Break-induced replication: A review and an example in budding yeast

Break-induced replication (BIR) is a nonreciprocal recombination-dependent replication process that is an effective mechanism to repair a broken chromosome. We review key roles played by BIR in maintaining genome integrity, including restarting DNA replication at broken replication forks and maintaining telomeres in the absence of telomerase. Previous studies suggested that gene targeting does not occur by simple crossings-over between ends of the linearized transforming fragment and the target chromosome, but involves extensive new DNA synthesis resembling BIR. We examined gene targeting in Saccharomyces cerevisiae where only one end of the transformed DNA has homology to chromosomal sequences. Linearized, centromere-containing plasmid DNA with the 5′ end of the LEU2 gene at one end was transformed into a strain in which the 5′ end of LEU2 was replaced by ADE1, preventing simple homologous gene replacement to become Leu2+. Ade1+ Leu2+ transformants were recovered in which the entire LEU2 gene and as much as 7 kb of additional sequences were found on the plasmid, joined by microhomologies characteristic of nonhomologous end-joining (NHEJ). In other experiments, cells were transformed with DNA fragments lacking an ARS and homologous to only 50 bp of ADE2 added to the ends of a URA3 gene. Autonomously replicating circles were recovered, containing URA3 and as much as 8 kb of ADE2-adjacent sequences, including a nearby ARS, copied from chromosomal DNA. Thus, the end of a linearized DNA fragment can initiate new DNA synthesis by BIR in which the newly synthesized DNA is displaced and subsequently forms circles by NHEJ.

The [(G/C)3NN]n motif: a common DNA repeat that excludes nucleosomes.

Nucleosomes, the basic structural elements of chromosomes, consist of 146 bp of DNA coiled around an octamer of histone proteins, and their presence can strongly influence gene expression. Considerations of the anisotropic flexibility of nucleotide triplets containing 3 cytosines or guanines suggested that a [5'(G/C)3 NN3']n motif might resist wrapping around a histone octamer. To test this, DNAs were constructed containing a 5'-CCGNN-3' pentanucleotide repeat with the Ns varied. Using in vitro nucleosome reconstitution and electron microscopy, a plasmid with 48 contiguous CCGNN repeats strongly excluded nucleosomes in the repeat region. Competitive reconstitution gel retardation experiments using DNA fragments containing 12, 24, or 48 CCGNN repeats showed that the propensity to exclude nucleosomes increased with the length of the repeat. Analysis showed that a 268-bp DNA containing a (CCGNN)48 block is 4.9 +/- 0.6-fold less efficient in nucleosome assembly than a similar length pUC19 fragment and approximately 78-fold less efficient than a similar length (CTG)n sequence, based on results from previous studies. Computer searches against the GenBank database for matches with a [(G/C)3NN]48 sequence revealed numerous examples that frequently were present in the control regions of "TATA-less" genes, including the human ETS-2 and human dihydrofolate reductase genes. In both cases the (G/C)3NN repeat, present in the promoter region, co-maps with loci previously shown to be nuclease hypersensitive sites.

The adipocyte specific transcription factor C/EBPalpha modulates human ob gene expression.

The ob gene product, leptin, apparently exclusively expressed in adipose tissue, is a signaling factor regulating body weight homeostasis and energy balance. ob gene expression is increased in obese rodents and regulated by feeding, insulin, and glucocorticoids, which supports the concept that ob gene expression is under hormonal control, which is expected for a key factor controlling body weight homeostasis and energy balance. In humans, ob mRNA expression is increased in gross obesity; however, the effects of the above factors on human ob expression are unknown. We describe the structure of the human ob gene and initial functional analysis of its promoter. The human ob gene's three exons cover approximately 15 kb of genomic DNA. The entire coding region is contained in exons 2 and 3, which are separated by a 2-kb intron. The first small 30-bp untranslated exon is located >10.5 kb upstream of the initiator ATG codon. Three kilobases of DNA upstream of the transcription start site has been cloned and characterized. Only 217 bp of 5' sequence are required for basal adipose tissue-specific expression of the ob gene as well as enhanced expression by C/EBPalpha. Mutation of the single C/EBPalpha site in this region abolished inducibility of the promoter by C/EBPalpha in cotransfection assays. The gene structure will facilitate our analysis of ob mutations in human obesity, whereas knowledge of sequence elements and factors regulating ob gene expression should be of major importance in the prevention and treatment of obesity.

ndhF sequence evolution and the major clades in the sunflower family.

An extensive sequence comparison of the chloroplast ndhF gene from all major clades of the largest flowering plant family (Asteraceae) shows that this gene provides approximately 3 times more phylogenetic information than rbcL. This is because it is substantially longer and evolves twice as fast. The 5' region (1380 bp) of ndhF is very different from the 3' region (855 bp) and is similar to rbcL in both the rate and the pattern of sequence change. The 3' region is more A+T-rich, has higher levels of nonsynonymous base substitution, and shows greater transversion bias at all codon positions. These differences probably reflect different functional constraints on the 5' and 3' regions of ndhF. The two patterns of base substitutions of ndhF are particularly advantageous for phylogenetic reconstruction because the conserved and variable segments can be used for older and recent groups, respectively. Phylogenetic analyses of 94 ndhF sequences provided much better resolution of relationships than previous molecular and morphological phylogenies of the Asteraceae. The ndhF tree identified five major clades: (i) the Calyceraceae is the sister family of Asteraceae; (ii) the Barnadesioideae is monophyletic and is the sister group to the rest of the family; (iii) the Cichorioideae and its two basal tribes Mutisieae and Cardueae are paraphyletic; (iv) four tribes of Cichorioideae (Lactuceae, Arctoteae, Liabeae, and Vernonieae) form a monophyletic group, and these are the sister clade of the Asteroideae; and (v) the Asteroideae is monophyletic and includes three major clades.

O imaginário das ilhas atlânticas no universo medieval islâmico-cristão

O pensamento cultural medieval aparece-nos como herdeiro da Antiguidade Clássica, da sua filosofia, ciência, arte e mitos. Todos estes conceitos traduzem-se com facilidade para as elites intelectuais cristãs e muçulmanas, que os conservam e integram em elementos da sua própria cultura. A ideia do mar, em especial o mar dito ‘aberto’ como o Oceano Atlântico, é marcada pelo maravilhoso. Em plena Idade Média o Oceano Atlântico surge como território de Caos, envolto em mistério. O Oceano Atlântico é local das mais variadas manifestações do fantástico. Desta forma, as ilhas atlânticas, contidas neste vasto oceano, são elas próprias impregnadas de um carácter maravilhoso. Tentaremos, ao longo desta dissertação de mestrado, abordar a questão das ilhas atlânticas e das suas características a nível de imaginário. Este exercício será feito, sempre que possível, fazendo o cruzamento de fontes de origem islâmica e de origem cristã. Desta maneira, surgirá uma imagem comum em relação ao imaginário do Oceano Atlântico e, em especial, das ilhas neste contidas. O objetivo principal deste trabalho é verdadeiramente demonstrar pontos de aproximação entre relatos e mapas, de origem cristã e islâmica, ligados a ilhas fantásticas e, ao mesmo tempo, reais. Veremos que as duas categorias, do real e do imaginário, sobrepõem-se diversas vezes, sendo que não se conseguem muitas vezes distinguir a nível das fontes. Desta forma, relatos de navegações atlânticas como a de São Brandão (de origem celto-cristã) ou a dos Aventureiros de Lisboa (originária no al-Andalus,) são reveladoras das atitudes e ideias na Idade Média em relação ao Atlântico e às suas ilhas.

Nel giorno XIX luglio MDCCCXLVI faustissimo e felicissimo, pel solenne ingresso di monsignore Bartolommeo de' conti Romilli alla sede vescovile di Cremona : omaggio di esultanza e d'amore.

Acquisition made accessible thanks to a 2015-2017 grant from the Council on Libraries and Information Resources.

S. Aurelii Augustini Confessiones.

Mode of access: Internet.

Libri decem explanationis Ecclesiastæ, graece primum & cum latina interpretatione ac commentariis vulgati /

"Appendix ... De aetate b. Gregorii ... dissertatio Joannis Lancea Panormitani": p. [296]-320.

Th. C. Cypriani De Oratione Dominica = St. Cyprian on the Lord's prayer /

Mode of access: Internet.

How I made $2,000,000 in the stock market.

Mode of access: Internet.

De civitate Dei : selections with notes and glossary /

A textbook for colleges, universities and seminaries.

Quae ratio inter Vitas Lysiae Dionysiacam, pseudo-Plutarcheam, Photianam intercedat, quaesivit A.Z.

Disbound Original Held in Oak Street Library Facility.

Opera omnia.

Mode of access: Internet.

Omelie mistagogiche e catechetice /

Text of the homilies in Latin; commentary in Italian. Appendix contains Italian translation of the homilies.

A Démétrien /

Includes bibliographical references (p. [59]-65) and indexes.