The fragility of a structurally diverse duplication block triggers recurrent genomic amplification.

The human genome contains hundreds of large, structurally diverse blocks that are insufficiently represented in the reference genome and are thus not amenable to genomic analyses. Structural diversity in the human population suggests that these blocks are unstable in the germline; however, whether or not these blocks are also unstable in the cancer genome remains elusive. Here we report that the 500 kb block called KRTAP_region_1 (KRTAP-1) on 17q12-21 recurrently demarcates the amplicon of the ERBB2 (HER2) oncogene in breast tumors. KRTAP-1 carries numerous tandemly-duplicated segments that exhibit diversity within the human population. We evaluated the fragility of the block by cytogenetically measuring the distances between the flanking regions and found that spontaneous distance outliers (i.e DNA breaks) appear more frequently at KRTAP-1 than at the representative common fragile site (CFS) FRA16D. Unlike CFSs, KRTAP-1 is not sensitive to aphidicolin. The exonuclease activity of DNA repair protein Mre11 protects KRTAP-1 from breaks, whereas CtIP does not. Breaks at KRTAP-1 lead to the palindromic duplication of the ERBB2 locus and trigger Breakage-Fusion-Bridge cycles. Our results indicate that an insufficiently investigated area of the human genome is fragile and could play a crucial role in cancer genome evolution.

Comparative Analysis of Simplified, Objective Nutrition-Associated Markers in Patients Undergoing Hemodialysis.

OBJECTIVE: Protein-energy wasting is prevalent among patients undergoing dialysis. Hence, identifying an optimal index is necessary for the comprehensive measurement of nutritional status. This study evaluated and compared the prognostic significance of the modified creatinine index (mCI) and geriatric nutritional risk index (GNRI), with the principal aim to identify markers that are more closely associated with clinical events in patients undergoing hemodialysis. METHODS: We performed a retrospective cohort study of 472 patients undergoing maintenance hemodialysis (mean age, 66.4 years; 62.9% males). We evaluated the mCI, GNRI, and their respective rates of change over a 1-year period. The outcome analysis included all-cause death, number and duration of all-cause hospitalizations, and number and duration of hospitalizations due to cardiovascular disease. In addition, we analyzed the associations of the mCI, GNRI, and their trajectories with clinical outcomes using Cox proportional hazard regression and negative binomial regression. RESULTS: Over a median 3.6-year follow-up, both the lower mCI (hazard ratio 3.00; 95% confidence interval 2.19, 4.09) and lower GNRI (hazard ratio 1.76; 95% confidence interval 1.45, 2.13) per 1 standard deviation decrease were associated with a higher risk of all-cause death. However, a lower mCI was consistently associated with a higher risk of hospitalization, whereas the GNRI was poorly associated with the risk of hospitalization after adjusting for covariates. Furthermore, although a decline in the mCI over time was associated with a higher risk of each adverse event, a significant association between the change in GNRI and clinical events was not detected. CONCLUSION: The mCI at one timepoint and its trajectory had consistently stronger associations with clinical events than the GNRI in patients undergoing hemodialysis. This study further emphasizes the importance of risk screening using a marker of nutritional status in patients undergoing hemodialysis.

Determinants of Health-Related Quality of Life and Physical Performance-Based Components of Frailty in Patients Undergoing Hemodialysis.

OBJECTIVES: Health-related quality of life (HRQoL) measures capture the patient's experience of the burden of chronic disease and are strongly associated with adverse health-related outcomes across multiple populations. The SF-36 score is the most widely used HRQoL measure among patients with end-stage renal disease. Current understanding of determinants of the physical component summary (PCS) and the mental component summary (MCS) and their association with objectively measured physical performance and activity is limited. METHODS: As an index of HRQoL, we prospectively examined the association of SF-36 and its component scores with physical function among 155 incident dialysis patients from the Hemodialysis Center. We investigated associations of HRQoL with the physical performance-based components of the frailty using multivariate linear and logistic regression after adjustment for confounders. Impaired physical performance was defined as having either slow usual gait speed or weak handgrip strength based on standardized and validated criteria derived from a large cohort study of older adults. RESULTS: The patients had a mean age of 65 ± 11 years, and 52.3% were male. After adjusting confounders, lower PCS was independently associated with decreased physical performance and reduced physical activity, but MCS was not associated. Among the PCS subscales, only physical functioning 10 (PF-10) was consistently associated with outcomes, and every 1 point increase in PF-10 score was associated with 4% lower odds of impaired physical performance (95% confidence interval 2-7, P = .01) after adjustment. CONCLUSIONS: SF-36, especially PF-10, is a valid surrogate that discriminates low physical performance and physical inactivity in the absence of formal physical function testing in patients on hemodialysis. The routine implementation of the PF-10 in clinical care has important clinical implications for medical management and therapeutic decision-making in patients undergoing hemodialysis.

Modified Creatinine Index and Clinical Outcomes of Hemodialysis Patients: An Indicator of Sarcopenia?

OBJECTIVE: Sarcopenia (especially muscle mass assessed using gold standard techniques) has been suggested as a poorer predictor of mortality than muscle function in patients undergoing hemodialysis. Appropriate methods to estimate muscle mass for use as a good predictor of clinical outcomes remain to be established. We investigated whether the modified creatinine index (mCI), which is a surrogate marker of muscle mass, could predict mortality and cardiovascular (CV) hospitalizations independent of muscle function and other confounders in patients on hemodialysis. DESIGN AND METHODS: In this retrospective study, outpatients (n = 542; mean age, 65.3 years; 60% men; median dialysis vintage, 29 months; mean BMI, 22.0 kg/m2) undergoing hemodialysis were investigated. The mCI, handgrip strength, and gait speed were assessed and related to all-cause mortality and a composite of CV hospitalizations and all-cause mortality. Cox proportional and mixed-effects negative binomial models were fit for mortality and the composite outcomes. RESULTS: Patients were followed up for a median 3 years (interquartile range: 1.5-5.7). Each per SD increase of mCI (HR:0.63, 95% CI:0.62-0.65), handgrip strength (HR:0.51, 95% CI:0.48-0.54), and gait speed (HR:0.60, 95% CI:0.56-0.64) were significantly associated with lower all-cause mortality rates after adjusting for covariates. The mCI was consistently found to be an independent predictor of mortality after additional adjustment for handgrip strength or gait speed. Furthermore, sarcopenic conditions [i.e., lower mCI, and lower handgrip strength (HR:3.79, 95% CI:2.09-6.87) or slower gait speed (HR:4.20, 95% CI:2.38-7.41)] were significantly associated with a higher risk of mortality after adjusting for covariates. Associations of mCI with multiple CV hospitalizations and mortality were similar to those between mCI and mortality. CONCLUSION: The mCI was a good predictor of clinical outcomes and was comparable to muscle function, including handgrip strength and gait speed. The mCI is likely to provide additional diagnostic and prognostic values for sarcopenia in patients on hemodialysis.

Impact of Physical Activity on Dialysis and Nondialysis Days and Clinical Outcomes Among Patients on Hemodialysis.

OBJECTIVE: Patients undergoing hemodialysis (HD) have different physical activity (PA) patterns on HD and non-HD days. Nonetheless, whether these differences are associated with clinical outcomes remains unclear. We examined the association of PA levels on HD and non-HD days with cardiovascular (CV) hospitalizations and mortality. METHODS: Outpatients undergoing HD from 2002 to 2019 were retrospectively enrolled. The number of steps performed over 3 HD days and 4 non-HD days was recorded via accelerometry. Outcomes were all-cause mortality and a composite of CV hospitalizations and mortality. Patients were divided into two groups, each according to the median number of steps performed on HD (2371 steps/day) and non-HD days (3752 steps/day). Further, we categorized them into 4 groups according to each median values: "more active on HD/more active on non-HD (MM)," "more active on HD/less active on non-HD (ML)," "less active on HD/more active on non-HD (LM)," and "less active on HD/less active on non-HD (LL)." Cox and mixed-effects Poisson regression models were used for these outcomes. RESULTS: We analyzed 512 patients (median follow-up, 3.4 years). Higher PA on HD (hazard ratio [HR], 0.59; 95% confidence interval [CI], 0.54-0.65), and non-HD (HR, 0.84; 95% CI, 0.80-0.88) was associated with lower mortality risk, respectively. Further, the ML group (HR, 1.20; 95% CI, 1.13-1.28), LM group (HR, 1.82; 95% CI, 1.53-2.17), and LL group (HR, 1.83; 95% CI, 1.65-2.02) had higher mortality risks than the MM group. Associations of PA with multiple CV hospitalizations and mortality were similar to those between PA and mortality. CONCLUSIONS: Higher PA on HD and non-HD days was associated with lower risks of CV hospitalizations and mortality. However, higher PA levels on either HD or non-HD days alone did not improve clinical outcomes.

Trajectory of Lean Body Mass Assessed Using the Modified Creatinine Index and Mortality in Hemodialysis Patients.

RATIONALE & OBJECTIVE: Although a declining body mass index (BMI) is associated with higher mortality in patients on hemodialysis, BMI cannot distinguish lean body mass from fat mass. It remains unclear whether changes over time in lean body mass are associated with mortality. We examined the prognostic significance of changes in the modified creatinine index, a proxy for lean body mass. STUDY DESIGN: Retrospective cohort study. SETTING & PARTICIPANTS: Outpatients (n=349; mean age, 67.4 years; 60% men) undergoing maintenance hemodialysis 3 times a week at a treatment center. PREDICTOR: Modified creatinine index and BMI trajectories over a 1-year period. OUTCOMES: All-cause mortality. ANALYTICAL APPROACH: We calculated the percentage of change in modified creatinine index and BMI over a 1-year period. Patients were categorized according to change in modified creatinine index/BMI: no decline (≥0%) or decline (<0%). Kaplan-Meier and Cox proportional hazard analyses were performed to examine whether modified creatinine index and BMI trajectories were associated with mortality. RESULTS: During follow-up (median, 1,157 days), 79 patients died. Decreasing modified creatinine index (HR, 1.31; 95% CI, 1.11-1.54) and BMI (HR, 1.25; 95% CI, 1.01-1.54) over time, measured as continuous variables and expressed per 1-standard deviation decrease, were independently associated with higher risk for all-cause mortality. The decline in modified creatinine index/no decline in BMI group (HR, 2.14; 95% CI, 1.04-4.45) and the decline in modified creatinine index/decline in BMI group (HR, 3.05; 95% CI, 1.58-5.90) had higher rates of mortality compared to the no decline in modified creatinine index/decline in BMI group. LIMITATIONS: The absence of a direct measure of lean body and fat mass and limited generalizability to non-Japanese hemodialysis populations. CONCLUSIONS: The modified creatinine index trajectory is independently associated with mortality and provides additional prognostic information to the BMI trajectory in patients on hemodialysis.

Complex repeat structure promotes hyper-amplification and amplicon evolution through rolling-circle replication.

Inverted repeats (IRs) are abundant in genomes and frequently serve as substrates for chromosomal aberrations, including gene amplification. In the early stage of amplification, repeated cycles of chromosome breakage and rearrangement, called breakage-fusion-bridge (BFB), generate a large inverted structure, which evolves into highly-amplified, complex end products. However, it remains to be determined how IRs mediate chromosome rearrangements and promote subsequent hyper-amplification and amplicon evolutions. To dissect the complex processes, we constructed repetitive structures in a yeast chromosome and selected amplified cells using genetic markers with limited expression. The genomic architecture was associated with replication stress and produced extra-/intra-chromosomal amplification. Genetic analysis revealed structure-specific endonucleases, Mus81 and Rad27, and post-replication DNA repair protein, Rad18, suppress the amplification processes. Following BFB cycles, the intra-chromosomal products undergo intensive rearrangements, such as frequent inversions and deletions, indicative of rolling-circle replication. This study presents an integrated view linking BFB cycles to hyper-amplification driven by rolling-circle replication.

Association between frailty and bone loss in patients undergoing maintenance hemodialysis.

Frailty is significantly associated with bone loss in the general population. However, it is unclear whether this association also exists in patients undergoing hemodialysis who have chronic kidney disease-mineral and bone disorder (CKD-MBD). This study aimed to assess the association between frailty and bone loss in patients undergoing hemodialysis. This cross-sectional study included 214 (90 women, 124 men) Japanese outpatients undergoing maintenance hemodialysis three times per week, with a mean age of 67.1 years (women) and 66.8 years (men). Frailty was defined based on criteria set forth by the Cardiovascular Health Study (CHS)-19 (21.1%) women and 47 (37.9%) men were robust, 41 (45.6%) women and 43 (34.7%) men were pre-frail, and 30 (33.3%) women and 34 (27.4%) men were frail. For bone mass, quantitative ultrasound (QUS) parameters (speed of sound, broadband ultrasound attenuation, stiffness index) of the calcaneus were measured. The association between frailty and QUS parameters was determined separately for women and men using multivariate analysis of covariance (ANCOVA), with adjustments for clinical characteristics including age, body mass index, hemodialysis vintage, diabetes, current smoking, serum albumin, phosphate, corrected calcium, intact parathyroid hormone, and medication for CKD-MBD (vitamin D receptor activator, calcimimetics). ANCOVA revealed that all QUS parameters declined significantly with increasing levels of frailty in both sexes (P < 0.05). In conclusion, frailty (as defined by CHS criteria) should be considered a risk factor for bone loss in patients undergoing hemodialysis.

Utility of Regular Management of Physical Activity and Physical Function in Hemodialysis Patients.

BACKGROUND/AIMS: Several clinical practice guidelines recommend regular assessment of physical activity and physical function as part of routine care in hemodialysis patients. However, there is no clear evidence to support these recommendations. We investigated whether the proportion of attendance at a regular program for management of physical activity and physical function can predict all-cause mortality and cardiovascular events in hemodialysis patients. METHODS: This retrospective cohort study consisted of 266 hemodialysis patients participating in the management program at least once. Participants were tracked for 3 years after their first attendance at the management program to determine their attendance proportion. The main study outcomes included all-cause mortality and a composite of fatal and nonfatal cardiovascular events. RESULTS: Median patient age was 64.5 (interquartile range, 56.8 - 72.0) years, 45% were women, and the median time on hemodialysis was 35.5 (interquartile range, 12.0 - 114.3) months at baseline. Sixty-five patients died over a median follow-up of 79 months. The incidence of cardiovascular events was 60 over a median follow-up of 68 months. Even after adjusting for any of the prognostic models, participants who attended ≤ 75% of sessions (n = 140) had higher risks of mortality (hazard ratio (HR), 1.79; 95% confidence interval (CI): 1.00 - 3.36; P = 0.049) and cardiovascular events (HR, 1.84; 95% CI: 1.07 - 3.48; P = 0.03) than those attending > 75% of sessions (n = 126). CONCLUSION: Hemodialysis patients in whom physical activity and physical function could be assessed more regularly had better prognosis than those with only intermittent assessment.

Combined Contribution of Reduced Functional Mobility, Muscle Weakness, and Low Serum Albumin in Prediction of All-Cause Mortality in Hemodialysis Patients: A Retrospective Cohort Study.

OBJECTIVES: The combined effects of reduced functional mobility, muscle weakness, and low serum albumin on mortality in hemodialysis patients have not been clarified. Here, we examined the associations of reduced functional mobility, muscle weakness, and low serum albumin-both alone and in combination-with all-cause mortality in hemodialysis patients. METHODS: A total of 490 patients treated between July 2010 and October 2016 were enrolled retrospectively in this study. The independent prognostic effect of the combination of reduced functional mobility, muscle weakness, and low serum albumin on survival was estimated by Cox proportional hazard regression analysis. We calculated the increases in predictive capacity by combining the associations of reduced functional mobility, muscle weakness, and low serum albumin in comparison to each component alone based on the receiver-operating characteristic curves, continuous net reclassification improvement (NRI), and integrated discrimination improvement (IDI). RESULTS: The final study population consisted of 314 hemodialysis patients, and 56 patients died during the 6.5-year follow-up period. The high Combined score group showed a significantly lower cumulative survival rate than the low Combined score group (hazard ratio, 3.30; 95% confidence interval, 1.59-6.87; P = .001). Both NRI and IDI suggested that the addition of Combined score to patient characteristics improved discrimination of patients at high risk of mortality (NRI, 0.038 95% CI: 0.096 - 0.064, P < .001 IDI, 0.029 95% CI: 0.004 - 0.055, P = .025). CONCLUSIONS: The combined assessment of reduced functional mobility, muscle weakness, and low serum albumin was associated with poorer prognosis in patients on hemodialysis. The results presented here indicated that the combination of reduced functional mobility, muscle weakness, and low serum albumin is useful for accurate prediction of prognosis in hemodialysis patients.

Physical Activity Dose for Hemodialysis Patients: Where to Begin? Results from a Prospective Cohort Study.

OBJECTIVE: Greater physical activity is associated with lower risk of mortality in persons with kidney disease; however, little is known about the appropriate dose of physical activity among hemodialysis patients. Here detected the minimum level of habitual physical activity to help inform interventions aimed at improving outcomes in the dialysis population. DESIGN: The design was prospective cohort study. SUBJECTS: Clinically stable outpatients in a hemodialysis unit from October 2002 to March 2014 were assessed for their eligibility to be included in this 7-year prospective cohort study. We used the Youden index to determine the optimal cutoff points for physical activity. The prognostic effect of physical activity on survival was estimated by Cox proportional hazards regression analysis. The number of steps per nondialysis day was recorded by accelerometer at study entry. MAIN OUTCOME MEASURE: The main outcome measure was all-cause mortality. RESULTS: There were 282 participants who had a mean age of 65 ± 11 years and 45% were female. A total of 56 deaths occurred during the follow-up period (56 months [interquartile range: 29-84 months]). The cutoff value for the physical activity discriminating those at high risk of mortality was 3,752 steps. After adjustment for the effect of confounders, the hazard ratio in the group of <4,000 steps was 2.37 (95% confidence interval: 1.22-4.60, P = .01) compared with the others. CONCLUSIONS: Engaging in physical activity is associated with decreased mortality risk among hemodialysis patients. Our findings of a substantial mortality benefit among those who engage in at least 4,000 steps provide a basis for as a minimum initial recommendation kidney health providers can provide for mobility disability-free hemodialysis patients.

Changes in physical activity and risk of all-cause mortality in patients on maintence hemodialysis: a retrospective cohort study.

BACKGROUND: A previous cohort study indicated a significant association of lower baseline level of physical activity in hemodialysis patients with elevated risks of mortality. However, there have been no reports regarding the association between changes in physical activity over time and mortality in hemodialysis patients. This study was performed to examine the prognostic significance of physical activity changes in hemodialysis patients. METHODS: This retrospective cohort study was performed in 192 hemodialysis patients with a 7-year follow-up. The average number of steps taken per non-dialysis day was used as a measure of physical activity. Forty (20.8%) patients had died during the follow-up period. The percentage change in physical activity between baseline and 12 months was determined, and patients were divided into three categories according to changes in physical activity. A decrease or increase in physical activity > 30% was defined as becoming less or more active, respectively, while decrease or increase in physical activity < 30% were classified as stable. RESULTS: Forty seven (24.5%), 51 (26.6%), and 94 (49.0%) patients were classified as becoming less active, becoming more active, and stable, respectively. The hazard ratio on multivariate analysis in patients with decreased physical activity was 3.68 (95% confidence interval, 1.55-8.78; P < 0.01) compared to those with increased physical activity. CONCLUSIONS: Reductions in physical activity were significantly associated with poor prognosis independent of not only patient characteristics but also baseline physical activity. Therefore, improved prognosis in hemodialysis patients requires means of preventing a decline in physical activity over time.

Replication fork integrity and intra-S phase checkpoint suppress gene amplification.

Gene amplification is a phenotype-causing form of chromosome instability and is initiated by DNA double-strand breaks (DSBs). Cells with mutant p53 lose G1/S checkpoint and are permissive to gene amplification. In this study we show that mammalian cells become proficient for spontaneous gene amplification when the function of the DSB repair protein complex MRN (Mre11/Rad50/Nbs1) is impaired. Cells with impaired MRN complex experienced severe replication stress and gained substrates for gene amplification during replication, as evidenced by the increase of replication-associated single-stranded breaks that were converted to DSBs most likely through replication fork reversal. Impaired MRN complex directly compromised ATM/ATR-mediated checkpoints and allowed cells to progress through cell cycle in the presence of DSBs. Such compromised intra-S phase checkpoints promoted gene amplification independently from mutant p53. Finally, cells adapted to endogenous replication stress by globally suppressing genes for DNA replication and cell cycle progression. Our results indicate that the MRN complex suppresses gene amplification by stabilizing replication forks and by securing DNA damage response to replication-associated DSBs.

Measurement of brain tissue oxygen saturation in term infants using a new portable near-infrared spectroscopy device.

BACKGROUND: A small oximeter with the probe attached to the examiner's finger has been developed. The aim of this study was to determine the feasibility of measuring regional oxygenation of the brain tissue using this device in healthy term infants immediately after birth. METHODS: We conducted a prospective observational study. Using a new near-infrared spectroscopy (NIRS) device, we measured changes in regional cerebral tissue oxygen saturation (crSO2 ) during the first 10 min of life in 32 healthy term infants after delivery. Arterial oxygen saturation (SpO2 ) was also simultaneously measured. RESULTS: Median crSO2 increased from 43% (1 min after birth) to 49% (4 min after birth); thereafter, no significant changes were observed. Median SpO2 increased constantly from min 3 to min 7, from 77% to 92% and did not change significantly after 8 min. A stable oxygen saturation signal was measured in 59% of infants (crSO2 ) and in 0% of infants (SpO2 ) at 1 min, and in 97% (crSO2 ) and in 78% (SpO2 ) at 3 min. CONCLUSIONS: During the transition after birth, crSO2 can be more easily and quickly measured in healthy newborn infants using the novel NIRS device than SpO2 .

Sex-related differences in long-term pulmonary outcomes of neonatal hyperoxia in mice.

AIM: Premature infants are often exposed to hyperoxia to maintain adequate oxygenation, which may lead to the development of bronchopulmonary dysplasia (BPD). Sex-specific differences exist in the development and severity of BPD. Only a few studies have examined the mechanisms underlying these sex-related differences. The aim of the present study is to examine the sex-related long-term effects of neonatal hyperoxia on the lungs of adult mice. MATERIALS AND METHODS: Newborn mice were exposed to 95% oxygen (hyperoxia) for 96 hours and were allowed to recover in room air to adulthood (8 weeks of age). Lung tissues were excised at 4 days, 14 days, or 8 weeks of age. Short-term effects of neonatal hyperoxia on the mouse lung and sex-related differences in pulmonary function, airway hyper-responsiveness, and lung structure in adult mice were assessed. RESULTS: Neonatal hyperoxia was found to have no differential effect on body weight, muscarinic acetylcholine receptor gene expression, or bronchiolar epithelial thickness in adult mice. Respiratory resistance was increased and sensitivity to methacholine was decreased in male adult mice following exposure to neonatal hyperoxia, whereas delayed alveolarization was observed in female adult mice following exposure to neonatal hyperoxia. CONCLUSIONS: The findings of the present study demonstrate that neonatal hyperoxia differentially affects pulmonary outcome in female and male adult mice.

[Laparoscopic Gastrectomy for Gastric Adenocarcinoma of the Fundic Gland Type - Report of a Case].

A 69-year-old man underwent esophagogastroduodenoscopy, which showed a slightly depressed lesion at the greater curvature of the gastric body. We diagnosed gastric adenocarcinoma of the fundic gland type(GA-FG)from examination of the biopsy specimen. Endoscopic submucosal dissection(ESD)was performed for curative resection. The pathological examination revealed a positive vertical margin. Consequently, laparoscopic gastrectomy was additionally performed. GA-FG has recently been proposed as a new entity of gastric adenocarcinoma. GA-FG mostly develops without Helicobacter pylori infection and often invades the submucosa, regardless of size. However, GA-FG rarely demonstrates lymphatic and venous invasion despite deep submucosal invasion. Since most GA-FG cases undergo ESD, few reports of surgical resection exist. Here, we report our experience of laparoscopic gastrectomy for GA-FG.

Homology-mediated end-capping as a primary step of sister chromatid fusion in the breakage-fusion-bridge cycles.

Breakage-fusion-bridge (BFB) cycle is a series of chromosome breaks and duplications that could lead to the increased copy number of a genomic segment (gene amplification). A critical step of BFB cycles leading to gene amplification is a palindromic fusion of sister chromatids following the rupture of a dicentric chromosome during mitosis. It is currently unknown how sister chromatid fusion is produced from a mitotic break. To delineate the process, we took an integrated genomic, cytogenetic and molecular approach for the recurrent MCL1 amplicon at chromosome 1 in human tumor cells. A newly developed next-generation sequencing-based approach identified a cluster of palindromic fusions within the amplicon at ∼50-kb intervals, indicating a series of breaks and fusions by BFB cycles. The physical location of the amplicon (at the end of a broken chromosome) further indicated BFB cycles as underlying processes. Three palindromic fusions were mediated by the homologies between two nearby inverted Alu repeats, whereas the other two fusions exhibited microhomology-mediated events. Such breakpoint sequences indicate that homology-mediated fold-back capping of broken ends followed by DNA replication is an underlying mechanism of sister chromatid fusion. Our results elucidate nucleotide-level events during BFB cycles and end processing for naturally occurring mitotic breaks.

Gene amplification system based on double rolling-circle replication as a model for oncogene-type amplification.

Gene amplification contributes to a variety of biological phenomena, including malignant progression and drug resistance. However, details of the molecular mechanisms remain to be determined. Here, we have developed a gene amplification system in yeast and mammalian cells that is based on double rolling-circle replication (DRCR). Cre-lox system is used to efficiently induce DRCR utilizing a recombinational process coupled with replication. This system shows distinctive features seen in amplification of oncogenes and drug-resistance genes: (i) intra- and extrachromosomal amplification, (ii) intensive chromosome rearrangement and (iii) scattered-type amplification resembling those seen in cancer cells. This system can serve as a model for amplification of oncogenes and drug-resistance genes, and improve amplification systems used for making pharmaceutical proteins in mammalian cells.

Physical function and physical activity in hemodialysis patients with peripheral artery disease.

INTRODUCTION: Peripheral artery disease (PAD) is commonly observed in patients undergoing hemodialysis. PAD impairs the vasculature and leads to pathophysiologic changes in the skeletal muscles, causing physical function impairment and physical inactivity in general. However, it is unclear whether PAD adversely affects physical function and physical activity in patients on hemodialysis. METHODS: We performed a cross-sectional study with a retrospective review of the data to determine whether PAD is associated with impaired physical function and physical activity in patients undergoing hemodialysis. The study population comprised 310 patients and 88 healthy subjects. PAD was diagnosed based on an ankle-brachial index of <1.00 in patients on hemodialysis. Measurements of physical function included maximum walking speed, muscle strength in the lower extremities, and balance while standing. FINDINGS: Of the 310 patients, 84 (27.1%) had PAD. When patients undergoing hemodialysis were divided into those without PAD and those with PAD, both groups had poorer physical function and physical activity than the healthy control subjects. After adjustments for potential confounders, it was found that patients on hemodialysis with PAD had slower walking speed, poorer standing balance, and less physical activity than those without PAD. However, there was no significant difference in lower extremity muscle strength between the two groups. DISCUSSION: PAD diagnosed based on an ankle-brachial index of <1.00 was independently associated with impaired physical function and reduced physical activity in patients undergoing hemodialysis.

Mid-Holocene expansion of the Indian Ocean warm pool documented in coral Sr/Ca records from Kenya.

Proxy reconstructions suggest that mid-Holocene East African temperatures were warmer than today between 8 and 5 ka BP, but climate models cannot replicate this warming. Precessional forcing caused a shift of maximum insolation from boreal spring to fall in the mid-Holocene, which may have favored intense warming at the start of the warm season. Here, we use three Porites corals from Kenya that represent time windows from 6.55 to 5.87 ka BP to reconstruct past sea surface temperature (SST) seasonality from coral Sr/Ca ratios in the western Indian Ocean during the mid-Holocene. Although the Indian monsoon was reportedly stronger in the mid-Holocene, which should have amplified the seasonal cycle of SST in the western Indian Ocean, the corals suggest reduced seasonality (mean 3.2 °C) compared to the modern record (mean 4.3 °C). Warming in austral spring is followed by a prolonged period of warm SSTs, suggesting that an upper limit of tropical SSTs under mid-Holocene conditions was reached at the start of the warm season, and SSTs then remained stable. Similar changes are seen at the Seychelles. Bootstrap estimates suggest a reduction in SST seasonality of 1.3 ± 0.22 °C at Kenya and 1.7 ± 0.32 °C at the Seychelles. SST seasonality at Kenya corresponds to present-day SST seasonality at 55° E-60° E, while SST seasonality at the Seychelles corresponds to present day SST seasonality at ~ 65° E. This implies a significant westward expansion of the Indian Ocean warm pool. Furthermore, the coral data suggests that SST seasonality deviates from seasonal changes in orbital insolation due to ocean-atmosphere interactions.