Rif1 controls DNA replication by directing Protein Phosphatase 1 to reverse Cdc7-mediated phosphorylation of the MCM complex.

Initiation of eukaryotic DNA replication requires phosphorylation of the MCM complex by Dbf4-dependent kinase (DDK), composed of Cdc7 kinase and its activator, Dbf4. We report here that budding yeast Rif1 (Rap1-interacting factor 1) controls DNA replication genome-wide and describe how Rif1 opposes DDK function by directing Protein Phosphatase 1 (PP1)-mediated dephosphorylation of the MCM complex. Deleting RIF1 partially compensates for the limited DDK activity in a cdc7-1 mutant strain by allowing increased, premature phosphorylation of Mcm4. PP1 interaction motifs within the Rif1 N-terminal domain are critical for its repressive effect on replication. We confirm that Rif1 interacts with PP1 and that PP1 prevents premature Mcm4 phosphorylation. Remarkably, our results suggest that replication repression by Rif1 is itself also DDK-regulated through phosphorylation near the PP1-interacting motifs. Based on our findings, we propose that Rif1 is a novel PP1 substrate targeting subunit that counteracts DDK-mediated phosphorylation during replication. Fission yeast and mammalian Rif1 proteins have also been implicated in regulating DNA replication. Since PP1 interaction sites are evolutionarily conserved within the Rif1 sequence, it is likely that replication control by Rif1 through PP1 is a conserved mechanism.

The Elg1 replication factor C-like complex functions in PCNA unloading during DNA replication.

The ring-shaped complex PCNA coordinates DNA replication, encircling DNA to act as a polymerase clamp and a sliding platform to recruit other replication proteins. PCNA is loaded onto DNA by replication factor C, but it has been unknown how PCNA is removed from DNA when Okazaki fragments are completed or the replication fork terminates. Here we show that the Elg1 replication factor C-like complex (Elg1-RLC) functions in PCNA unloading. Using an improved degron system we show that without Elg1, PCNA accumulates on Saccharomyces cerevisiae chromatin during replication. The accumulated PCNA can be removed from chromatin in vivo by switching on Elg1 expression. We find moreover that treating chromatin with purified Elg1-RLC causes PCNA unloading in vitro. Our results demonstrate that Elg1-RLC functions in unloading of both unmodified and SUMOylated PCNA during DNA replication, while the genome instability of an elg1Δ mutant suggests timely PCNA unloading is critical for chromosome maintenance.

Effective mismatch repair depends on timely control of PCNA retention on DNA by the Elg1 complex.

Proliferating cell nuclear antigen (PCNA) is a sliding clamp that acts as a central co-ordinator for mismatch repair (MMR) as well as DNA replication. Loss of Elg1, the major subunit of the PCNA unloader complex, causes over-accumulation of PCNA on DNA and also increases mutation rate, but it has been unclear if the two effects are linked. Here we show that timely removal of PCNA from DNA by the Elg1 complex is important to prevent mutations. Although premature unloading of PCNA generally increases mutation rate, the mutator phenotype of elg1Δ is attenuated by PCNA mutants PCNA-R14E and PCNA-D150E that spontaneously fall off DNA. In contrast, the elg1Δ mutator phenotype is exacerbated by PCNA mutants that accumulate on DNA due to enhanced electrostatic PCNA-DNA interactions. Epistasis analysis suggests that PCNA over-accumulation on DNA interferes with both MMR and MMR-independent process(es). In elg1Δ, over-retained PCNA hyper-recruits the Msh2-Msh6 mismatch recognition complex through its PCNA-interacting peptide motif, causing accumulation of MMR intermediates. Our results suggest that PCNA retention controlled by the Elg1 complex is critical for efficient MMR: PCNA needs to be on DNA long enough to enable MMR, but if it is retained too long it interferes with downstream repair steps.

Identification of Elg1 interaction partners and effects on post-replication chromatin re-formation.

Elg1, the major subunit of a Replication Factor C-like complex, is critical to ensure genomic stability during DNA replication, and is implicated in controlling chromatin structure. We investigated the consequences of Elg1 loss for the dynamics of chromatin re-formation following DNA replication. Measurement of Okazaki fragment length and the micrococcal nuclease sensitivity of newly replicated DNA revealed a defect in nucleosome organization in the absence of Elg1. Using a proteomic approach to identify Elg1 binding partners, we discovered that Elg1 interacts with Rtt106, a histone chaperone implicated in replication-coupled nucleosome assembly that also regulates transcription. A central role for Elg1 is the unloading of PCNA from chromatin following DNA replication, so we examined the relative importance of Rtt106 and PCNA unloading for chromatin reassembly following DNA replication. We find that the major cause of the chromatin organization defects of an ELG1 mutant is PCNA retention on DNA following replication, with Rtt106-Elg1 interaction potentially playing a contributory role.

Analysis of modulation factor to shorten the delivery time in helical tomotherapy.

A low modulation factor (MF) maintaining a good dose distribution contributes to the shortening of the delivery time and efficiency of the treatment plan in helical tomotherapy. The purpose of this study was to reduce the delivery time using initial values and the upper limit values of MF. First, patients with head and neck cancer (293 cases) or prostate cancer (181 cases) treated between June 2011 and July 2015 were included in the analysis of MF values. The initial MF value (MFinitial ) was defined as the average MFactual value, and the upper limit of the MF value (MFUL ) was defined according the following equation: MFUL = 2 × standard deviation of MFactual value + the average MFactual Next, a treatment plan was designed for patients with head and neck cancer (62 cases) and prostate cancer (13 cases) treated between December 2015 and June 2016. The average MFactual value for the nasopharynx, oropharynx, hypopharynx, and prostate cases decreased from 2.1 to 1.9 (p = 0.0006), 1.9 to 1.6 (p < 0.0001), 2.0 to 1.7 (p < 0.0001), and 1.8 to 1.6 (p = 0.0004) by adapting the MFinitial and the MFUL values, respectively. The average delivery time for the nasopharynx, oropharynx, hypopharynx, and prostate cases also decreased from 19.9 s cm-1 to 16.7 s cm-1 (p < 0.0001), 15.0 s cm-1 to 13.9 s cm-1 (p = 0.025), 15.1 s cm-1 to 13.8 s cm-1 (p = 0.015), and 23.6 s cm-1 to 16.9 s cm-1 (p = 0.008) respectively. The delivery time was shortened by the adaptation of MFinitial and MFUL values with a reduction in the average MFactual for head and neck cancer and prostate cancer cases.

Definition of the transcription factor TdIF1 consensus-binding sequence through genomewide mapping of its binding sites.

TdIF1 was originally identified as a protein that directly binds to terminal deoxynucleotidyltransferase, TdT. Through in vitro selection assays (SELEX), we recently showed that TdIF1 recognizes both AT-tract and a specific DNA sequence motif, 5'-TGCATG-3', and can up-regulate the expression of RAB20 through the latter motif. However, whether TdIF1 binds to these sequences in the cells has not been clear and its other target genes remain to be identified. Here, we determined in vivo TdIF1-binding sequences (TdIF1-invivoBMs) on the human chromosomes through ChIP-seq analyses. The result showed a 160-base pair cassette containing 'AT-tract~palindrome (inverted repeat)~AT-tract' as a likely target sequence of TdIF1. Interestingly, the core sequence of the palindrome in the TdIF1-invivoBMs shares significant similarity to the above 5'-TGCATG-3' motif determined by SELEX in vitro. Furthermore, spacer sequences between AT-tract and the palindrome contain many potential transcription factor binding sites. In luciferase assays, TdIF1 can up-regulate transcription activity of the promoters containing the TdIF1-invivoBM, and this effect is mainly through the palindrome. Clusters of this motif were found in the potential target genes. Gene ontology analysis and RT-qPCR showed the enrichment of some candidate targets of TdIF1 among the genes involved in the regulation of ossification. Potential modes of transcription activation by TdIF1 are discussed.

Ameliorative effect of membrane-associated estrogen receptor G protein coupled receptor 30 activation on object recognition memory in mouse models of Alzheimer's disease.

Membrane-associated estrogen receptor "G protein-coupled receptor 30" (GPR30) has been implicated in spatial recognition memory and protection against neuronal death. The present study investigated the role of GPR30 in object recognition memory in an Alzheimer's disease (AD) mouse model (5XFAD) by using novel object recognition (NOR) test. Impairment of long-term (24 h) recognition memory was observed in both male and female 5XFAD mice. Selective GPR30 agonist, G-1, ameliorated this impairment in female 5XFAD mice, but not in male mice. Our study demonstrated the ameliorative role of GPR30 in NOR memory impaired by AD pathology in female mice.

Establishment of the Commissioning Procedure for Modifying the Beam Model of Helical Tomotherapy.

Although much evidence about the helical tomotherapy system are available, there is not a document about the procedure of quality assurance (QA) for changing the beam model. This study establishes the commissioning procedure for modifying the beam model of helical tomotherapy. Firstly, some intensity-modulated radiotherapy (IMRT) plans were created, and compared them with the calculated dose and the measured dose. Secondly, the absorbed doses to water in the machine-specific reference field and the plan-class specific reference field with a protocol in Japan; Standard Dosimetry of Absorbed Dose to Water in External Beam Radiotherapy (Standard Dosimetry 12) were measured. Thirdly, we reconfirmed patient-specific quality assurance. The recommended commissioning procedure after the change of the beam model was shown through three verification processes. This report would be helpful for not only changing the beam model of helical tomotherapy but also introducing Standard Dosimetry 12 to a clinic.

Quantitative proteomic analysis of yeast DNA replication proteins.

Chromatin is dynamically regulated, and proteomic analysis of its composition can provide important information about chromatin functional components. Many DNA replication proteins for example bind chromatin at specific times during the cell cycle. Proteomic investigation can also be used to characterize changes in chromatin composition in response to perturbations such as DNA damage, while useful information is obtained by testing the effects on chromatin composition of mutations in chromosome stability pathways. We have successfully used the method of stable isotope labeling by amino acids in cell culture (SILAC) for quantitative proteomic analysis of normal and pathological changes to yeast chromatin. Here we describe this proteomic method for analyzing changes to Saccharomyces cerevisiae chromatin, illustrating the procedure with an analysis of the changes that occur in chromatin composition as cells progress from a G1 phase block (induced by alpha factor) into S phase (in the presence of DNA replication inhibitor hydroxyurea).

Quantitative proteomic analysis of chromatin reveals that Ctf18 acts in the DNA replication checkpoint.

Yeast cells lacking Ctf18, the major subunit of an alternative Replication Factor C complex, have multiple problems with genome stability. To understand the in vivo function of the Ctf18 complex, we analyzed chromatin composition in a ctf18Δ mutant using the quantitative proteomic technique of stable isotope labeling by amino acids in cell culture. Three hundred and seven of the 491 reported chromosomal proteins were quantitated. The most marked abnormalities occurred when cells were challenged with the replication inhibitor hydroxyurea. Compared with wild type, hydroxyurea-treated ctf18Δ cells exhibited increased chromatin association of replisome progression complex components including Cdc45, Ctf4, and GINS complex subunits, the polymerase processivity clamp PCNA and the single-stranded DNA-binding complex RPA. Chromatin composition abnormalities observed in ctf18Δ cells were very similar to those of an mrc1Δ mutant, which is defective in the activating the Rad53 checkpoint kinase in response to DNA replication stress. We found that ctf18Δ cells are also defective in Rad53 activation, revealing that the Ctf18 complex is required for engagement of the DNA replication checkpoint. Inappropriate initiation of replication at late origins, because of loss of the checkpoint, probably causes the elevated level of chromatin-bound replisome proteins in the ctf18Δ mutant. The role of Ctf18 in checkpoint activation is not shared by all Replication Factor C-like complexes, because proteomic analysis revealed that cells lacking Elg1 (the major subunit of a different Replication Factor C-like complex) display a different spectrum of chromatin abnormalities. Identification of Ctf18 as a checkpoint protein highlights the usefulness of chromatin proteomic analysis for understanding the in vivo function of proteins that mediate chromatin transactions.

Use of Nuclear and Chromatin Enrichment Procedures for Quantitation of Yeast DNA Replication Proteins Using SILAC.

DNA replication is a highly complex process that achieves the faithful transmission of genetic information from parent to progeny. Recruitment of DNA replication proteins to DNA is dynamically regulated during the cell cycle and in response to replication stresses. For a large-scale analysis of DNA replication proteins, I established a method for analysis of chromatin-bound proteins by SILAC (stable isotope labeling by amino acids in cell culture)-based quantitative proteomics. Here I describe a detailed methodology for SILAC labeling of budding yeast Saccharomyces cerevisiae, then nuclear isolation and chromatin preparation from synchronized yeast cells, prior to quantitative proteomic analysis of DNA replication proteins.

[A Bibliometric Analysis of Research Paper Productivity of Japanese Pharmacy Schools].

Since the early 2000s, Japan has been frequently noted as being the only country among about 20 major countries where the publication of academic papers has stagnated. During this period, there have been major changes especially with regards to the Japanese pharmacy schools, such as the shift to a six-year schooling system and the rapid increase in the number of private pharmacy schools. However, few studies have focused on academic productivity specifically among pharmacy schools. Therefore, this study analyzed the outputs associated with the publication of peer-reviewed scholarly articles in Scopus search engine per faculty member in pharmacy schools nationwide in 2020. Professors, associate professors, and lecturers were considered as faculty members. The average number of papers published per the faculty member was 3.13 for national and public universities and 1.15 for private universities, with a significant difference between these universities. Dividing the pharmacy schools of private universities into schools established in and after 2003 and schools established before that, the production coefficient of the former was 0.98 and that of the latter was 1.33. Newly established pharmacy schools were thus found to be slightly less productive in terms of published papers than traditional schools. The paper productivity of private university pharmacy schools is stagnant; the increase in the number of private schools that have adopted a six-year schooling system has contributed to large extent to the creation of clinically competent pharmacists, but it has also brought to light concerns related to the decline in basic research capabilities of Japanese pharmaceutical academia.

Correlations between atrophy of the entorhinal cortex and cognitive function in patients with Alzheimer's disease and mild cognitive impairment.

AIMS: In order to confirm the utility of the voxel-based specific regional analysis system for Alzheimer's disease (VSRAD) in assessing the atrophy of the entorhinal cortex, we investigated whether there were correlations between VSRAD and the scores of neuropsychological tests in the patients with Alzheimer's disease (AD) and mild cognitive impairment. METHODS: Thirty patients, including 18 AD and 12 mild cognitive impairment patients, were included in this study. VSRAD was performed to assess the atrophy of the entorhinal cortex. The patients were carefully screened with the neuropsychological tests, including Wechsler Adult Intelligence Scale-III (WAIS-III), the Wechsler Memory Scale-Revised, the Alzheimer's Disease Assessment Scale-Cognitive Part (ADAS-cog) and the revised version of Hasegawa's Dementia Scale. RESULTS: All patients showed atrophy with different degrees in the entorhinal cortex except one case. Z-scores had significant positive correlation with ADAS-cog, and negative correlation with Information subset of WAIS-III (respectively, P = 0.0129 and P = 0.0294). The revised version of Hasegawa's Dementia Scale and the Similarities subsets of the WAIS-III had a tendency of negatively correlating with Z-scores of VSRAD (respectively, P = 0.0532 and P = 0.0635). The Delayed Visual Reproduction subset of the Wechsler Memory Scale-Revised was also found to have a weak negative correlation with Z-scores (P = 0.0609). CONCLUSIONS: Z-scores of VSRAD were revealed to have a close relation with many neuropsychological tests, especially ADAS-cog and the Information subset of WAIS-III. The results meant that VSRAD was a useful indictor of early diagnosis of AD, closely correlating with the changes of cognitive functions and the progression of the disease.

SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes.

The Pleiotropic Drug Resistance (PDR) network is central to the drug response in fungi, and its overactivation is associated with drug resistance. However, gene regulation of the PDR network is not well understood. Here, we show that the histone chaperone Rtt106 and the chromatin remodeller SWI/SNF control expression of the PDR network genes and confer drug resistance. In Saccharomyces cerevisiae, Rtt106 specifically localises to PDR network gene promoters dependent on transcription factor Pdr3, but not Pdr1, and is essential for Pdr3-mediated basal expression of the PDR network genes, while SWI/SNF is essential for both basal and drug-induced expression. Also in the pathogenic fungus Candida glabrata, Rtt106 and SWI/SNF regulate drug-induced PDR gene expression. Consistently, loss of Rtt106 or SWI/SNF sensitises drug-resistant S. cerevisiae mutants and C. glabrata to antifungal drugs. Since they cooperatively drive PDR network gene expression, Rtt106 and SWI/SNF represent potential therapeutic targets to combat antifungal resistance.

Age-dependent impairment of memory and neurofibrillary tangle formation and clearance in a mouse model of tauopathy.

Insoluble, fibrillar intraneuronal accumulation of the tau protein termed neurofibrillary tangles (NFTs), are characteristic hallmarks of Alzheimer's disease (AD). They play a significant role in the behavioral phenotypes of AD. Certain mice (rTg4510) constitutively express mutant human tau until transgene expression is inactivated by the administration of doxycycline (DOX). The present study aimed to determine the timing of the onset of memory impairment in rTg4510 mice and define the relationship between the extent of memory deficit and the duration of NFT overexpression. In 6-month-old (young) rTg4510 mice, both spatial memory and object recognition memory were impaired. These impairments were prevented by pre-treatment with DOX for 2 months. In parallel, the expression of NFTs decreased in the DOX-treated group. Ten-month-old (aged) rTg4510 mice showed severe impairments in memory performance. Pretreatment with DOX did not prevent these impairments. Increasing levels of NFTs were observed in aged rTg4510 mice. DOX treatment did not prevent tau pathology in aged rTg4510 mice. Expression of the autophagy markers LC3A and LC3B increased in rTg4510 mice, along with an increase in NFT formation. These results suggest that the clearance mechanisms of NFTs are impaired at 10 months of age.

Flexible electrochromic devices based on tungsten oxide and Prussian blue nanoparticles for automobile applications.

Smart windows, which control the amount of light entering buildings, houses, and automobiles, are promising in terms of energy conservation and their low environmental impact. Particularly, a next-generation smart window for automobiles will require high optical modulation, along with flexibility to adapt to various intelligent designs. We have previously fabricated electrochromic devices (ECDs) by wet coating glass substrates with nanoparticles (NPs), such as water-dispersive ink containing tungsten oxide (WO3), and Prussian blue (PB), and have evaluated and confirmed the various electrochromic (EC) properties, such as optical modulation, cyclic durability, and colouration efficiency, of the ECDs. However, glass substrates are heavy and difficult to adapt by deformation to meet the demand of next-generation automobiles. In this study, we aim to prepare complementary ECDs by wet coating WO3 and PB thin films on indium tin oxide (ITO)-coated flexible polyethylene terephthalate (PET) substrates. Chromaticity and haze of ECDs were investigated in detail as evaluation indexes to verify specifications for practical use in automotive applications. Repeated switching, bending, and twisting did not degrade the ECD properties, thereby demonstrating its durability and mechanical robustness. These excellent electrochromic properties of the flexible ECDs suggest that they are promising materials for application in next-generation smart windows for automobiles.

Spatial and latent memory data in PS2Tg2576 alzheimer's disease mouse model after memantine treatment.

We herein present behavioral data on whether memantine, an adamantane derivative and medical NMDA-receptor antagonist, improves spatial and latent learning deficits in amyloid precursor protein/presenilin 2 double-transgenic mice (PS2Tg2576 mice). In PS2Tg2576 mice, early amyloid-ß protein (Aß) deposition at 2-3 months of age and progressive accumulation at about 5 months of age has been shown. Thus, PS2Tg2576 mice were subjected to Morris water maze (MWM) test for spatial memory and the water-finding test for latent memory testing at ages 3 and 5-6 months. In addition, memantine (30 mg/kg/day, p.o.) was administered 3-4 weeks before commencing the behavioral tasks to check for effects on cognitive function. The information provided in this paper adds to the literature and can be used for the selection of animal models and behavioral paradigms for Alzheimer's disease (AD) research.

Ligation of newly replicated DNA controls the timing of DNA mismatch repair.

Mismatch repair (MMR) safeguards genome stability through recognition and excision of DNA replication errors.1-4 How eukaryotic MMR targets the newly replicated strand in vivo has not been established. MMR reactions reconstituted in vitro are directed to the strand containing a preexisting nick or gap,5-8 suggesting that strand discontinuities could act as discrimination signals. Another candidate is the proliferating cell nuclear antigen (PCNA) that is loaded at replication forks and is required for the activation of Mlh1-Pms1 endonuclease.7-9 Here, we discovered that overexpression of DNA ligase I (Cdc9) in Saccharomyces cerevisiae causes elevated mutation rates and increased chromatin-bound PCNA levels and accumulation of Pms1 foci that are MMR intermediates, suggesting that premature ligation of replication-associated nicks interferes with MMR. We showed that yeast Pms1 expression is mainly restricted to S phase, in agreement with the temporal coupling between MMR and DNA replication.10 Restricting Pms1 expression to the G2/M phase caused a mutator phenotype that was exacerbated in the absence of the exonuclease Exo1. This mutator phenotype was largely suppressed by increasing the lifetime of replication-associated DNA nicks, either by reducing or delaying Cdc9 ligase activity in vivo. Therefore, Cdc9 dictates a window of time for MMR determined by transient DNA nicks that direct the Mlh1-Pms1 in a strand-specific manner. Because DNA nicks occur on both newly synthesized leading and lagging strands,11 these results establish a general mechanism for targeting MMR to the newly synthesized DNA, thus preventing the accumulation of mutations that underlie the development of human cancer.

TdT interacting factor 1 enhances TdT ubiquitylation through recruitment of BPOZ-2 into nucleus from cytoplasm.

We isolated human cDNA clone encoding Bood POZ containing gene type 2 (BPOZ-2) as a gene with a product that binds to TdT interacting factor 1 (TdIF1) using a yeast two-hybrid system. BPOZ-2 is an adaptor for E3 ligase CUL3 and participates in developmental processes. The binding between BPOZ-2 and TdIF1 was confirmed by GST pull-down and immunoprecipitation assays using specific antibodies against BPOZ-2 and TdIF1 in vitro and in vivo. Although when BPOZ-2 solely was expressed in COS7 cells, BPOZ-2 was observed mainly within the cytoplasm, co-transfection of pEGFP-BPOZ-2 and pDsRed-TdIF1 into COS7 cells resulted in co-localization of EGFP-BPOZ-2 and DsRed-TdIF1 within the nucleus. TdIF1 may recruit BPOZ-2 into the nucleus from the cytoplasm by directly binding to BPOZ-2. BPOZ-2 enhanced TdT ubiquitylation when TdIF1 was expressed together with BPOZ-2 in 293T cells, strongly suggesting that the recruitment of BPOZ-2 into the nucleus from the cytoplasm is significant for the TdT ubiquitylation within the nucleus.

Correlations between Z-scores of VSRAD and regional cerebral blood flow of SPECT in patients with Alzheimer's disease and mild cognitive impairment.

AIMS: The purpose of the present study was to investigate whether there were correlations between atrophy of the entorhinal cortex and individual regional cerebral blood flow (rCBF) in patients with Alzheimer's disease (AD) and amnestic mild cognitive impairment (MCI) to better clarify the relationships between morphological and functional changes in AD. METHODS: Twenty-six patients including sixteen AD and 10 amnestic MCI patients were enrolled. Z scores of voxel-based specific regional analysis system for AD (VSRAD) were determined to assess the degree of atrophy of the entorhinal cortex. Single-photon emission computed tomography (SPECT) and 3-D stereotaxic region of interest template (3DSRT) were used to quantify absolute rCBF. RESULTS: The Z scores of the entorhinal cortex were found to have significant negative correlations with the absolute rCBF in the bilateral hippocampus, thalamus and temporal regions. A negative correlation between Z scores and rCBF of the cerebellum region, especially on the right side, was also noted. CONCLUSIONS: Atrophy of the entorhinal cortex had an obvious functional relationship with rCBF changes in the hippocampus, thalamus, temporal lobe and cerebellum in AD and MCI patients, which was attributed to their close anatomical and physiological connections.