Meiotic crossing over in each of two linked intervals may be correlated. The coefficient of coincidence is a measure of that correlation. Letting R1 be the recombinant frequency for interval 1 determined without regard to interval 2, R2 be that for interval 2 determined without regard to interval 1, and R12 be the frequency of the haploid meiotic products that are recombinant simultaneously in the two intervals, the expectation for no correlation is R12 = R1R2. When the expectation is not realized, introduction of a factor, C (the coefficient of coincidence), allows the equation R12 = CR1R2. A C value of unity implies no correlation, values of zero to unity imply negative correlation, and values greater than unity imply positive correlation.

In a two-factor cross (AB × ab), recombination is reciprocal when the two recombinant types (Ab and aB) are produced in the same event. Such reciprocality characterizes meiotic recombination as well as certain site-specific recombination events well studied in prokaryotes.

For some genes, the meiotic conversion frequency for different genetic markers within the same gene varies as a function of the position of the marker within the gene. Commonly in fungi, conversion frequencies are relatively high near one end of the gene and fall monotonically to a lower value at the other end (this is known as the conversion gradient, often called polarity gradient, defining a segment of a chromosome as a polaron).

Previously published, and some unpublished, tetrad data from budding yeast (Saccharomyces cerevisiae) are analyzed for disparity in gene conversion, in which one allele is more often favored than the other (conversion disparity). One such disparity, characteristic of a bias in the frequencies of meiotic double-strand DNA breaks at the hotspot near the His4 locus, is found in diploids that undergo meiosis soon after their formation, but not in diploids that have been cloned and frozen. Altered meiotic DNA breakability associated with altered metabolism-related chromatin states has been previously reported. However, the above observations imply that such differing parental chromatin states can persist through at least one chromosome replication, and probably more, in a common environment. This conclusion may have implications for interpreting changes in allele frequencies in populations.

The study of homologous recombination between plasmids, or between a plasmid and the chromosome, revealed that the RecFOR pathway is less of a poor cousin than first thought. When the exquisite sensitivity to DNA damage of the first recombination-deficient mutants was found, it became clear that homologous recombination might be the only way to repair certain DNA lesions. Generally, the stronger the defect in homologous recombination, the higher the sensitivity to DNA damage. In Escherichia coli, chromosomal lesions are repaired by homology-guided strand exchange between sister chromatids. The evidence in support of this notion comes in three forms. First, physical connections between parental and daughter strands, associated with lesion repair, can be detected. Second, repair of chromosomal lesions is not observed in recA mutants. Third, DNA damage stimulates homologous recombination although the structure of chromosomal lesions in this case is unspecified. Single-stranded DNA-binding protein (SSB) complexes single-stranded DNA (ssDNA), facilitating its subsequent use in replication and in degradation and repair pathways of DNA metabolism. Chromosomal dimerization in E. coli creates a chromosomal lesion, because it prevents segregation of the replicated chromosomes into daughter cells. The understanding of the formation of replication-dependent chromosomal lesions is still primitive. There is one in vivo study on the structure of stalled replication forks, a report documenting replication fork reversal in vivo, as well as a few reports of replication fork reversal in vitro, likely to be an artifact of DNA isolation.

The analysis of crossover interference in many creatures is complicated by the presence of two kinds of crossovers, interfering and noninterfering. In such creatures, the values of the traditional indicators of interference are subject not only to the strength of interference but also to the relative frequencies of crossing over contributed by the two kinds. We formalize the relationship among these variables and illustrate the possibilities and limitations of classical interference analysis with meiotic tetrad data from wild-type Saccharomyces cerevisiae and from mlh1 and ndj1 mutants.

Several apparently paradoxical observations regarding meiotic crossing over and gene conversion are readily resolved in a framework that recognizes the existence of two recombination pathways that differ in mismatch repair, structures of intermediates, crossover interference, and the generation of noncrossovers. One manifestation of these differences is that simultaneous gene conversion on both sides of a recombination-initiating DNA double-strand break (“two-sidedness”) characterizes only one of the two pathways and is promoted by mismatch repair. Data from previous work are analyzed quantitatively within this framework, and a molecular model for meiotic double-strand break repair based on the concept of sliding D-loops is offered as an efficient scheme for visualizing the salient results from studies of crossing over and gene conversion, the molecular structures of recombination intermediates, and the biochemical competencies of the proteins involved.

Gestational diabetes and impaired glucose tolerance in pregnancy were found to be important teratogenetic risk factors for the development of diabetes in the offspring. Mechanisms of action and prevention of maternofetal transmission of teratogenetic susceptibility to diabetes are presented. Gestational diabetes induced in the F0 generation produced the following effects in the F1 and/or F2 generation: Early postnatal hyperinsulinaemia, decreased noradrenaline and serotonin and increased endorphin concentrations in specific brain regions, permanent hypoplasia of the hypothalamic ventromedial nuclei, decreased insulin responsiveness to glucose, impaired glucose tolerance and increased diabetes susceptibility.

Interest in crossover interference in yeast has been spurred by the discovery and characterization of mutants that alter it as well as by the development and testing of models to explain it. This chapter describes methods for detecting and for measuring interference, with emphasis on those that exploit the ability to examine all four products of individual acts of meiosis.

spo16 mutants in yeast were reported to have reduced map lengths, a high frequency of nondisjunction in the first meiotic division, and essentially unchanged coefficients of coincidence. Were all crossing over in yeast subject to interference, such data would suggest that the “designation” of recombination events to become crossovers is separable from the “implementation” of that crossing over. In the presence of coexisting interference and noninterference phases of crossing over, however, lack of change in the coefficient of coincidence may show only that spo16 reduces crossing over in the two phases by a similar factor.

We demonstrate that recent data from human males are consistent with constant interference levels among chromosomes under the two-pathway model, whereas inappropriately fitting shape parameters of Gamma distributions to immunofluorescent interfoci distances observed on finite chromosomes generates false interpretations of higher levels of interference on shorter chromosomes. We provide appropriate statistical methodology.

Using small palindromes to monitor meiotic double-strand-break-repair (DSBr) events, we demonstrate that two distinct classes of crossovers occur during meiosis in wild-type yeast. We found that crossovers accompanying 5:3 segregation of a palindrome show no conventional (i.e., positive) interference, while crossovers with 6:2 or normal 4:4 segregation for the same palindrome, in the same cross, do manifest interference. Our observations support the concept of a “non”-interference class and an interference class of meiotic double-strand-break-repair events, each with its own rules for mismatch repair of heteroduplexes. We further show that deletion of MSH4 reduces crossover tetrads with 6:2 or normal 4:4 segregation more than it does those with 5:3 segregation, consistent with Msh4p specifically promoting formation of crossovers in the interference class. Additionally, we present evidence that an ndj1 mutation causes a shift of noncrossovers to crossovers specifically within the “non”-interference class of DSBr events. We use these and other data in support of a model in which meiotic recombination occurs in two phases—one specializing in homolog pairing, the other in disjunction—and each producing both noncrossovers and crossovers.

WHEN physicist Max Delbruck undertook the study of phage growth (Ellis and Delbruck 1939), he anticipated that phage would be the best model for elucidating biological reproduction and mutation, uncomplicated by sex (Delbruck 1970). This Perspectives traces Max's attempt to come to grips with realities that threatened that view, and it considers present-day relevance for yeast geneticists of two lessons that remain from his heroic effort. Readers should understand (or recall) that in 1939 essentially nothing of what we now know about the chemistry of either reproduction or mutation was even imagined—for nucleic acids, it was “known” only that most of the DNA is in the nucleus and most of the RNA is in the cytoplasm and, for proteins, only that some were enzymes and that they were probably the stuff that genes are made of. Furthermore, Max seemed to have little hope that the biochemistry of the day would ask the right questions (Delbruck 1949). (Overheard, one graduate of Max's phage course to another: “Would you want your daughter to marry a biochemist?”) I think Max hoped to solve the secret of life using physics and algebra along with open communication subject to tough criticism.

WHEN we stumbled over Chi in coliphage λ (in 1972?), it appeared to be a uniquely accessible example of a “recombination initiator,” whose existence was implied by gene-conversion gradients (polarons) of fungi. Hence, it promised to have wide significance for our understanding of meiotic as well as of prokaryotic recombination. For a time, Chi seemed to fulfill its promise, but things turned out otherwise. Nevertheless, Chi did elucidate basic aspects of genetic recombination and genome maintenance, played a role in the development of λ as a cloning vehicle, and continues to bring enzymological surprises. In this Perspectives, which reflects my rather personal memory of events, literature citations of work from our lab are omitted to improve readability. They can be found in older reviews (e.g., Myers and Stahl 1994; Smith 1998) or electronically. For those in a hurry, here is the bottom line: Escherichia coli's RecBCD enzyme enters duplex DNA at a double-strand break and travels in a destructive mode until it encounters a properly oriented octamer called Chi. This encounter civilizes the enzyme, which keeps on traveling, in a recombinagenic mode, recruiting E. coli's strand-invasion protein, RecA, to effect recombination when a homolog is available. The primary adaptive significance of Chi is likely to concern E. coli DNA replication, when breaks occur at the fork. Since these breaks are repaired by a RecBCD-promoted recombination-like reaction (usually between the two tines of the fork), Chi plays a role in the maintenance of the E. coli genome.

Sandy Lam*, Sarah R. Horn*, Sarah J. Radford, Elizabeth A. Housworth, Franklin W. Stahl and Gregory P. Copenhaver* * Department of Biology and The Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, Curriculum in Genetics and Molecular Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, Departments of Mathematics and Biology, Indiana University, Bloomington, IN 47405, Institute of Molecular Biology, University of Oregon, Eugene, OR 97403-1229

In most eukaryotes, crossovers are not independently distributed along the length of a chromosome. Instead, they appear to avoid close proximity to one another—a phenomenon known as crossover interference. Previously, for three of the five Arabidopsis chromosomes, we measured the strength of interference and suggested a model wherein some crossovers experience interference while others do not. Here we show, using the same model, that the fraction of interference-insensitive crossovers is significantly smaller on the remaining two chromosomes. Since these two chromosomes bear the Arabidopsis NOR domains, the possibility that these chromosomal regions influence interference is discussed.

We previously proposed a "counting model" for meiotic crossover interference, in which double-strand breaks occur independently and a fixed number of noncrossovers occur between neighboring crossovers. Whereas in some organisms (group I) this simple model alone describes the crossover distribution, in other organisms (group II) an additional assumption--that some crossovers lack interference--improves the fit. Other differences exist between the groups: Group II needs double-strand breaks and some repair functions to achieve synapsis, while repair in group I generally occurs after synapsis is achieved; group II, but not group I, has recombination proteins Dmc1, Mnd1, and Hop2. Here we report experiments in msh4 mutants that are designed to test predictions of the revised model in a group II organism. Further, we interpret these experiments, the above-mentioned differences between group I and II meiosis, and other data to yield the following proposal: Group II organisms use the repair of leptotene breaks to promote synapsis by generating double-Holliday-junction intermediates that lock homologs together (pairing pathway). The possible crossover or noncrossover resolution products of these structures lack interference. In contrast, for both group I and group II, repair during pachytene (disjunction pathway) is associated with interference and generates only two resolution types, whose structures suggest that the Holliday junctions of the repair intermediates are unligated. A crossover arises when such an intermediate is stabilized by a protein that prevents its default resolution to a noncrossover. The protein-binding pattern required for interference depends on clustering of sites that have received, or are normally about to receive, meiotic double-strand breaks.

Gene conversions and crossing over were analyzed along 10 intervals in a 405-kb region comprising nearly all of the left arm of chromosome VII in Saccharomyces cerevisiae. Crossover interference was detected in all intervals as measured by a reduced number of nonparental ditypes. We have evaluated interference between crossovers in adjacent intervals by methods that retain the information contained in tetrads as opposed to single segregants. Interference was seen between intervals when the distance in the region adjacent to a crossover was < approximately 35 cM (90 kb). At the met13 locus, which exhibits approximately 9% gene conversions, those gene conversions accompanied by crossing over exerted interference in exchanges in an adjacent interval, whereas met13 gene conversions without an accompanying exchange did not show interference. The pattern of exchanges along this chromosome arm can be represented by a counting model in which there are three nonexchange events between adjacent exchanges; however, maximum-likelihood analysis suggests that approximately 8-12% of the crossovers on chromosome VII arise by a separate, noninterfering mechanism.

On June 27, two months after Ira Herskowitz's death from cancer, more than 300 of his family, friends, and colleagues gathered at the Legion of Honor in San Francisco to reflect on Ira's remarkable life. The memorial, like Ira himself, celebrated science, music, and the art of mentoring, and it reminded us that, even in today's competitive climate, straight talk combined with a generous spirit is compatible with accomplishment and recognition. Figure 1 Ira and his identical twin, Joel, were born in 1946 in Brooklyn to parents Reida and Irwin. They attended high school in Missouri, while their father, a Drosophila geneticist, was a member of the Genetics Department at St. Louis University. Ira was an undergraduate at Caltech where his interactions with Jean Weigle and Sandy Parkinson directed him toward bacteriophage λ as a system for gaining insight into developmental processes. After graduating in 1967, Ira continued studies of developmental phage genetics at MIT with Ethan Signer. Ira's PhD thesis (1971) “Control of late genes, early genes, the cI gene, and replication in bacteriophage λ” revealed, by its very title, both the breadth and the intensity of Ira's interests. It also revealed his modus operandi: using simple genetics to ask and answer big questions. In 1971, in his last year of graduate school, Ira accepted an Assistant Professorship in the University of Oregon's Institute of Molecular Biology, deferring his arrival to spend a year at MIT with David Botstein to gear up for work on yeast. At Eugene, Ira continued his passionate interest in λ lifestyle decisions—studying how λ determined whether to lyse its host or reside peacefully within it. He also began his study of how yeast makes lifestyle decisions, choosing as his entry point a most important issue—cell type specification. How do yeast decide to switch from the a cell type to the α cell type so that mating can occur? His incisive genetic experiments suggested a novel mechanism—insertion of a new cassette with opposite mating type information. In 1977, the significance and potential of that work was recognized by Jim Watson, who convinced two of Ira's earliest students (Jeff Strathern and Jim Hicks) to join with Amar Klar to create a year-round program in yeast genetics at Cold Spring Harbor. Among the accomplishments of this Cold Spring Harbor Yeast group, which attracted the best and brightest of young collaborators, was the demonstration that mating type interconversion was achieved by genetic recombination, initiated by a DNA double-strand break. Figure 2 In 1981, Ira was enticed to move to San Francisco, where he remained for the rest of his life. At UCSF, he continued to study cell type specification, dissecting the molecular circuits responsible for mating type switching. He also broadened his sphere of inquiry. He investigated morphogenetic questions, determining how bud sites are selected and cell polarity established, touched on signal transduction by studying crosstalk between pathways, and examined sporulation as a developmental program. Recently, Ira began using yeast to directly learn about human genetics, performing a “proof of principle” study showing that yeast and mammals share similar mechanisms of resistance to the anticancer drug cisplatin. Finally, Ira developed a new love—pharmocogenomics. Stymied by the inability to carry out genetic experiments in humans, Ira spearheaded a study of whether inherited differences in membrane transporters correlated with altered response to drugs. Ira was an inspiring scientist with a generous heart. His hallmark was the ability to use simple genetics, supplemented in later years by the judicial application of molecular biological, genomic, and bioinformatic tools, to ask big questions. His genius was his ability to look at the data and formulate elegant hypotheses, often with universal implications. His driving force was an intense desire to understand the workings of life and derive the truth, almost akin to the drive of a Talmudic scholar. In this pursuit, he cared little whether it was his idea or someone else's that provided the key to understanding. As Ira never failed to acknowledge the contributions of others, both competitors and collaborators were drawn together in the search for understanding. It is completely in character that Ira orchestrated the award of the 2001 Thomas Hunt Morgan Medal to Yasuji Oshima (Herskowitz and O'Shea 2002Herskowitz I. O'Shea E. Genetics. 2002; 160: 367-368PubMed Google Scholar) so that Oshima's contributions to mating type switching would be forever acknowledged. Not surprisingly, Ira was also an inspiring mentor, able to instill in his associates both a big approach to science and an appreciation of hypotheses, while facilitating the development of their own personal styles. His success was astounding. Many continued working on problems started in his lab. Others used the approaches learned from Ira to tackle new organisms or problems. Ira's dedication to science education was manifested in both imaginable and unimaginable ways. Who could forget Ira's whimsical, but highly informative, pictorial summary of λ's control circuits (shrink-wrapped with the 1983 Cold Spring Harbor volume Lambda II)? Or Ira's guitar/vocal performances of Joel's “Double Talking Helix Blues” (available from Cold Spring Harbor Laboratory Press)? In review articles, he presented his understanding of λ and yeast development and their wider applications to a grateful community (Herskowitz 1973Herskowitz I. Annu. Rev. Genet. 1973; 7: 289-324Crossref PubMed Scopus (88) Google Scholar, Herskowitz 1987Herskowitz I. Nature. 1987; 329: 219-222Crossref PubMed Scopus (841) Google Scholar, Herskowitz 1989Herskowitz I. Nature. 1989; 342: 749-757Crossref PubMed Scopus (377) Google Scholar, Herskowitz 1997Herskowitz I. Cold Spring Harb. Symp. Quant. Biol. 1997; 62: 57-63Crossref PubMed Google Scholar, Herskowitz and Hagen 1980Herskowitz I. Hagen D. Annu. Rev. Genet. 1980; 14: 399-445Crossref PubMed Scopus (199) Google Scholar), which rewarded him with the National Academy of Sciences Award for Excellence in Scientific Reviewing in 1985. As course director of Genetics at UCSF for eighteen years, Ira's success in instilling generations of graduate students (and their faculty mentors) with awareness of the “awesome power of yeast genetics” was legendary. His impact can be measured by the fact that hardly a single UCSF laboratory, regardless of research orientation, was immune to the logic of this approach. More than anyone else we know, Ira's spirit combined competition with generosity. To illustrate—upon his arrival in Eugene, Ira quickly scooped up all graduate students who had not yet chosen labs (and some who had). The brain-drain suffered by less talented faculty was more than compensated for by the help Ira gave us—from advice on the nitty-gritty of phage and yeast development to a vision of the future for our program. And we all enjoyed watching this brilliant, interactive Pied Piper rapidly achieve worldwide scientific recognition with one hand, while beating us at ping-pong with the other. When Ira left Eugene, he cried and so did we. Ira was equally valued in San Francisco, where students and postdocs vied to join his laboratory or to secure him as a member of their thesis committee, and faculty relied upon him for incisive suggestions and for leadership in new directions. When Ira died, UCSF mourned the loss of one of its anchors. But the students said it best. Although policies of the University of California may prevent it from happening, a remarkable document from the UCSF graduate students asked that a building at Mission Bay be named Herskowitz Hall “in memory and remembrance of a truly inspiring and excellent member of the UCSF family. His overall presence, ranging from whistling down the hall to teaching Genetics to singing the DNA Blues, are memories that have touched us all forever. We would like to see this wonderful person honored in such a way that his spirit lives on forever at UCSF. He was the heart and soul of the UCSF community.” Sentiments of Ira's colleagues at Eugene and UCSF were widely shared. By the time Ira died at the age of 56, he was an elected member of the Institute of Medicine, the National Academy of Sciences, and the American Academy of Arts and Sciences, and he had been honored by a MacArthur Fellowship, an Eli Lilly Award in Microbiology and Immunology, a Genetics Society of America Medal, a Thomas Hunt Morgan Medal for Lifetime Contribution to Genetics, and a Rosenstiel Award.

Crossing-over between homologous chromosomes facilitates proper disjunction of chromosomes during meiosis I. In many organisms, gene functions that are essential to crossing-over also facilitate the intimate chromosome pairing called "synapsis." Many organisms--including budding yeast, humans, zebrafish, Drosophila, and Arabidopsis--regulate the distribution of crossovers, so that, most of the time, each chromosome bundle gets at least one crossover while the mean number of crossovers per chromosome remains modest. This regulation is obtained through crossover interference. Recent evidence suggests that the organisms that use recombination functions to achieve synapsis have two classes of crossovers, only one of which is subject to interference. We statistically test this two-pathway hypothesis in the CEPH data and find evidence to support the two-pathway hypothesis in humans.