Although the proteins that read the gene regulatory code, transcription factors (TFs), have been largely identified, it is not well known which sequences TFs can recognize. We have analyzed the ...sequence-specific binding of human TFs using high-throughput SELEX and ChIP sequencing. A total of 830 binding profiles were obtained, describing 239 distinctly different binding specificities. The models represent the majority of human TFs, approximately doubling the coverage compared to existing systematic studies. Our results reveal additional specificity determinants for a large number of factors for which a partial specificity was known, including a commonly observed A- or T-rich stretch that flanks the core motifs. Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated. We further describe a binding model incorporating these features that is required to understand binding of TFs to DNA.
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► High-resolution binding profiles representing most human transcription factors ► High-throughput SELEX can identify long and dimeric sites ► Full-length protein and DNA-binding domain specificities are similar ► Adjacent bases affect TF-DNA binding more than previously thought
High-throughput SELEX is used to determine high-resolution binding profiles representing most human transcription factors. Base-stacking interactions, and dimer orientation and spacing preferences, have a larger role in TF-DNA binding than previously appreciated.
FLASH radiotherapy is the delivery of ultra-high dose rate radiation several orders of magnitude higher than what is currently used in conventional clinical radiotherapy, and has the potential to ...revolutionize the future of cancer treatment. FLASH radiotherapy induces a phenomenon known as the FLASH effect, whereby the ultra-high dose rate radiation reduces the normal tissue toxicities commonly associated with conventional radiotherapy, while still maintaining local tumor control. The underlying mechanism(s) responsible for the FLASH effect are yet to be fully elucidated, but a prominent role for oxygen tension and reactive oxygen species production is the most current valid hypothesis. The FLASH effect has been confirmed in many studies in recent years, both
and
, with even the first patient with T-cell cutaneous lymphoma being treated using FLASH radiotherapy. However, most of the studies into FLASH radiotherapy have used electron beams that have low tissue penetration, which presents a limitation for translation into clinical practice. A promising alternate FLASH delivery method is via proton beam therapy, as the dose can be deposited deeper within the tissue. However, studies into FLASH protons are currently sparse. This review will summarize FLASH radiotherapy research conducted to date and the current theories explaining the FLASH effect, with an emphasis on the future potential for FLASH proton beam therapy.
A
bstract
We examine the Regge limit of holographic 4-point correlation functions in AdS
3
× S
3
involving two heavy and two light operators. In this kinematic regime such correlators can be ...reconstructed from the bulk phase shift accumulated by the light probe as it traverses the geometry dual to the heavy operator. We work perturbatively — but to arbitrary orders — in the ratio of the heavy operator’s conformal dimension to the dual CFT
2
’s central charge, thus going beyond the low order results of 1 and 2. In doing so, we derive all-order relations between the bulk phase shift and the Regge limit OPE data of a class of heavy-light multi-trace operators exchanged in the cross-channel. Furthermore, we analyse two examples for which the relevant 4-point correlators are known explicitly to all orders: firstly the case of heavy operators dual to AdS
3
conical defect geometries and secondly the case of non-trivial smooth geometries representing microstates of the two-charge D1-D5 black hole.
Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from ...multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.
Systemic lupus erythematosus D'Cruz, David P, Dr; Khamashta, Munther A, FRCP; Hughes, Graham RV, FRCP
The Lancet (British edition),
02/2007, Letnik:
369, Številka:
9561
Journal Article
Recenzirano
Summary Systemic lupus erythematosus is an autoimmune connective-tissue disorder with a wide range of clinical features, which predominantly affects women, especially from certain ethnic groups. ...Diagnosis is based on clinical assessment supported by investigations, including the finding of autoantibodies. Treatments range from antimalarial agents to corticosteroids and immunosuppressive agents. This Seminar draws attention to advances in the epidemiology, genetics, cardiovascular risks, lupus nephritis, CNS disease, the antiphospholipid syndrome, assessment of disease activity and damage, and pregnancy related and quality of life issues. New therapeutic approaches, such as biological agents and mycophenolate mofetil, will also be discussed.
Abstract The “hardening hypothesis” states tobacco control activities have mostly influenced those smokers who found it easier to quit and, thus, remaining smokers are those who are less likely to ...stop smoking. This paper first describes a conceptual model for hardening. Then the paper describes important methodological distinctions (quit attempts vs. ability to remain abstinent as indicators, measures of hardening per se vs. measures of causes of hardening, and dependence measures that do vs. do not include cigarettes per day (cigs/day).) After this commentary, the paper reviews data from prior reviews and new searches for studies on one type of hardening: the decreasing ability to quit due to increasing nicotine dependence. Overall, all four studies of the general population of smokers found no evidence of decreased ability to quit; however, both secondary analyses of treatment-seeking smokers found quit rates were decreasing over time. Cigs/day and time-to-first cigarette measures of dependence did not increase over time; however, two studies found that DSM-defined dependence appeared to be increasing over time. Although these data suggest hardening may be occurring in treatment seekers but not in the general population of smokers, this conclusion may be premature given the small number of data sets and indirect measures of quit success and dependence in the data sets. Future studies should include questions about quit attempts, ability to abstain, treatment use, and multi-item dependence measures.
The membrane attack complex of complement (MAC), apart from its classical role of lysing cells, can also trigger a range of non-lethal effects on cells, acting as a drive to inflammation. In the ...present study, we chose to investigate these non-lethal effects on inflammasome activation. We found that, following sublytic MAC attack, there is increased cytosolic Ca(2+) concentration, at least partly through Ca(2+) release from the endoplasmic reticulum lumen via the inositol 1,4,5-triphosphate receptor (IP3R) and ryanodine receptor (RyR) channels. This increase in intracellular Ca(2+) concentration leads to Ca(2+) accumulation in the mitochondrial matrix via the 'mitochondrial calcium uniporter' (MCU), and loss of mitochondrial transmembrane potential, triggering NLRP3 inflammasome activation and IL-1β release. NLRP3 co-localises with the mitochondria, probably sensing the increase in calcium and the resultant mitochondrial dysfunction, leading to caspase activation and apoptosis. This is the first study that links non-lethal effects of sublytic MAC attack with inflammasome activation and provides a mechanism by which sublytic MAC can drive inflammation and apoptosis.
The relative preference of nucleosomes to form on individual DNA sequences plays a major role in genome packaging. A wide variety of DNA sequence features are believed to influence nucleosome ...formation, including periodic dinucleotide signals, poly-A stretches and other short motifs, and sequence properties that influence DNA structure, including base content. It was recently shown by Kaplan et al. that a probabilistic model using composition of all 5-mers within a nucleosome-sized tiling window accurately predicts intrinsic nucleosome occupancy across an entire genome in vitro. However, the model is complicated, and it is not clear which specific DNA sequence properties are most important for intrinsic nucleosome-forming preferences.
We find that a simple linear combination of only 14 simple DNA sequence attributes (G+C content, two transformations of dinucleotide composition, and the frequency of eleven 4-bp sequences) explains nucleosome occupancy in vitro and in vivo in a manner comparable to the Kaplan model. G+C content and frequency of AAAA are the most important features. G+C content is dominant, alone explaining approximately 50% of the variation in nucleosome occupancy in vitro.
Our findings provide a dramatically simplified means to predict and understand intrinsic nucleosome occupancy. G+C content may dominate because it both reduces frequency of poly-A-like stretches and correlates with many other DNA structural characteristics. Since G+C content is enriched or depleted at many types of features in diverse eukaryotic genomes, our results suggest that variation in nucleotide composition may have a widespread and direct influence on chromatin structure.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Lifting of two-mode states in the D1-D5 CFT Hughes, Marcel R. R.; Mathur, Samir D.; Mehta, Madhur
The journal of high energy physics,
01/2024, Letnik:
2024, Številka:
1
Journal Article
Recenzirano
Odprti dostop
A
bstract
We consider D1-D5-P states in the untwisted sector of the D1-D5 orbifold CFT where one copy of the seed CFT has been excited by a pair of oscillators, each being either bosonic or ...fermionic. While such states are BPS at the orbifold point, they will in general ‘lift’ as the theory is deformed towards general values of the couplings. We compute the expectation value of this lift at second order in the deformation parameter for the above mentioned states. We write this lift in terms of a fixed number of nested contour integrals on a given integrand; this integrand depends on the mode numbers of the oscillators in the state. We evaluate these integrals to obtain the explicit value of the lift for various subfamilies of states. At large mode numbers one observes a smooth increase of the lift with the dimension of the state
h
; this increase appears to follow
a
∼
h
behavior similar to that found analytically in earlier computations for other classes of states.
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