evolution of species-type specificity in the global DNA sequence organization of mitochondrial genomes
Authors: Hill Kathleen A. , Singh Shiva M.
Published: May 2008

Prokaryote genomes and nuclear genomes of eukaryotes have a global DNA sequence organization that is species type specific, determined primarily by nearest-neighbor nucleotide associations, and independent of gene function and sequence length. The determinants of such a global structure have remained largely uncharacterized. The monophyletic and endosymbiotic origin of mitochondria permit examination of the influence of evolutionary time and host species type. Different global structures were seen among (i) protozoan and plant, (ii) fungal, (iii) algal (iv) nematode, (v) echinoderm, (vi) insect, and (vii) vertebrate species following examination of 28 complete mitochondrial genomes using chaos representation and measures of short-sequence representation. The mitochondrial genomes have biases in single-nucleotide and dinucleotide representation, specifically, an overrepresentation of A and T nucleotides and CC/GG and AG/CT dinucleotides and a deficiency of CG dinucleotides, in all but one genome. Dinucleotide representation is similar among (i) mitochondrial genomes of more closely related species; (ii) mitochondrial genomes and the Mycoplasma capricolum genome, a proposed progenitor of mitochondrial genomes; and (iii) mitochondrial genomes of diverse species, more so than between the mitochondrial and the nuclear genome of the same or a closely related species. It is hypothesized that sufficient evolutionary time has permitted host-specific constraints to affect nuclear and mitochondrial genomes and that different species type specific constraints influence nuclear and mitochondrial genome global structure.Key words: chaos representation, mitochondrial genomes, primary sequence organization, oligonucleotide frequencies.
Molecular cytogenetic analysis of durum wheat × tritordeum hybrids
Authors: Lima-Brito J. , Guedes-Pinto H. , Harrison G. E. , Heslop-Harrison J. S.
Published: May 2008

Southern and in situ hybridization were used to examine the chromosome constitution, genomic relationships, repetitive DNA sequences, and nuclear architecture in durum wheat × tritordeum hybrids (2n = 5x = 35), where tritordeum is the fertile amphiploid (2n = 6x = 42) between Hordeum chilense and durum wheat. Using in situ hybridization, H. chilense total genomic DNA hybridized strongly to the H. chilense chromosomes and weakly to the wheat chromosomes, which showed some strongly labelled bands. pHcKB6, a cloned repetitive sequence isolated from H. chilense, enabled the unequivocal identification of each H. chilense chromosome at metaphase. Analysis of chromosome disposition in prophase nuclei, using the same probes, showed that the chromosomes of H. chilense origin were in individual domains with only limited intermixing with chromosomes of wheat origin. Six major sites of 18S–26S rDNA genes were detected on the chromosomes of the hybrids. Hybridization to Southern transfers of restriction enzyme digests using genomic DNA showed some variants of tandem repeats, perhaps owing to methylation. Both techniques gave complementary information, extending that available from phenotypic, chromosome morphology, or isozyme analysis, and perhaps are useful for following chromosomes or chromosome segments during further crossing of the lines in plant breeding programs.Key words: In situ hybridization, molecular cytogenetics, plant breeding, Hordeum chilense, Southern hybridization, durum wheat, hybrids.