Genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature.

We report the genome sequences of 31 mycobacteriophages isolated on Mycobacterium smegmatis mc2155 at room temperature. The genomes add to the diversity of Clusters A, B, C, G, and K. Collectively, the genomes include 70 novel protein-coding genes that have no close relatives among the actinobacteriophages.

The impact of holistic review on correlations between doctoral student outcomes, and GPA and GRE scores in the biomedical sciences.

Graduate admissions committees throughout the United States examine both quantitative and qualitative data from applicants to make admissions determinations. A number of recent studies have examined the ability of commonly used quantitative metrics such as the GRE and undergraduate GPA to predict the likelihood of applicant success in graduate programs. We examined whether an admissions committee could predict applicant success at The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences based on quantitative metrics. We analyzed the predictive validity of admissions scores, undergraduate GPA, and the GRE for student success. We observed nuanced differences based on gender, ethnicity, race, and citizenship status. The scores assigned to applicants by the admissions committee could not predict time to degree in PhD students regardless of demographic group. Undergraduate GPA was correlated with time to degree in some instances. Interestingly, while GRE scores could predict time to degree, GRE percentile scores could predict both time to degree and PhD candidacy examination results. These findings suggest that there is a level of nuance that is required for interpretation of these quantitative metrics by admissions committees.

Ubiquitination-Linked Phosphorylation of the FANCI S/TQ Cluster Contributes to Activation of the Fanconi Anemia I/D2 Complex.

Repair of interstrand crosslinks by the Fanconi anemia (FA) pathway requires both monoubiquitination and de-ubiquitination of the FANCI/FANCD2 (FANCI/D2) complex. In the standing model, the phosphorylation of six sites in the FANCI S/TQ cluster domain occurs upstream of, and promotes, FANCI/D2 monoubiquitination. We generated phospho-specific antibodies against three different S/TQ cluster sites (serines 556, 559, and 565) on human FANCI and found that, in contrast to the standing model, distinct FANCI sites were phosphorylated either predominantly upstream (ubiquitination independent; serine 556) or downstream (ubiquitination-linked; serines 559 and 565) of FANCI/D2 monoubiquitination. Ubiquitination-linked FANCI phosphorylation inhibited FANCD2 de-ubiquitination and bypassed the need to de-ubiquitinate FANCD2 to achieve effective interstrand crosslink repair. USP1 depletion suppressed ubiquitination-linked FANCI phosphorylation despite increasing FANCI/D2 monoubiquitination, providing an explanation of why FANCD2 de-ubiquitination is important for function of the FA pathway. Our work results in a refined model of how FANCI phosphorylation activates the FANCI/D2 complex.

NEK8 regulates DNA damage-induced RAD51 foci formation and replication fork protection.

Proteins essential for homologous recombination play a pivotal role in the repair of DNA double strand breaks, DNA inter-strand crosslinks and replication fork stability. Defects in homologous recombination also play a critical role in the development of cancer and the sensitivity of these cancers to chemotherapy. RAD51, an essential factor for homologous recombination and replication fork protection, accumulates and forms immunocytochemically detectable nuclear foci at sites of DNA damage. To identify kinases that may regulate RAD51 localization to sites of DNA damage, we performed a human kinome siRNA library screen, using DNA damage-induced RAD51 foci formation as readout. We found that NEK8, a NIMA family kinase member, is required for efficient DNA damage-induced RAD51 foci formation. Interestingly, knockout of Nek8 in murine embryonic fibroblasts led to cellular sensitivity to the replication inhibitor, hydroxyurea, and inhibition of the ATR kinase. Furthermore, NEK8 was required for proper replication fork protection following replication stall with hydroxyurea. Loading of RAD51 to chromatin was decreased in NEK8-depleted cells and Nek8-knockout cells. Single-molecule DNA fiber analyses revealed that nascent DNA tracts were degraded in the absence of NEK8 following treatment with hydroxyurea. Consistent with this, Nek8-knockout cells showed increased chromosome breaks following treatment with hydroxyurea. Thus, NEK8 plays a critical role in replication fork stability through its regulation of the DNA repair and replication fork protection protein RAD51.