| 1. |
- Ederle, Joerg, et al.
(författare)
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Carotid artery stenting compared with endarterectomy in patients with symptomatic carotid stenosis (International Carotid Stenting Study): an interim analysis of a randomised controlled trial
- 2010
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Ingår i: The Lancet. - 1474-547X. ; 375:9719, s. 985-997
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Tidskriftsartikel (refereegranskat)abstract
- Background Stents are an alternative treatment to carotid endarterectomy for symptomatic carotid stenosis, but previous trials have not established equivalent safety and efficacy. We compared the safety of carotid artery stenting with that of carotid endarterectomy. Methods The International Carotid Stenting Study (ICSS) is a multicentre, international, randomised controlled trial with blinded adjudication of outcomes. Patients with recently symptomatic carotid artery stenosis were randomly assigned in a 1:1 ratio to receive carotid artery stenting or carotid endarterectomy. Randomisation was by telephone call or fax to a central computerised service and was stratified by centre with minimisation for sex, age, contralateral occlusion, and side of the randomised artery. Patients and investigators were not masked to treatment assignment. Patients were followed up by independent clinicians not directly involved in delivering the randomised treatment. The primary outcome measure of the trial is the 3-year rate of fatal or disabling stroke in any territory, which has not been analysed yet. The main outcome measure for the interim safety analysis was the 120-day rate of stroke, death, or procedural myocardial infarction. Analysis was by intention to treat (ITT). This study is registered, number ISRCTN25337470. Findings The trial enrolled 1713 patients (stenting group, n=855; endarterectomy group, n=858). Two patients in the stenting group and one in the endarterectomy group withdrew immediately after randomisation, and were not included in the ITT analysis. Between randomisation and 120 days, there were 34 (Kaplan-Meier estimate 4.0%) events of disabling stroke or death in the stenting group compared with 27 (3.2%) events in the endarterectomy group (hazard ratio [HR] 1.28, 95% CI 0.77-2.11). The incidence of stroke, death, or procedural myocardial infarction was 8.5% in the stenting group compared with 5.2% in the endarterectomy group (72 vs 44 events; HR 1.69, 1.16-2.45, p=0.006), Risks of any stroke (65 vs 35 events; HR 1.92, 1.27-2.89) and all-cause death (19 vs seven events; HR 2.76, 1.16-6.56) were higher in the stenting group than in the endarterectomy group. Three procedural myocardial infarctions were recorded in the stenting group, all of which were fatal, compared with four, all non-fatal, in the endarterectomy group. There was one event of cranial nerve palsy in the stenting group compared with 45 in the endarterectomy group. There were also fewer haematomas of any severity in the stenting group than in the endarterectomy group (31 vs 50 events; p=0.0197). Interpretation Completion of long-term follow-up is needed to establish the efficacy of carotid artery stenting compared with endarterectomy. In the meantime, carotid endarterectomy should remain the treatment of choice for patients suitable for surgery.
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| 2. |
- Lissek, T, et al.
(författare)
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Building Bridges through Science
- 2017
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Ingår i: Neuron. - : Elsevier BV. - 1097-4199 .- 0896-6273. ; 96:4, s. 730-735
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Tidskriftsartikel (refereegranskat)
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| 3. |
- Mavaddat, Nasim, et al.
(författare)
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Prediction of Breast Cancer Risk Based on Profiling With Common Genetic Variants
- 2015
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 1460-2105 .- 0027-8874. ; 107:5, s. 036-036
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Tidskriftsartikel (refereegranskat)abstract
- Background: Data for multiple common susceptibility alleles for breast cancer may be combined to identify women at different levels of breast cancer risk. Such stratification could guide preventive and screening strategies. However, empirical evidence for genetic risk stratification is lacking. Methods: We investigated the value of using 77 breast cancer-associated single nucleotide polymorphisms (SNPs) for risk stratification, in a study of 33 673 breast cancer cases and 33 381 control women of European origin. We tested all possible pair-wise multiplicative interactions and constructed a 77-SNP polygenic risk score (PRS) for breast cancer overall and by estrogen receptor (ER) status. Absolute risks of breast cancer by PRS were derived from relative risk estimates and UK incidence and mortality rates. Results: There was no strong evidence for departure from a multiplicative model for any SNP pair. Women in the highest 1% of the PRS had a three-fold increased risk of developing breast cancer compared with women in the middle quintile (odds ratio [OR] = 3.36, 95% confidence interval [CI] = 2.95 to 3.83). The ORs for ER-positive and ER-negative disease were 3.73 (95% CI = 3.24 to 4.30) and 2.80 (95% CI = 2.26 to 3.46), respectively. Lifetime risk of breast cancer for women in the lowest and highest quintiles of the PRS were 5.2% and 16.6% for a woman without family history, and 8.6% and 24.4% for a woman with a first-degree family history of breast cancer. Conclusions: The PRS stratifies breast cancer risk in women both with and without a family history of breast cancer. The observed level of risk discrimination could inform targeted screening and prevention strategies. Further discrimination may be achievable through combining the PRS with lifestyle/environmental factors, although these were not considered in this report.
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| 4. |
- Kapoor, Pooja Middha, et al.
(författare)
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Combined associations of a polygenic risk score and classical risk factors with breast cancer risk
- 2021
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 113:3, s. 329-337
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Tidskriftsartikel (refereegranskat)abstract
- We evaluated the joint associations between a new 313-variant PRS (PRS313) and questionnaire-based breast cancer risk factors for women of European ancestry, using 72 284 cases and 80 354 controls from the Breast Cancer Association Consortium. Interactions were evaluated using standard logistic regression and a newly developed case-only method for breast cancer risk overall and by estrogen receptor status. After accounting for multiple testing, we did not find evidence that per-standard deviation PRS313 odds ratio differed across strata defined by individual risk factors. Goodness-of-fit tests did not reject the assumption of a multiplicative model between PRS313 and each risk factor. Variation in projected absolute lifetime risk of breast cancer associated with classical risk factors was greater for women with higher genetic risk (PRS313 and family history) and, on average, 17.5% higher in the highest vs lowest deciles of genetic risk. These findings have implications for risk prevention for women at increased risk of breast cancer.
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| 5. |
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| 6. |
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| 7. |
- Daebes, HL, et al.
(författare)
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Association between triage level and outcomes at Médecins Sans Frontières trauma hospital in Kunduz, Afghanistan, 2015
- 2021
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Ingår i: Emergency medicine journal : EMJ. - : BMJ. - 1472-0213 .- 1472-0205. ; 39:8, s. 628-633
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Tidskriftsartikel (refereegranskat)abstract
- Five million people die annually due to injuries; an increasing part is due to armed conflict in low-income and middle-income countries, demanding resolute emergency trauma care. In Afghanistan, a low-income country that has experienced conflict for over 35 years, conflict related trauma is a significant public health problem. To address this, the non-governmental organisation Médecins Sans Frontières (MSF) set up a trauma centre in Kunduz (Kunduz Trauma Centre (KTC)). MSF’s standardised emergency operating procedures include the South African Triage Scale (SATS). To date, there are few studies that assess how triage levels correspond with outcome in low-resource conflict settingsAimThis study aims to assess to what extent SATS triage levels correlated to outcomes in terms of hospital admission, intensive care unit (ICU) admission and mortality for patients treated at KTC.Method and materialsThis retrospective study used routinely collected data from KTC registries. A total of 17 970 patients were included. The outcomes were hospital admission, ICU admission and mortality. The explanatory variable was triage level. Covariates including age, gender and delay to arrival were used. Logistic regression was used to study the correlation between triage level and outcomes.ResultsOut of all patients seeking care, 28.7% were triaged as red or orange. The overall mortality was 0.6%. In total, 90% of those that died and 79% of ICU-admitted patients were triaged as red.ConclusionThe risk of positive and negative outcomes correlated with triage level. None of the patients triaged as green died or were admitted to the ICU whereas 90% of patients who died were triaged as red.
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| 8. |
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| 9. |
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| 10. |
- Kuchenbaecker, Karoline B., et al.
(författare)
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Evaluation of polygenic risk scores for breast and ovarian cancer risk prediction in BRCA1 and BRCA2 mutation carriers
- 2017
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Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 109:7
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genome-wide association studies (GWAS) have identified 94 common single-nucleotide polymorphisms (SNPs) associated with breast cancer (BC) risk and 18 associated with ovarian cancer (OC) risk. Several of these are also associated with risk of BC or OC for women who carry a pathogenic mutation in the high-risk BC and OC genes BRCA1 or BRCA2. The combined effects of these variants on BC or OC risk for BRCA1 and BRCA2 mutation carriers have not yet been assessed while their clinical management could benefit from improved personalized risk estimates. Methods: We constructed polygenic risk scores (PRS) using BC and OC susceptibility SNPs identified through population-based GWAS: for BC (overall, estrogen receptor [ER]-positive, and ER-negative) and for OC. Using data from 15 252 female BRCA1 and 8211 BRCA2 carriers, the association of each PRS with BC or OC risk was evaluated using a weighted cohort approach, with time to diagnosis as the outcome and estimation of the hazard ratios (HRs) per standard deviation increase in the PRS. Results: The PRS for ER-negative BC displayed the strongest association with BC risk in BRCA1 carriers (HR = 1.27, 95% confidence interval [CI] = 1.23 to 1.31, P = 8.2 × 10-53). InBRCA2 carriers, the strongest association with BC risk was seen for the overall BCPRS (HR = 1.22, 95% CI = 1.17 to 1.28, P = 7.2 × 10-20). The OC PRS was strongly associated with OC risk for both BRCA1 and BRCA2 carriers. These translate to differences in absolute risks (more than 10% in each case) between the top and bottom deciles of the PRS distribution; for example, the OC risk was 6% by age 80 years for BRCA2 carriers at the 10th percentile of the OC PRS compared with 19% risk for those at the 90th percentile of PRS. Conclusions: BC and OC PRS are predictive of cancer risk in BRCA1 and BRCA2 carriers. Incorporation of the PRS into risk prediction models has promise to better inform decisions on cancer risk management.
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| 11. |
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| 12. |
- Garg, Parie, et al.
(författare)
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Idling by DNA polymerase delta maintains a ligatable nick during lagging-strand DNA replication.
- 2004
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Ingår i: Genes & Development. - : Cold Spring Harbor Laboratory. - 0890-9369 .- 1549-5477. ; 18:22, s. 2764-2773
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Tidskriftsartikel (refereegranskat)abstract
- During each yeast cell cycle, ∼100,000 nicks are generated during lagging-strand DNA replication. Efficient nick processing during Okazaki fragment maturation requires the coordinated action of DNA polymerase δ (Pol δ) and the FLAP endonuclease FEN1. Misregulation of this process leads to the accumulation of double-stranded breaks and cell lethality. Our studies highlight a remarkably efficient mechanism for Okazaki fragment maturation in which Pol δ by default displaces 2–3 nt of any downstream RNA or DNA it encounters. In the presence of FEN1, efficient nick translation ensues, whereby a mixture of mono- and small oligonucleotides are released. If FEN1 is absent or not optimally functional, the ability of Pol δ to back up via its 3′–5′-exonuclease activity, a process called idling, maintains the polymerase at a position that is ideal either for ligation (in case of a DNA–DNA nick) or for subsequent engagement by FEN1 (in case of a DNA–RNA nick). Consistent with the hypothesis that DNA polymerase ϵ is the leading-strand enzyme, we observed no idling by this enzyme and no cooperation with FEN1 for creating a ligatable nick.
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| 13. |
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| 14. |
- Farahini, Nasim, et al.
(författare)
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Parallel distributed scalable runtime address generation scheme for a coarse grain reconfigurable computation and storage fabric
- 2014
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Ingår i: Microprocessors and microsystems. - : Elsevier BV. - 0141-9331 .- 1872-9436. ; 38:8, s. 788-802
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents a hardware based solution for a scalable runtime address generation scheme for DSP applications mapped to a parallel distributed coarse grain reconfigurable computation and storage fabric. The scheme can also deal with non-affine functions of multiple variables that typically correspond to multiple nested loops. The key innovation is the judicious use of two categories of address generation resources. The first category of resource is the low cost AGU that generates addresses for given address bounds for affine functions of up to two variables. Such low cost AGUs are distributed and associated with every read/write port in the distributed memory architecture. The second category of resource is relatively more complex but is also distributed but shared among a few storage units and is capable of handling more complex address generation requirements like dynamic computation of address bounds that are then used to configure the AGUs, transformation of non-affine functions to affine function by computing the affine factor outside the loop, etc. The runtime computation of the address constraints results in negligibly small overhead in latency, area and energy while it provides substantial reduction in program storage, reconfiguration agility and energy compared to the prevalent pre-computation of address constraints. The efficacy of the proposed method has been validated against the prevalent address generation schemes for a set of six realistic DSP functions. Compared to the pre-computation method, the proposed solution achieved 75% average code compaction and compared to the centralized runtime address generation scheme, the proposed solution achieved 32.7% average performance improvement.
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| 15. |
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| 16. |
- Forslund, Josefin M. E., 1988-
(författare)
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The consequences of DNA lesions for mitochondrial DNA maintenance
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Eukaryotic cells have their own energy-producing organelles called mitochondria. The energy is stored in the adenosine triphosphate (ATP) molecule and is produced via the oxidative phosphorylation process inside the mitochondria. Thirteen of the essential proteins required for this process are encoded on the mitochondrial DNA (mtDNA). To ensure sufficient energy production it is therefore important to maintain mtDNA integrity. MtDNA maintenance is dependent on several factors, which include the replicative DNA polymerase. In humans, the main mitochondrial polymerase is DNA polymerase gamma (Pol γ), whereas in S. cerevisiae the homolog is called Mip1. Defects in the mitochondrial DNA polymerase and mtDNA replication in general cause mitochondrial dysfunction, reduced energy production and, in humans, mitochondrial diseases. DNA damage and non-standard nucleotides are frequently forming obstacles to the DNA replication machinery. One of the proteins that assists the nuclear replication machinery in dealing with DNA damage is the primase-polymerase PrimPol, performing either translesion DNA synthesis or alternatively priming replication restart after DNA damage. More recently, PrimPol was also identified inside the mitochondria. We therefore investigated the potential role of PrimPol to assist the mtDNA replication machinery at the site of mtDNA damage. Our results suggest that PrimPol does not work as a conventional translesion DNA polymerase at oxidative damage in the mitochondria, but instead interacts with the mtDNA replication machinery to support restart after replication stalling.Stalling of DNA replication can also occur at wrongly inserted nucleotides. In this study, we pay extra attention to ribonucleotides, which are non-standard nucleotides in the context of DNA. Ribonucleotides (rNTPs) are normally building blocks for RNA but are occasionally utilized by DNA polymerases during DNA replication. Ribonucleotides are more reactive compared to dNTPs as they have an additional hydroxyl group (-OH). Their presence in the genome can lead to replication stress and genomic instability. In nuclear DNA, ribonucleotides are efficiently removed by the Ribonucleotide Excision Repair (RER) pathway and failure to remove them leads to human disease (e.g., Aicardi-Goutières syndrome). We investigated if ribonucleotides are removed from mtDNA and if not, how the replication machinery can tolerate the presence of ribonucleotides in the mtDNA. By using several yeast strains with altered dNTP pools, we found that the RER pathway is not active in mitochondria. Instead, mitochondria have an innate tolerance to ribonucleotide incorporation in mtDNA and under normal cellular conditions mature human mtDNA contains ~50 ribonucleotides per genome. We show that this ribonucleotide tolerance is the result of human Pol γ’s remarkable abilities to 1) efficiently bypass ribonucleotides in the DNA template and 2) proficiently discriminate against the incorporation of free ribonucleotides during mtDNA replication. Pol γ’s discrimination capability against free ribonucleotides comes with a price. In the presence of high rNTP levels, Pol γ is inhibited in DNA synthesis and could eventually lead to frequent replication stalling. Together, these studies are in line with our hypothesis that ribonucleotides in mtDNA can be tolerated, with the consequence that mtDNA replication is in particular vulnerable to imbalances in rNTP/dNTP ratios.In summary, this study shows that we cannot simply extrapolate our knowledge of nuclear DNA replication stress management to the mtDNA maintenance, highlighting the need to study the molecular mechanism by which the mtDNA replication machinery is able to cope with DNA lesions to prevent loss of mtDNA integrity and disease development.
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| 17. |
- Fusté, Javier Miralles, et al.
(författare)
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In Vivo Occupancy of Mitochondrial Single-Stranded DNA Binding Protein Supports the Strand Displacement Mode of DNA Replication
- 2014
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Ingår i: Plos Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 10:12
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Tidskriftsartikel (refereegranskat)abstract
- Mitochondrial DNA (mtDNA) encodes for proteins required for oxidative phosphorylation, and mutations affecting the genome have been linked to a number of diseases as well as the natural ageing process in mammals. Human mtDNA is replicated by a molecular machinery that is distinct from the nuclear replisome, but there is still no consensus on the exact mode of mtDNA replication. We here demonstrate that the mitochondrial single-stranded DNA binding protein (mtSSB) directs origin specific initiation of mtDNA replication. MtSSB covers the parental heavy strand, which is displaced during mtDNA replication. MtSSB blocks primer synthesis on the displaced strand and restricts initiation of light-strand mtDNA synthesis to the specific origin of light-strand DNA synthesis (OriL). The in vivo occupancy profile of mtSSB displays a distinct pattern, with the highest levels of mtSSB close to the mitochondrial control region and with a gradual decline towards OriL. The pattern correlates with the replication products expected for the strand displacement mode of mtDNA synthesis, lending strong in vivo support for this debated model for mitochondrial DNA replication.
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| 18. |
- Ghasemzadeh, Nasim
(författare)
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Application of Artificial Gel Antibodies for the Detection and Quantification of Proteins in Biological Fluids
- 2010
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The molecular-imprinting method has previously been used for the synthesis of artificial gel antibodies, highly selective for various proteins. In present study, we have synthesized artificial gel antibodies against haemoglobin, albumin and different forms of growth hormone with the aim to develop a simple and rapid procedure to measure the concentration of these protein biomarkers in samples of clinical interest. A spectrophotometric method was developed to design a standard curve in the form of a straight line, whereby the true absorption (not the recorded “apparent” absorption) was plotted against a known protein concentration. The procedure, applied to quantitative analysis of albumin in human plasma and cerebrospinal fluid (CSF) from patients with ALS, indicated that the concentration of this protein was significantly enhanced in CSF from patients with amyotrophic lateral sclerosis (ALS), compared to control samples. A low level of albumin was observed in plasma from ALS patients compared to controls. Additionally, free zone electrophoresis was employed to detect human growth hormone (GH) activity in hormone preparations purified from human pituitaries. We have successfully synthesized antibodies capable of discriminating between dimeric and monomeric GH in samples of clinical origin. To quantify these proteins a calibration curve has been designed, i.e. a plot of the electrophoretic mobility of the complex GH/gel antibody against the protein concentration in the sample, for instance serum or CSF. This method was also employed for qualitative and quantitative determinations of Somatropin, a non-glycosylated GH and glycosylated-GH in a body liquid. Our results indicate that by this technique one can “fish out” with high accuracy various proteins from both body fluids containing a great number of other proteins. It might well apply also to biomarker proteins for other diseases.
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| 19. |
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| 20. |
- Jafri, Syed M. A. H., et al.
(författare)
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Architecture and Implementation of Dynamic Parallelism, Voltage and Frequency Scaling (PVFS) on CGRAs
- 2015
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Ingår i: ACM Journal on Emerging Technologies in Computing Systems. - : Association for Computing Machinery (ACM). - 1550-4832 .- 1550-4840. ; 11:4
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Tidskriftsartikel (refereegranskat)abstract
- In the era of platforms hosting multiple applications with arbitrary performance requirements, providing a worst-case platform-wide voltage/frequency operating point is neither optimal nor desirable. As a solution to this problem, designs commonly employ dynamic voltage and frequency scaling (DVFS). DVFS promises significant energy and power reductions by providing each application with the operating point (and hence the performance) tailored to its needs. To further enhance the optimization potential, recent works interleave dynamic parallelism with conventional DVFS. The induced parallelism results in performance gains that allow an application to lower its operating point even further (thereby saving energy and power consumption). However, the existing works employ costly dedicated hardware (for synchronization) and rely solely on greedy algorithms to make parallelism decisions. To efficiently integrate parallelism with DVFS, compared to state-of-the-art, we exploit the reconfiguration (to reduce DVFS synchronization overheads) and enhance the intelligence of the greedy algorithm (to make optimal parallelism decisions). Specifically, our solution relies on dynamically reconfigurable isolation cells and an autonomous parallelism, voltage, and frequency selection algorithm. The dynamically reconfigurable isolation cells reduce the area overheads of DVFS circuitry by configuring the existing resources to provide synchronization. The autonomous parallelism, voltage, and frequency selection algorithm ensures high power efficiency by combining parallelism with DVFS. It selects that parallelism, voltage, and frequency trio which consumes minimum power to meet the deadlines on available resources. Synthesis and simulation results using various applications/algorithms (WLAN, MPEG4, FFT, FIR, matrix multiplication) show that our solution promises significant reduction in area and power consumption (23% and 51%) compared to state-of-the-art.
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| 21. |
- Jafri, Syed. M. A. H., et al.
(författare)
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Energy-Aware Coarse-Grained Reconfigurable Architectures using Dynamically Reconfigurable Isolation Cells
- 2013
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Ingår i: Proceedings Of The Fourteenth International Symposium On Quality Electronic Design (ISQED 2013). - 9781467349529 ; , s. 104-111
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Konferensbidrag (refereegranskat)abstract
- This paper presents a self adaptive architecture to enhance the energy efficiency of coarse-grained reconfigurable architectures (CGRAs). Today, platforms host multiple applications, with arbitrary inter-application communication and concurrency patterns. Each application itself can have multiple versions (implementations with different degree of parallelism) and the optimal version can only be determined at runtime. For such scenarios, traditional worst case designs and compile time mapping decisions are neither optimal nor desirable. Existing solutions to this problem employ costly dedicated hardware to configure the operating point at runtime (using DVFS). As an alternative to dedicated hardware, we propose exploiting the reconfiguration features of modern CGRAs. Our solution relies on dynamically reconfigurable isolation cells (DRICs) and autonomous parallelism, voltage, and frequency selection algorithm (APVFS). The DRICs reduce the overheads of DVFS circuitry by configuring the existing resources as isolation cells. APVFS ensures high efficiency by dynamically selecting the parallelism, voltage and frequency trio, which consumes minimum power to meet the deadlines on available resources. Simulation results using representative applications (Matrix multiplication, FIR, and FFT) showed up to 23% and 51% reduction in power and energy, respectively, compared to traditional DVFS designs. Synthesis results have confirmed significant reduction in area overheads compared to state of the art DVFS methods.
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| 22. |
- McDonald, Karin R., et al.
(författare)
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Pfh1 Is an Accessory Replicative Helicase that Interacts with the Replisome to Facilitate Fork Progression and Preserve Genome Integrity
- 2016
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Ingår i: PLOS Genetics. - : Copernicus GmbH. - 1553-7390 .- 1553-7404. ; 12:9
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Tidskriftsartikel (refereegranskat)abstract
- Replicative DNA helicases expose the two strands of the double helix to the replication apparatus, but accessory helicases are often needed to help forks move past naturally occurring hard-to-replicate sites, such as tightly bound proteins, RNA/DNA hybrids, and DNA secondary structures. Although the Schizosaccharomyces pombe 5'-to-3' DNA helicase Pfh1 is known to promote fork progression, its genomic targets, dynamics, and mechanisms of action are largely unknown. Here we address these questions by integrating genome-wide identification of Pfh1 binding sites, comprehensive analysis of the effects of Pfh1 depletion on replication and DNA damage, and proteomic analysis of Pfh1 interaction partners by immunoaffinity purification mass spectrometry. Of the 621 high confidence Pfh1-binding sites in wild type cells, about 40% were sites of fork slowing (as marked by high DNA polymerase occupancy) and/or DNA damage (as marked by high levels of phosphorylated H2A). The replication and integrity of tRNA and 5S rRNA genes, highly transcribed RNA polymerase II genes, and nucleosome depleted regions were particularly Pfh1-dependent. The association of Pfh1 with genomic integrity at highly transcribed genes was S phase dependent, and thus unlikely to be an artifact of high transcription rates. Although Pfh1 affected replication and suppressed DNA damage at discrete sites throughout the genome, Pfh1 and the replicative DNA polymerase bound to similar extents to both Pfh1-dependent and independent sites, suggesting that Pfh1 is proximal to the replication machinery during S phase. Consistent with this interpretation, Pfh1 co-purified with many key replisome components, including the hexameric MCM helicase, replicative DNA polymerases, RPA, and the processivity clamp PCNA in an S phase dependent manner. Thus, we conclude that Pfh1 is an accessory DNA helicase that interacts with the replisome and promotes replication and suppresses DNA damage at hard-to-replicate sites. These data provide insight into mechanisms by which this evolutionarily conserved helicase helps preserve genome integrity.
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| 23. |
- Mudie, Deanna M., et al.
(författare)
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Selection of In Vivo Predictive Dissolution Media Using Drug Substance and Physiological Properties
- 2020
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Ingår i: AAPS Journal. - : SPRINGER. - 1550-7416. ; 22:2
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Tidskriftsartikel (refereegranskat)abstract
- The rate and extent of drug dissolution in the gastrointestinal (GI) tract are highly dependent upon drug physicochemical properties and GI fluid properties. Biorelevant dissolution media (BDM), which aim to facilitate in vitro prediction of in vivo dissolution performance, have evolved with our understanding of GI physiology. However, BDM with a variety of properties and compositions are available, making the choice of dissolution medium challenging. In this tutorial, we describe a simple and quantitative methodology for selecting practical, yet physiologically relevant BDM representative of fasted humans for evaluating dissolution of immediate release formulations. Specifically, this methodology describes selection of pH, buffer species, and concentration and evaluates the importance of including bile salts and phospholipids in the BDM based upon drug substance log D, pK(a), and intrinsic solubility. The methodology is based upon a mechanistic understanding of how three main factors affect dissolution, including (1) drug ionization at gastrointestinal pH, (2) alteration of surface pH by charged drug species, and (3) drug solubilization in mixed lipidic aggregates comprising bile salts and phospholipids. Assessment of this methodology through testing and comparison with literature reports showed that the recommendations correctly identified when a biorelevant buffer capacity or the addition of bile salts and phospholipids to the medium would appreciably change the drug dissolution profile. This methodology can enable informed decisions about when a time, complexity, and/or cost-saving buffer is expected to lead to physiologically meaningful in vitro dissolution testing, versus when a more complex buffer would be required.
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| 24. |
- Sabouri, Nasim, et al.
(författare)
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DNA replication through hard-to-replicate sites, including both highly transcribed RNA Pol II and Pol III genes, requires the S. pombe Pfh1 helicase
- 2012
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Ingår i: Genes & Development. - : Cold Spring Harbor Laboratory. - 0890-9369 .- 1549-5477. ; 26:6, s. 581-593
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Tidskriftsartikel (refereegranskat)abstract
- Replication forks encounter impediments as they move through the genome, including natural barriers due to stable protein complexes and highly transcribed genes. Unlike lesions generated by exogenous damage, natural barriers are encountered in every S phase. Like humans, Schizosaccharomyces pombe encodes a single Pif1 family DNA helicase, Pfh1. Here, we show that Pfh1 is required for efficient fork movement in the ribosomal DNA, the mating type locus, tRNA, 5S ribosomal RNA genes, and genes that are highly transcribed by RNA polymerase II. In addition, converged replication forks accumulated at all of these sites in the absence of Pfh1. The effects of Pfh1 on DNA replication are likely direct, as it had high binding to sites whose replication was impaired in its absence. Replication in the absence of Pfh1 resulted in DNA damage specifically at those sites that bound high levels of Pfh1 in wild-type cells and whose replication was slowed in its absence. Cells depleted of Pfh1 were inviable if they also lacked the human TIMELESS homolog Swi1, a replisome component that stabilizes stalled forks. Thus, Pfh1 promotes DNA replication and separation of converged replication forks and suppresses DNA damage at hard-to-replicate sites.
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