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Accurate DNA replication is essential for genomic stability and cancer prevention. Homologous recombination is important for high-fidelity DNA damage tolerance during replication. How the homologous recombination machinery is recruited to replication intermediates is unknown. Here, we provide evidence that a Rad51 paralog-containing complex, the budding yeast Shu complex, directly recognizes and enables tolerance of predominantly lagging strand abasic sites. We show that the Shu complex becomes chromatin associated when cells accumulate abasic sites during S phase. We also demonstrate that purified recombinant Shu complex recognizes an abasic analog on a double-flap substrate, which prevents AP endonuclease activity and endonuclease-induced double-strand break formation. Shu complex DNA binding mutants are sensitive to methyl methanesulfonate, are not chromatin enriched, and exhibit increased mutation rates. We propose a role for the Shu complex in recognizing abasic sites at replication intermediates, where it recruits the homologous recombination machinery to mediate strand specific damage tolerance. The homologous recombination machinery needs to be recruited at replication intermediates for accurate functioning. Here, the authors reveal that a Rad51 paralog-containing complex, called the Shu complex, recognizes and enables tolerance of predominantly lagging strand abasic sites.

Three-methyl cytosine (3meC) are toxic DNA lesions, blocking base pairing. Bacteria and humans express members of the AlkB enzymes family, which directly remove 3meC. However, other organisms, including budding yeast, lack this class of enzymes. It remains an unanswered evolutionary question as to how yeast repairs 3meC, particularly in single-stranded DNA. The yeast Shu complex, a conserved homologous recombination factor, aids in preventing replication-associated mutagenesis from DNA base damaging agents such as methyl methanesulfonate (MMS). We found that MMS-treated Shu complex-deficient cells exhibit a genome-wide increase in A:T and G:C substitutions mutations. The G:C substitutions displayed transcriptional and replicational asymmetries consistent with mutations resulting from 3meC. Ectopic expression of a human AlkB homolog in Shu-deficient yeast rescues MMS-induced growth defects and increased mutagenesis. Thus, our work identifies a novel homologous recombination-based mechanism mediated by the Shu complex for coping with alkylation adducts.

Background Over the last several decades, the average age of first-time mothers has risen steadily. With increasing maternal age comes a decrease in fertility, which in turn has led to an increase in the use of assisted reproductive technologies by these women. Assisted reproductive technologies (ARTs), including superovulation and embryo culture, have been shown separately to alter imprinted DNA methylation maintenance in blastocysts. However, there has been little investigation on the effects of advanced maternal age, with or without ARTs, on genomic imprinting. We hypothesized that ARTs and advanced maternal age, separately and together, alter imprinted methylation in mouse preimplantation embryos. For this study, we examined imprinted methylation at three genes, Snrpn , Kcnq1ot1 , and H19 , which in humans are linked to ART-associated methylation errors that lead to imprinting disorders. Results Our data showed that imprinted methylation acquisition in oocytes was unaffected by increasing maternal age. Furthermore, imprinted methylation was normally acquired when advanced maternal age was combined with superovulation. Analysis of blastocyst-stage embryos revealed that imprinted methylation maintenance was also not affected by increasing maternal age. In a comparison of ARTs, we observed that the frequency of blastocysts with imprinted methylation loss was similar between the superovulation only and the embryo culture only groups, while the combination of superovulation and embryo culture resulted in a higher frequency of mouse blastocysts with maternal imprinted methylation perturbations than superovulation alone. Finally, the combination of increasing maternal age with ARTs had no additional effect on the frequency of imprinted methylation errors. Conclusion Collectively, increasing maternal age with or without superovulation had no effect of imprinted methylation acquisition at Snrpn , Kcnq1ot1 , and H19 in oocytes. Furthermore, during preimplantation development, while ARTs generated perturbations in imprinted methylation maintenance in blastocysts, advanced maternal age did not increase the burden of imprinted methylation errors at Snrpn , Kcnq1ot1 , and H19 when combined with ARTs. These results provide cautious optimism that advanced maternal age is not a contributing factor to imprinted methylation errors in embryos produced in the clinic. Furthermore, our data on the effects of ARTs strengthen the need to advance clinical methods to reduce imprinted methylation errors in in vitro-produced embryos.

Gordonia phages Bowser and Schwabeltier are newly isolated phages infecting Gordonia terrae 3612. Bowser and Schwabeltier have similar siphoviral morphologies and their genomes are related to each other, but not to other phages. Their lysis cassettes are atypically situated among virion tail genes, and Bowser encodes two tyrosine integrases.

Emalyn is a newly isolated bacteriophage of Gordonia terrae 3612 and has a double-stranded DNA genome 43,982 bp long with 67 predicted protein-encoding genes, 32 of which we can assign putative functions. Emalyn has a prolate capsid and has extensive nucleotide similarity with several previously sequenced phages.

BetterKatz is a bacteriophage isolated from a soil sample collected in Pittsburgh, Pennsylvania using the host Gordonia terrae 3612. BetterKatz’s genome is 50,636 bp long and contains 75 predicted protein-coding genes, 35 of which have been assigned putative functions. BetterKatz is not closely related to other sequenced Gordonia phages.

Three-methyl cytosine (3meC) are toxic DNA lesions, blocking base pairing. Bacteria and humans, express members of the AlkB enzymes family, which directly remove 3meC. However, other organisms, including budding yeast, lack this class of enzymes. It remains an unanswered evolutionary question as to how yeast repairs 3meC, particularly in single-stranded DNA. The yeast Shu complex, a conserved homologous recombination factor, aids in preventing replication-associated mutagenesis from DNA base damaging agents such as methyl methanesulfonate (MMS). We found that MMS-treated Shu complex-deficient cells, exhibit a genome-wide increase in A:T and G:C substitutions mutations. The G:C substitutions displayed transcriptional and replicational asymmetries consistent with mutations resulting from 3meC. Ectopic expression of a human AlkB homolog in Shu-deficient yeast rescues MMS-induced growth defects and increased mutagenesis. Finally, the Shu complex exhibits increased affinity for 3meC-containing DNA. Thus, our work identifies a novel mechanism for coping with alkylation adducts.

Lesson study (LS), a teacher-oriented, student-focused professional development (PD) approach that originated in Japan, has spread globally. However, existing literature on the implementation of LS and its effectiveness provides inconsistent results, suggesting a need to review current research on LS. With a focus on LS in mathematics education, we examined 75 recent LS studies using Lewis’s (ZDM Mathematics Education 48:571–580, 2016. https://doi.org/10.1007/s11858-016-0792-x ) framework to understand how LS is implemented and the pathways by which LS can impact teaching practice and student learning. We found that new developments have taken place in LS implementation, although challenges persist throughout its process. Regarding the implementation of LS, even though the examined LS studies generally contained four phases (study, plan, teach, and reflect), we found many LS lacked a research question, and the study of teaching materials was sometimes invisible. Across phases, studies shared a consensus that it is most critical to focus on students’ thinking and learning, yet reported challenges in maintaining this focus. In addition, the role of knowledgeable others (KOs) was recognized but inconsistently understood. Collaboration was also widely reported as a challenge. Finally, there were large variations in LS duration, with some LS implementing overly brief cycles. Regarding LS impact, the literature has more frequently reported changes in teachers’ knowledge and beliefs and less frequently in curriculum, learning community/professional norms, teaching practice, and student learning outcomes. The above challenges reflect a need for culturally relevant systemic support for developing sustainable and large-scale LS. We suggest future directions for continued research and practice improvement.

The patient-physician relationship, especially in the case of severely ill patients, is often fraught with anxiety, grief, and guilt in the physician who may come to feel that he or she has failed the patient and thereby becomes a “second victim.” This notion was first explored in a 1973 publication (Artiss and Levine N Engl J Med 288(23):1210-4, 1973 ) that described a novel interactive seminar series for oncology fellows that had been designed to address and possibly remedy the frequent disquiet experienced by young physicians in this setting. Fifty years later, the medical student co-authors of this Perspective enrolled in an elective course that comprised a similar series of interactive seminars, now addressing the contemporary patient-physician relationship. The earlier paper was employed as a historical background, and the framework of the course then broadened such that the students considered the current environmental changes in medical practice (social, cultural, financial, legal, policy) that may be linked to the character of individual patient-physician relationships. This essay reports on the students’ perception of such relationships, and on the environmental elements that may be helpful or harmful to the well-being of both patients and physicians.

Introduction: Influenza and COVID-19 vaccination rates remain suboptimal, demanding new community-centric approaches that improve targeted counseling and increase vaccine uptake. Notably, racially diverse communities show high vaccine hesitancy, yet most existing vaccine studies focus on white, college-educated cohorts. Objective: Here, we identify factors influencing vaccination decisions of patients at Turtle Creek Primary Care clinic in Turtle Creek, PA, a racially-diverse borough. Design: A retrospective mixed-methods study of the predominantly non-white patient population at Turtle Creek Primary Care clinic, a clinic caring for >70% minority patients. Results: Fourteen factors emerged that patients reported were crucial to vaccine decision-making. Of these factors, top reasons for COVID-19 vaccine hesitancy were trust in vaccines, vaccine side effects, perceived vaccine knowledge, and faith/religion. Top reasons for influenza vaccine hesitancy were perceived need, vaccine side effects, trust in vaccines, and habitual behaviors. We also uncovered correlations between vaccine decision factors and sociodemographic factors. Participants > 65-years-old were more likely to cite personal safety in choosing to get the COVID-19 vaccine, while non-white participants were more likely to cite others’ safety. Participants > 65-years-old were also more likely to cite personal safety in influenza vaccine decision-making, and non-female participants were more likely to cite perceived need for influenza vaccines. Conclusions: These data uncover targetable factors contributing to vaccine hesitancy and aid in developing community-centered, personalized vaccine education approaches in Turtle Creek and analogous minority communities.