Quantum Chromodynamics in extreme environments

In this thesis, various aspects of Quantum Chromodynamics(QCD) at extreme conditions and heavy-ion collisions phenomenology have been studies. The description of chiral charge transport in non-equilibirum conditions within the framework of kinetic theory is established. Effects of chiral anomaly are encoded in Berry curvature which affects the classical equation of motion of chiral fermions. A novel method is introduced to study the longitudinal expansion of heavy-ion collisions. By applying, for the first time in heavy-ion physics, the maximum entropy method, the longitudinal freeze-out surface is reconstructed from particle spectrum data. Insights on temperature-flow profile of the longitudinal expansion are extracted by evolving the system backward, from freeze-out time to early time, by solving the 1 + 1 ideal hydrodynamic equations analytically with initial condition fixed by the reconstructed freeze-out surface. The electrical conductivity is an important parameter characterizing the transport properties of quark-gluon plasma(QGP). The first direct estimation of the electrical conductivity of QGP based on soft photon production data with realistic hydrodynamics simulation is reported. A physically intuitive and computational convenient method to solve anomalous hydrodynamic equation of axial/vector current on top of general hydrodynamic background is developed. As an application, contribution of chiral anomaly to charge dependent pion elliptic flow as observed in experiment is simulated quantitatively. The techniques of gauge/gravity correspondence have been applied to study the relation between the electrical conductivity and other me-stable modes of the medium as well as the fate of moving charmonium in QGP

System to monitor crossovers on chromosome XII.

<p>A diploid was constructed with heterozygous markers immediately centromere-proximal to the ribosomal RNA (rRNA) gene clusters (<i>HYG</i>), within the rRNA gene cluster (<i>TRP1</i>), and immediately centromere-distal to the cluster (<i>URA3</i>) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003894#pgen.1003894-Casper1" target="_blank">[34]</a>. G1-synchronized cells were treated with UV, plated on solid medium and grown non-selectively. The resulting colonies were replica-plated to medium lacking uracil, tryptophan, or containing hygromycin as described in the text. A. Sectoring pattern expected for a crossover centromere-proximal to the <i>HYG</i> marker. B. Sectoring pattern expected for a crossover within the rRNA gene cluster centromere-proximal to <i>TRP1</i>. C. Sectoring pattern expected for a crossover within the rRNA gene cluster centromere-distal to <i>TRP1</i>.</p

Frequency of sectored colonies in unirradiated and UV-irradiated wild-type and <i>rad14</i> strains.¹

<p>¹As discussed in the text, red/white sectored colonies result from mitotic crossovers between <i>SUP4-o</i> and the centromere. The diploids used in our analysis had <i>SUP4-o</i> located near the left end of chromosome V or the right end of chromosome IV.</p><p>²Data from Lee <i>et al</i>. (2009).</p><p>³The selective method used in Lee <i>et al</i>. (2009) prevented the growth of cells without a recombination event on chromosome V.</p><p>⁴Data from Yin and Petes (2013). For the samples irradiated with 15 J/m², we included only those samples grown in the absence of canavanine, and incubated at 30⁰ following irradiation.</p><p>⁵Data from St. Charles and Petes (2013).</p><p>⁶As described in the text, most of the pink/red/white colonies in the wild-type strains reflect the plating of two adjacent cells, one with a crossover and one with unassociated events.</p><p>⁷Relative to the unirradiated wild-type strain PG311, the increase is 4309-fold.</p><p>⁸Relative to the unirradiated wild-type strain JSC25, the increase is 986-fold. Note that the unirradiated <i>rad14</i> strains YYy37.6 and YYy37.8 are hyper-Rec.</p><p>Frequency of sectored colonies in unirradiated and UV-irradiated wild-type and <i>rad14</i> strains.<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005026#t001fn001" target="_blank">¹</a></p

System to monitor crossovers on chromosome XII.

<p>A diploid was constructed with heterozygous markers immediately centromere-proximal to the ribosomal RNA (rRNA) gene clusters (<i>HYG</i>), within the rRNA gene cluster (<i>TRP1</i>), and immediately centromere-distal to the cluster (<i>URA3</i>) <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003894#pgen.1003894-Casper1" target="_blank">[34]</a>. G1-synchronized cells were treated with UV, plated on solid medium and grown non-selectively. The resulting colonies were replica-plated to medium lacking uracil, tryptophan, or containing hygromycin as described in the text. A. Sectoring pattern expected for a crossover centromere-proximal to the <i>HYG</i> marker. B. Sectoring pattern expected for a crossover within the rRNA gene cluster centromere-proximal to <i>TRP1</i>. C. Sectoring pattern expected for a crossover within the rRNA gene cluster centromere-distal to <i>TRP1</i>.</p

Mechanisms for generating UV-induced recombinogenic DSBs.

<p>At the top part of the figure, chromosomal DNA molecules are depicted as unreplicated double-stranded DNA molecules. Newly-synthesized DNA is depicted as gray dashed lines. UV-induced pyrimidine dimers are shown as triangles, and centromeres of replicated chromosomes are shown as ovals. A. Excision of a dimer results in a small gap and replication produces one broken and one unbroken sister chromatid. B. During replication of a DNA molecule with an unexcised dimer, a DSB occurs in one of the two sister chromatids. C. Excision of two closely-opposed dimers results in a short (<6 bp) unstable double-stranded region between the excision tracts. The resulting broken chromosome is replicated to form two broken sister chromatids. D. As in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003894#pgen-1003894-g009" target="_blank">Figure 9C</a>, two closely-opposed dimers are excised. One of the resulting short gaps is expanded by the 5′ to 3′ Exo1p nuclease (shown in green) to generate a broken chromosome. Replication of this chromosome results in two broken sister chromatids. E. The tract resulting form excision of a single dimer is expanded, leaving a large single-stranded DNA gap. An endonuclease cleaves this single-stranded region, resulting in two broken sister chromatids.</p

Recombination events induced by persistent UV damage in NER-deficient yeast strains.

<p>UV treatment results in the formation of a pyrimidine dimer (circle). A. Generation of a recombinogenic DSB. We suggest that the dimer-associated replication fork block can be converted into a DSB by the structure-nuclease Mus81p. The resulting DSB can be repaired either by recombination with the homolog, resulting in a detectable LOH event (boxed in grey), or by recombination with the sister chromatid which does not lead to LOH. B. Error-free bypass of lesions. When the 3’ end on the leading strand encounters a dimer, it can invade the sister chromatid (template switch), and continue replication. This branch of the post-replication repair requires Mms2p. We think that this pathway mainly involves interaction between sister chromatids without causing LOH and suppresses recombination between homologs.</p

Numbers of unselected UV-induced LOH events and other genomic changes in single colonies derived from <i>rad14</i>, <i>rad14 mus81</i>, <i>rad14 yen1</i>, and <i>rad14 mms2</i> diploids treated with 1 J/m² of UV.

<p>¹One isolate also had a translocation.</p><p>²p<0.0001 compared to <i>rad14</i>.</p><p>³<u>p</u><0.001 compared to <i>rad14</i>.</p><p>⁴<u>p</u><0.01 compared to <i>rad14</i>.</p><p>Numbers of unselected UV-induced LOH events and other genomic changes in single colonies derived from <i>rad14</i>, <i>rad14 mus81</i>, <i>rad14 yen1</i>, and <i>rad14 mms2</i> diploids treated with 1 J/m² of UV.</p

Pathways of homologous recombination.

<p>We depict recombination events initiated by a double-stranded DNA break (DSB) with each chromosome shown as a double-stranded DNA molecule. All pathways are initiated by the invasion of the 3’ end of the broken DNA molecule. Dotted lines denote DNA synthesis primed by the invading end. Regions in which a red strand and black strand are paired (in blue boxes) represent heteroduplexes; repair of mismatches within the heteroduplexes can generate gene conversion events. In synthesis-dependent strand annealing (SDSA), following DNA synthesis primed from the invading strand, the invading strand is displaced, hybridizing to the other broken end. This pathway produces a gene conversion that is not associated with a crossover (NCO). In Holliday junction (HJ) containing intermediates, an association of both broken ends with the intact template molecule can result in formation of a single Holliday junction (sHJ), a nicked Holliday junction, or a double Holliday junction (dHJ). Cleavage of these junctions by resolvases can produce either non-crossovers (NCO) or crossovers (CO). For both CO and NCO products, both molecules contain heteroduplexes located in <i>trans</i>. In contrast, if the HJ is resolved by dissolution, the heteroduplex regions are located in <i>cis</i>. In break-induced replication (BIR) events, the invading end copies the intact homolog by conservative DNA replication, resulting in a large terminal LOH event.</p

Recombination between Homologous Chromosomes Induced by Unrepaired UV-Generated DNA Damage Requires Mus81p and Is Suppressed by Mms2p

<div><p>DNA lesions caused by UV radiation are highly recombinogenic. In wild-type cells, the recombinogenic effect of UV partially reflects the processing of UV-induced pyrimidine dimers into DNA gaps or breaks by the enzymes of the nucleotide excision repair (NER) pathway. In this study, we show that unprocessed pyrimidine dimers also potently induce recombination between homologs. In NER-deficient <i>rad14</i> diploid strains, we demonstrate that unexcised pyrimidine dimers stimulate crossovers, noncrossovers, and break-induced replication events. The same dose of UV is about six-fold more recombinogenic in a repair-deficient strain than in a repair-proficient strain. We also examined the roles of several genes involved in the processing of UV-induced damage in NER-deficient cells. We found that the resolvase Mus81p is required for most of the UV-induced inter-homolog recombination events. This requirement likely reflects the Mus81p-associated cleavage of dimer-blocked replication forks. The error-free post-replication repair pathway mediated by Mms2p suppresses dimer-induced recombination between homologs, possibly by channeling replication-blocking lesions into recombination between sister chromatids.</p></div

Numbers of unselected UV-induced LOH events, deletions/duplications, and chromosome number changes in sectored colonies derived from UV-treated wild-type, <i>rad14</i>, <i>mus81</i>, and <i>yen1</i> diploids.¹

<p>¹For all strains, we examined <u>unselected</u> LOH events and other genomic changes in sectored colonies resulting from crossovers on chromosome V.</p><p>²We operationally define a BIR event as a terminal LOH event that is present in one sector but not the other. As discussed in the text, since we purify single colonies from each sector, we cannot exclude the possibility that some of the putative BIR events are actually crossovers that occur in the second division after irradiation.</p><p>³<u>p</u><0.001 compared to wild-type cells treated at 1 J/m².</p><p>⁴<u>p</u><0.01 compared to wild-type cells treated at 15 J/m².</p><p>⁵<u>p</u><0.01 compared to wild-type cells treated at 1 J/m².</p><p>Numbers of unselected UV-induced LOH events, deletions/duplications, and chromosome number changes in sectored colonies derived from UV-treated wild-type, <i>rad14</i>, <i>mus81</i>, and <i>yen1</i> diploids.<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005026#t002fn001" target="_blank">¹</a></p