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Understanding the plasticity of genomes has been greatly aided by assays for recombination, repair and mutagenesis. These assays have been developed in microbial systems that provide the advantages of genetic and molecular reporters that can readily be manipulated. Cellular assays comprise genetic, molecular, and cytological reporters. The assays are powerful tools but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.

To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.cell.2008.08.037 Byline: Zhu Zhu (1), Woo-Hyun Chung (1), Eun Yong Shim (2), Sang Eun Lee (2), Grzegorz Ira (1) Keywords: DNA Abstract: Formation of single-strand DNA (ssDNA) tails at a double-strand break (DSB) is a key step in homologous recombination and DNA-damage signaling. The enzyme(s) producing ssDNA at DSBs in eukaryotes remain unknown. We monitored 5'-strand resection at inducible DSB ends in yeast and identified proteins required for two stages of resection: initiation and long-range 5'-strand resection. We show that the Mre11-Rad50-Xrs2 complex (MRX) initiates 5' degradation, whereas Sgs1 and Dna2 degrade 5' strands exposing long 3' strands. Deletion of SGS1 or DNA2 reduces resection and DSB repair by single-strand annealing between distant repeats while the remaining long-range resection activity depends on the exonuclease Exo1. In exo1[DELTA]sgs1[DELTA] double mutants, the MRX complex together with Sae2 nuclease generate, in a stepwise manner, only few hundred nucleotides of ssDNA at the break, resulting in inefficient gene conversion and G2/M damage checkpoint arrest. These results provide important insights into the early steps of DSB repair in eukaryotes. Author Affiliation: (1) Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA (2) Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 15355 Lambda Drive, San Antonio, TX 78245, USA Article History: Received 15 May 2008; Revised 30 July 2008; Accepted 27 August 2008 Article Note: (miscellaneous) Published: September 18, 2008

3.6 MW (66 kV/55 A) high voltage power supply system was developed for the 170 GHz ECH&CD system in KSTAR. It consists of the cathode power supply (CPS), anode power supply (APS), and body power supply (BPS). Currently, modulation frequency of APS was limited to less than 1 kHz due to the parasitic capacitance of Zener diode circuit including gyrotron. In order to solve these lacks of controllability and high frequency modulation of APS, the existing APS is replaced by a new type of APS and it is tested for KSTAR 170 GHz gyrotron system. This paper presents the new APS design and characteristics and the test results for 170GHz gyrotron in KSTAR ECH system.

Research has been conducted on metazoan transcription elongation factor P-TEFb (CDK-9/cyclin T). The study of the P-TEFb functions in vivo has been carried out via the use of RNA interference in the Caenorhabditis elegans embryo and the results are presented.

Transcriptional repression by a Caenorhabditis elegans germ-line protein has been studied. In the early C. elegans embryo, PIE-1 protein, which is maternally expressed, is necessary in germ-line blastomeres to inhibit somatic differentiation, block phosphorylation of the RNA polymerase II large subunit (Pol II) carboxy-terminal domain (CTD) and maintain mRNA transcription absence. It has been found the PIE-1 can act as a transcriptional repressor in cell culture assays. A PIE-1 repression domain that seems to cut back transcriptional machinery directly has been identified. It seems repressor activity may be important for in vivo PIE-1 function.

Nucleosome positioning is still under investigation. The mice transcriptional enhancer of the serum albumin gene acts in the liver. There regulatory factors occupy target sites on three particles designated N1, N2 and N3. They are nucleosome-like. Winged helix transcription factor HNF3 binds to two near-center sites in the N1 particle. Dinucleosome templates using the albumin enhancer sequence were created. Site-specific binding of HNF3 protein brought nucleosome positioning in vitro like that seen in liver nuclei. Binding of a transcription factor can put in place an underlying nucleosome core.

A 3.6 MW (-66 kV/55 A) Gyrotron power supply system was developed for the 170 GHz ECH&CD gyrotron system in KSTAR. This power supply system consists of Cathode Power Supply(CPS), Anode Power Supply(APS) and Body Power Supply(BPS). The CPS is using the Pulse Step Modulation by the 32set of IGBT choppers. The respons time of Chopper is very fast. So the cathode voltaget is able to be controlled rapidly. The APS is a sort of voltage devider using zener and switch component. It was achieved 3kHz modulation operation. The BPS is combined the commercial power supply and special high voltage switches. It is very simple topology but 5kHz modulation was accomplished easily. Theses power supply system were installed and commissioned successfully in 2011. This paper presents the topology of the each power supply and test result for 170 GHz gyrotron in KSTAR.

The transcription factor HNF3 and linker histones H1 and H5 possess winged-helix DNA-binding domains, yet HNF3 and other fork head-related proteins activate genes during development whereas linker histones compact DNA in chromatin and repress gene expression. We compared how the two classes of factors interact with chromatin templates and found that HNF3 binds DNA at the side of nucleosome cores, similarly to what has been reported for linker histone. A nucleosome structural binding site for HNF3 is occupied at the albumin transcriptional enhancer in active and potentially active chromatin, but not in inactive chromatin in vivo. While wild-type HNF3 protein does not compact DNA extending from the nucleosome, as does linker histone, site-directed mutants of HNF3 can compact nucleosomal DNA if they contain basic amino acids at positions previously shown to be essential for nucleosomal DNA compaction by linker histones. The results illustrate how transcription factors can possess special nucleosome-binding activities that are not predicted from studies of factor interactions with free DNA. [ABSTRACT FROM AUTHOR]