Calculating the exclusion probability and paternity index for X-chromosomal loci in the presence of substructure

There has been recent interest in the use of X-chromosomal loci for forensic and relatedness testing casework, with many authors developing new X-linked short tandem repeat (STR) loci suitable for forensic use. Here we present formulae for two key quantities in paternity testing, the average probability of exclusion and the paternity index, which are suitable for Xchromosomal loci in the presence of population substructure.

Excision of anabaena PCC 7120 nifD element in escherichia coli: growth kinetics and RecA regulated xisA expression and DNA rearrangement

Anabaena PCC 7120 nifHDK operon is interrupted by an 11 kb DNA element which is excised during the development of heterocysts by Excisase A, encoded by the xisA gene residing on the element. The excision is a site-specific recombination event that occurs at the I I base pair direct repeats flanking the element. Earlier work showed the excision of the I I kb element in Escherichia coli at a frequency 0.3%. We report here the excision of this element at 1.1% and 1.98% in E. coli DH5 alpha, and 1.9% and 10.9% in E. coli JM 101 when grown on Luria broth and minimal media, respectively. Excision of nifD element in isogenic recA(-) (RK1) and recA(+) (RK2) E. coli JM101 P1 transductants, showed similar results to that of E. coli JM101 and DH5 alpha, respectively. A plasmid pMX32, carrying a xisA defective 11 kb element, showed no excision in E. coli RK2 strain. In contrast to Anabaena PCC 7120, excision of nifD element did not increase in E. call DH5 alpha grown in iron-deficient conditions. A PxisA::lacZ transcriptional fusion, used to detect the expression of elusive xisA gene, showed maximal beta-galactosidase activity in the stationary phase. The results suggest that the excision event in E. coli may involve additional factors, such as RecA and that the physiological status can influence the excision of nifD element. (C) 2007 Elsevier Ltd. All rights reserved.

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and ArnphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.

The chromosomal assessment of salt tolerant substituted tritipyrum using genomic fluorescent in situ hybridiization (FISH)

Wheat, although moderately tolerant to salt, can not be cultivated in many areas. However, in the triticeae tribe, some of the wild wheat relatives are highly tolerant, e.g. Thinopyrum bessarabicum, which grows on the sea shore. Eight primary hexaploid tritipyrum lines, amphiploids between Triticum durum and Thinopyrum bessarabicum have been produced which can set seed in at least 250 mM NaCl. These tritipyrums (2n=6x=42, AABBEbEb) due to reasons such as brittle rachis, continuous production of tillers, late maturity, tall stature and meiotic instability will not fulfill the requirements of a successful commercial salt tolerant crop. To overcome such problems the substituted tritipyrum, in which selected Eb chromosomes are replaced by D genome chromosomes of 6x wheat, was produced from 6x tritipyrum x 6x wheat hybrids (F1: 2n=6x=42, AABBDEb) followed by selfing and backcrossing with 6x tritipyrum. The fertile plants among the above progenies were screened by the genomic fluorescent in situ hybridization technique to identify their Eb and D chromosome constitution. This study showed that producing tritiprum with variable numbers of Eb and D genome chromosomes is feasible and that FISH is a useful technique for determining the number of Eb chromosomes present.

Copper(II)-catalyzed [2,3]-sigmatropic rearrangement of N-methyltetrahydropyridinium ylids

A ring-contractive and highly diastereoselective [2,3]-sigmatropic rearrangement occurs when N-methyl-1,2,3,6-tetrahydropyridine is treated with sub-stoichiometric amounts of copper or rhodium salts, in the presence of ethyl diazoacetate, giving ethyl cis-N-methyl-3-ethenyl proline (4).

Ring-rearrangement metathesis of bicyclic amino acid derivatives

In this letter, we describe the ring-rearrangement metathesis (RRM) of bicyclic amino acid derivatives. The procedure is of use for the synthesis of constrained amino acid and peptide derivatives with potential as reverse-turn inducers. (c) 2005 Elsevier Ltd. All rights reserved.

Structure dependent rearrangement of the cyclopropylmethyl cation - isolation of a bicyclo[3.2.0]heptene

Access to 7-allyl substituted norbornene derivatives for tandem olefin metathesis via cationic rearrangement of cyclopropylmethanol substituted norbornenes is shown to be structure dependent. In some cases products that arise from cationic rearrangement of a cyclopropylmethyl cation are furnished. Thionyl chloride is shown to be superior to silica for inducing the desired rearrangement. (c) 2007 Elsevier Ltd. All rights reserved.

Ring-rearrangement metathesis of substituted 2-aminonorbornenes

In this report we describe the ring-rearrangement metathesis of 2-aminonorbornene derivatives. Ail efficient ruthenium-catalysed metathesis reaction Occurs with a wide range of pendent alkenes and alkynes to generate bicyclic amines and amides.

Stereochemistry and rearrangement reactions of hydroxylignanolactones

Various conflicting data on the rearrangement and absolute stereochemistry of hydroxylignano-9,7'-lactones are resolved using O-18 labeled compounds, also confirmed by an X-ray analysis of a pure lignano-9,7'-lactone enantiomer, obtained for the first time. Under NaH/DMF rearrangement conditions a silyl protected hydroxylignano-9,9'-lactone underwent an unexpected silyl migration.

A new class of ammonium ylid for [2,3]-sigmatropic rearrangement reactions: ene-endo-spiro ylids

The first examples of sigmatropic rearrangements of ene-endo-spirocyclic, tetrahydropyridine-derived ammonium ylids are reported. Thus, spiro[6.7]-ylids rearrange primarily by a [2,3]-pathway, whereas the analogous [6.6]-ylids rearrange by [1,2]- and [2,3]-mechanisms in roughly equal proportions. This method serves as a rapid entry to the core of a range of alkaloids bearing a pyrrolo[1,2-a]azepine or octahydroindolizidine nucleus.

First efficient and general copper-catalyzed [2,3]-rearrangement of tetrahydropyridinium ylids

The factors affecting the copper-catalyzed rearrangement of ammonium ylids derived from tetrahydropyriclines and diazoesters; have been examined,and the first examples of high-yielding metal-catalyzed [2,3]-sigmatropic rearrangements of a wide range of such ylids are reported. The nature of the alpha-substituent in the diazo component of the reaction has a dramatic effect upon the yields of the reaction, with electron-withdrawing substituents enhancing the yield of the reaction.

A low-temperature ammonium ylid rearrangement: enhanced reactivity engendered by rigidity

Sigmatropic rearrangement of tetrahydropyridine-derived ammonium is a valuable method for the preparation of substituted prolines. These reaction normally require elevated temperatures to proceed, but bicyclic tetrahydropyridine-like ylid I undergoes rearrangement at -15 degrees C; the extra rigidity of the azabicyclo[3.3.0]octene system preorganizes the transition state and lowers the activation energy for rearrangement.

Asymmetric [2,3]-rearrangement of glycine-derived allyl ammonium ylids

The first examples of highly enantioselective [2,3]-sigmatropic rearrangements of acyclic allylic ammonium ylids are reported. Thus, a range of N-{2‘-[(N‘-allyl-N‘,N‘-dialkyl)ammonium]}acetyl camphor sultams undergo rearrangement at 0 °C in DME solution with high diastereofacial control (up to 99:1 dr) to give allylglycines in generally high yield. The power of the method has been demonstrated in a rapid and efficient synthesis of (R)-allyl glycine.

Complex history of a chromosomal paralogy region: insights from amphioxus aromatic amino acid hydroxylase genes and insulin-related genes

Aromatic amino acid hydroxylase (AAAH) genes and insulin-like genes form part of an extensive paralogy region shared by human chromosomes 11 and 12, thought to have arisen by tetraploidy in early vertebrate evolution. Cloning of a complementary DNA (cDNA) for an amphioxus (Branchiostoma floridae) hydroxylase gene (AmphiPAH) allowed us to investigate the ancestry of the human chromosome 11/12 paralogy region. Molecular phylogenetic evidence reveals that AmphiPAH is orthologous to vertebrate phenylalanine (PAH) genes; the implication is that all three vertebrate AAAH genes arose early in metazoan evolution, predating vertebrates. In contrast, our phylogenetic analysis of amphioxus and vertebrate insulin-related gene sequences is consistent with duplication of these genes during early chordate ancestry. The conclusion is that two tightly linked gene families on human chromosomes 11 and 12 were not duplicated coincidentally. We rationalize this paradox by invoking gene loss in the AAAH gene family and conclude that paralogous genes shared by paralogous chromosomes need not have identical evolutionary histories.

Optical genetic mapping defines regions of chromosomal variation in serovars of S. enterica subsp enterica of concern for human and animal health

Infections involving Salmonella enterica subsp. enterica serovars have serious animal and human health implications; causing gastroenteritis in humans and clinical symptoms, such as diarrhoea and abortion, in livestock. In this study an optical genetic mapping technique was used to screen 20 field isolate strains from four serovars implicated in disease outbreaks. The technique was able to distinguish between the serovars and the available sequenced strains and group them in agreement with similar data from microarrays and PFGE. The optical maps revealed variation in genome maps associated with antimicrobial resistance and prophage content in S. Typhimurium, and separated the S. Newport strains into two clear geographical lineages defined by the presence of prophage sequences. The technique was also able to detect novel insertions that may have had effects on the central metabolism of some strains. Overall optical mapping allowed a greater level of differentiation of genomic content and spatial information than more traditional typing methods.