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PubMed2025

Mapping early PRC2 nucleation sites upon Suz12 reintroduction reveals features of de novo Polycomb recruitment.

Polycomb domains safeguard cell identity by maintaining lineage-specific chromatin states enriched in repressive histone modifications, preserving the epigenetic memory of cell lineages. While Polycomb Repressive Complex 2 (PRC2) can re-establish its occupancy after perturbation, the mechanisms that guide de novo Polycomb recruitment remain unclear. To address this, we engineered an auxin-inducible degradation system to reversibly deplete and reintroduce the endogenous PRC2 core subunit Suz12 in mouse embryonic stem cells (mESCs). Genome-wide profiling at an early recovery time point revealed ~1,100 PRC2 nucleation sites, characterized by rapid Suz12 and histone H3K27me3 re-accumulation with strong signal, with minimal impact on gene expression. These sites were significantly enriched at bivalent promoters, coinciding with unmethylated CpG islands and chromatin states associated with developmental regulation, and were largely conserved in differentiated cells. Motif analysis identified G/C-rich DNA sequences associated with E2F and zinc-finger proteins, alongside strong co-occupancy with MTF2 and JARID2, two PRC2 cofactors previously implicated in Polycomb targeting. Notably, a subset of nucleation sites overlapped with long-range chromatin interaction anchors in histone H3K27me3 HiChIP datasets. These findings reveal that PRC2 de novo nucleation sites are associated with a combination of chromatin states, DNA sequence features, cofactor co-occupancy and spatial genome organization, suggesting that epigenetic memory can be re-established through defined genomic and chromatin features.

Epigenetic memory↗

PubMed2006

Genetic and epigenetic mechanisms in the early development of the vascular system.

The cardiovascular system plays a critical role in vertebrate development and homeostasis. Vascular development is a highly organized sequence of events that requires the correct spatial and temporal expression of specific sets of genes leading to the development of a primary vascular network. There have been intensive efforts to determine the molecular mechanisms regulating vascular growth and development, and much of the rationale for this has stemmed from the increasing clinical importance and therapeutic potential of modulating vascular formation during various disease states.

Animals↗

PubMed1991

Location of ribosomal genes in CHO cells; in situ hybridization with a non-isotopic DNA probe on G-banded chromosomes.

A novel in situ hybridization technique using sulfonated probes is described. This non-radioactive approach, which employs chemically modified DNA and immunocytochemical procedures, is compatible with pre-G-banding and allows a rapid localization of the hybridized sequences on chromosomal spreads with a high spatial resolution. Using this technique we have localised the Chinese hamster ribosomal genes in the telomeric region of ten chromosomes, and among them in the subtelomeric q region of the Z5 chromosome. These results are discussed, the genetic markers confirming and locating the origin of Z group chromosomes by rearrangements of Chinese hamster chromosomes.

Animals↗

PubMed1960

Induction of Fechner colors in black and white photographs.

Fechner colors are visible when two black and white photographs of a scene which have been taken with longwavelength and short-wavelength light, respectively, are viewed in an alternating sequence. Such colors may be combined with spatially induced, two-primary colors to enhance or reduce the vividness of the latter.

Color↗

PubMed2001

Unsupervised learning and temporal context to recall complex robot trajectories.

An unsupervised neural network is proposed to learn and recall complex robot trajectories. Two cases are considered: (i) A single trajectory in which a particular arm configuration (state) may occur more than once, and (ii) trajectories sharing states with each other. Ambiguities occur in both cases during recall of such trajectories. The proposed model consists of two groups of synaptic weights trained by competitive and Hebbian learning laws. They are responsible for encoding spatial and temporal features of the input sequences, respectively. Three mechanisms allow the network to deal with repeated or shared states: local and global context units, neurons disabled from learning, and redundancy. The network reproduces the current and the next state of the learned sequences and is able to resolve ambiguities. The model was simulated over various sets of robot trajectories in order to evaluate learning and recall, trajectory sampling effects and robustness.

Algorithms↗

PubMed1991

Changing patterns of synaptic input to subplate and cortical plate during development of visual cortex.

1. The development of excitatory activation in the visual cortex was studied in fetal and neonatal cats. During fetal and neonatal life, the immature cerebral cortex (the cortical plate) is sandwiched between two synaptic zones: the marginal zone above, and an area just below the cortical plate, the subplate. The subplate is transient and disappears by approximately 2 mo postnatal. Here we have investigated whether the subplate and the cortical plate receive functional synaptic inputs in the fetus, and when the adultlike pattern of excitatory synaptic input to the cortical plate appears during development. 2. Extracellular field potential recording to electrical stimulation of the optic radiation was performed in slices of cerebral cortex maintained in vitro. Laminar profiles of field potentials were converted by the current-source density (CSD) method to identify the spatial and temporal distribution of neuronal excitation within the subplate and the cortical plate. 3. Between embryonic day 47 (E47) and postnatal day 28 (P28; birth, E65), age-related changes occur in the pattern of synaptic activation of neurons in the cortical plate and the subplate. Early in development, at E47, E57, and P0, short-latency (probably monosynaptic) excitation is most obvious in the subplate, and longer latency (presumably polysynaptic) excitation can be seen in the cortical plate. Synaptic excitation in the subplate is no longer apparent at P21 and P28, a time when cell migration is finally complete and the cortical layers have formed. By contrast, excitation in the cortical plate is prominent in postnatal animals, and the temporal and spatial pattern has changed. 4. The adultlike sequence of synaptic activation in the different cortical layers can be seen by P28. It differs from earlier ages in several respects. First, short-latency (probably monosynaptic) excitation can be detected in cortical layer 4. Second, multisynaptic, long-lasting activation is present in layers 2/3 and 5. 5. Our results show that the subplate zone, known from anatomic studies to be a synaptic neurophil during development, receives functional excitatory inputs from axons that course in the developing white matter. Because the only mature neurons present in this zone are the subplate neurons, we conclude that subplate neurons are the principal, if not the exclusive, recipients of this input. The results suggest further that the excitation in the subplate in turn is relayed to neurons of the cortical plate via axon collaterals of subplate neurons.(ABSTRACT TRUNCATED AT 400 WORDS)

Aging↗

PubMed2001

Transcriptional regulation of vascular development.

Vascular development is a highly organized sequence of events that requires the correct spatial and temporal expression of specific sets of genes leading to the development of a primary vascular network. The first step in this process is the differentiation of pluripotent stem cells into endothelial cells. This is followed by endothelial proliferation, migration, and eventual formation of endothelial tubes. Maturation of these primitive tubes into fully developed blood vessels requires the recruitment of surrounding pericytes and their differentiation into vascular smooth muscle cells. Many of the events that occur during vasculogenesis are recapitulated during angiogenesis. Transcription factors have been shown to serve as master switches for regulating a number of developmental processes. Using a candidate gene approach, the genomic regulatory regions required to direct vascular-specific gene expression of several receptor tyrosine kinases that are critical for vasculogenesis have been characterized and some of the transcription factors that are involved in the regulation of these genes have recently been identified. Many of these factors are also involved in the regulation of hematopoiesis and may have overlapping functions in determining hematopoietic and endothelial differentiation. Targeted disruption of other transcription factors that were not previously thought to be involved in vascular development have also been recently shown to play a role in blood vessel development. The purpose of this review is to provide an update on the progress that has been made in our understanding of the transcriptional regulation of vascular development over the past few years.

Animals↗

PubMed2004

The coordination of signaling during Fc receptor-mediated phagocytosis.

Phagocytosis by macrophages can be initiated by Fcgamma receptors (FcR) in membranes that bind to Fc regions of immunoglobulin G (IgG). Activated FcR transduce signals to cytoplasm, which regulate the internalization of IgG-coated particles into plasma membrane-derived vacuoles, phagosomes. Particles internalized by phagocytosis are much larger than FcR, which prompts questions of if and how the receptors are coordinated with each other. FcR-mediated signal transduction entails recruitment of proteins from cytoplasm to the receptor, largely via protein phosphorylation. These FcR signaling complexes then activate proteins that regulate actin, myosin, membrane fusion, and the production of reactive oxygen intermediates. Recent fluorescence microscopic studies of phagocytosis in macrophages indicate that signaling by FcR occurs as a sequence of distinct stages, evident in the spatial and temporal patterns of phosphoinositides, protein kinase C, and Rho-family GTPase activation on forming phagosomes. The coordination of these stages may be regulated by lipids or lipid-anchored proteins, which diffuse away from FcR complexes. Lateral diffusion of FcR-derived signals could integrate FcR-dependent responses over large areas of membrane in the forming phagosome.

Animals↗

PubMed2004

After double-strand break induction by UV-A, homologous recombination and nonhomologous end joining cooperate at the same DSB if both systems are available.

After induction of DNA double-strand breaks (DSB) two repair systems, the error-prone 'nonhomologous end joining' (NHEJ) and the more accurate 'homologous recombination repair' (HRR) can compete for the same individual DSB site. In the human keratinocyte cell line, HaCaT, we have tested the spatial co-localisation and the temporal sequence of events. We used UV-A (365 nm) as a damaging agent, which can be applied in clearly defined doses and can lead to rare DSBs via propagation of clustered single-strand breaks (SSBs). DNA fragmentation and repair was measured by the Comet assay and persisting DSBs were quantified by the micronucleus assay. Direct DSB detection was performed by immunohistochemical labelling of gamma-H2AX, a phosphorylated histone that is assumed to form one foci per DSB. Intra- and inter-pathway interactions were quantified by co-localisation, FRET imaging and by co-immunoprecipitation (Co-IP) of XRCC4, DNA-PK and Ku70 as representatives of NHEJ, Rad51 and Rad52 for HRR and gamma-H2AX, Mre11 and Rad50 as representatives of both pathways. In G2 cells, where both systems are available, the temporal sequence after irradiation is: (1) gamma-H2AX (2) Mre11 (3) DNA-PK Rad51 (4) XRCC4. That is, the first two proteins involved in both pathways 'label' the damaged site and initiate repair, followed by the NHEJ, which is temporally overlapping with HRR activity. Taking all these observations together we suggest that a cell tries to repair DSBs with a combination of both HRR and NHEJ, if available.

Antigens, Nuclear↗

PubMed2006

Turbulence strength estimation from an arbitrary set of atmospherically degraded images.

In remote sensing, atmospheric turbulence and aerosols usually limit the image quality. For many practical cases, turbulence is shown to be dominant, especially for horizontal close-to-earth imaging in hot environments. In a horizontal long-range imaging, it is usually impractical to calculate path-averaged refractive index structure constant C(2)(n) (which characterizes the turbulence strength) with conventional equipment. We propose a method for estimating C(2)(n) from the available atmospherically degraded video sequence by calculating temporal intensity fluctuations in spatially high variance areas. Experimental comparison with C(2)(n) measurements using a scintillometer shows reliable estimation results.

Journal Article↗

PubMed1995

MR myelography: imaging findings.

MR myelography, heavily T2-weighted fast spin-echo imaging with fat suppression, enhances the signal intensity of CSF with subtraction of the surrounding background signal. Krudy [1], who first described the technique, used multiple projections per examination. We illustrate the findings in 80 patients who were examined with a modified MR imaging technique that provides increased spatial resolution and uses a single coronal sequence after the conventional MR study. This report illustrates the usefulness of MR myelography in cases of spinal stenosis or spinal block, in both the lumbar and thoracic regions.

Adolescent↗

PubMedDate not supplied

[Isolation and characteristics of antistreptokinase antibodies from blood serum of myocardial infarct patients treated with streptokinase].

Antistreptokinase IgG (antiSK IgG) from blood of 8 patients with acute myocardial infarction that were treated by streptokinase (SK) has been investigated. AntiSK IgG contained 1.8% of total serum IgG. They had high affinity to SK (K50% approximately 10 nM) and inhibited activation of plasminogen (Pg) by SK with K50% approximately 6 nM. AntiSK IgG were bound with chymothriptic fragments of SK with affinity decreased in the set of fragments: 47 > 36 > 30 > 17 > or = 11 > 7 kDa. 11 linear epitopes of antiSK IgG were localized in I1-S12, T43-M70, G139-Q152, T163-I190, T193-S222, F241-Y252, Y275-P286, T315-L336, I365-E376, S379-T390 and Y397-N410 sites of SK primary structure using SK decapeptides. 70% of antibodies were bound with T43-M70 (38.3%), T315-L336 (13.2%) and Y397-N410 (17.7%) SK sequences located in alpha and gamma SK domains. By depletion of antiSK IgG on Pg-SK complex it was shown that 80-85% of antiSK IgG bound to Pg-SK complex, 47.9% of that contained antibodies with epitopes located in I1-S12, T43-M70, T193-S222 and S379-T390 SK sequences, and rest of IgG had probably spatial epitopes. Unbound with Pg-SK complex antibodies inhibited activation of Pg by SK with higher affinity (Ki approximately 1.2 nM) in comparison with total antiSK IgG fraction. The role of different sites in antigenity of SK and in Pg-SK complex formation is discussed.

Antibodies↗

PubMedDate not supplied

Cardiac MR spectroscopy in the new millennium.

Spectroscopy is close to becoming an integral part of the clinical MR examination to achieve a complete morphological, functional, and metabolic evaluation of the human heart. 31P-NMR spectroscopy is used to noninvasively assess human myocardial energy metabolism. Abnormalities in the phosphocreatine (PCr) to ATP ratio are observed in ischemic heart disease, heart failure, transplanted hearts, and hypertrophic cardiomyopathy. NMR spectroscopy 31P spectra obtained at rest, during exercise or pharmacological stress allow the observation of the earliest metabolic responses of myocardial ischemia. 1 spectroscopy can evaluate the concentration of intracellular creatine and myocardial lipids as a means of evaluating myocardial viability. The increase in total 23Na in ischemic tissue provides information about the extent and location of viable tissue. Higher magnetic fields, gradient strength, and technological advances in pulse sequence and localization will result in better spatial and temporal resolution improving the clinical utility of the technique.

Animals↗

PubMed1994

[Magnetic resonance tomography of the hand: current status].

Magnetic resonance imaging (MRI) is an established imaging method in abnormalities of the wrist. Inherent advantages of this imaging method such as the lack of ionizing irradiation, the free choice of imaging planes and its excellent contrast resolution have been enhanced by the introduction of surface coils and new sequences. These developments result in an improved spatial resolution, allowing imaging of small structures such as the triangular fibrocartilage. There is a number of established indications for MRI of the wrist, e.g. diagnosis of avascular necrosis, follow-up after carpal tunnel surgery and imaging of soft tissue masses. Increasingly, MRI can be used for the diagnosis of intercarpal ligament tears as well. The diagnostic capabilities of MRI of the wrist are discussed, based on personal experience and a review of the literature.

Carpal Tunnel Syndrome↗

PubMed1996

Pax and vertebrate development.

Pax genes encode transcription factors sharing a highly conserved sequence, the paired box. Their temporally and spatially restricted expression patterns during development indicate that Pax genes are involved in important steps of nervous system formation. Mutations in Pax genes have been correlated with three mouse mutants (undulated, splotch, small eye) and two human diseases (Waardenburg syndrome, aniridia). Recent data demonstrated that deregulation of Pax genes contributes to tumor formation.

Animals↗

PubMedDate not supplied

[Possibility of biocompatibility of fullerene C60 with oligopeptides using a comparative analysis of their spatial form].

It was proposed to elucidate the mechanism of unique biological biocompatibility of carbon materials used for making endoprostheses for medicinal practice. For this purpose, a method of comparing the geometry of individual globular and fibrillar proteins and carbon structures (fullerenes) was advanced, and a comparative analysis of the spatial structure of fullerene C60 and the amino acid sequences of 286 proteins was made. Based on a high degree of similarity in the positions of atoms of the polypeptide chains of proteins and peptides and the corresponding atoms of fullerene and of other structural parameters revealed by the comparison of the spatial structures using mathematical simulation, the phenomenon of biological compatibility was interpreted as an "insertion" of fullerenes into the structure of protein molecules in place of structurally similar amino acid sequences, i.e., as a "prosthetics" at the molecular level. It is proposed that fullerenes can "simulate" structurally similar short peptides in biological processes. It was shown that noncarbon biogenic atoms play a large role in the formation of specific structure of protein molecules.

Amino Acid Sequence↗

PubMed2005

A motif-based framework for recognizing sequence families.

MOTIVATION: Many signals in biological sequences are based on the presence or absence of base signals and their spatial combinations. One of the best known examples of this is the signal identifying a core promoter--the site at which the basal transcription machinery starts the transcription of a gene. Our goal is a fully automatic pattern recognition system for a family of sequences, which simultaneously discovers the base signals, their spatial relationships and a classifier based upon them. RESULTS: In this paper we present a general method for characterizing a set of sequences by their recurrent motifs. Our approach relies on novel probabilistic models for DNA binding sites and modules of binding sites, on algorithms to study them from the data and on a support vector machine that uses the models studied to classify a set of sequences. We demonstrate the applicability of our approach to diverse instances, ranging from families of promoter sequences to a dataset of intronic sequences flanking alternatively spliced exons. On a core promoter dataset our results are comparable with the state-of-the-art McPromoter. On a dataset of alternatively spliced exons we outperform a previous approach. We also achieve high success rates in recognizing cell cycle regulated genes. These results demonstrate that a fully automatic pattern recognition algorithm can meet or exceed the performance of hand-crafted approaches. AVAILABILITY: The software and datasets are available from the authors upon request.

Algorithms↗

PubMed2004

Time-optimal multidimensional gradient waveform design for rapid imaging.

Magnetic resonance imaging (MRI) is limited in many cases by long scan times and low spatial resolution. Recent advances in gradient systems hardware allow very rapid imaging sequences, such as steady-state free precession (SSFP), which has repetition times (TRs) of 2-5 ms. The design of these rapid sequences demands time-optimal preparatory gradient waveforms to provide maximum readout duty-cycle, and preserve spatial resolution and SNR while keeping TRs low. Time-optimal gradient waveforms can be synthesized analytically for certain simple cases. However, certain problems, such as time-optimal 2D and 3D gradient design with moment constraints, either may not have a solution or must be solved numerically. We show that time-optimal gradient design is a convex-optimization problem, for which very efficient solution methods exist. These methods can be applied to solve gradient design problems for oblique gradient design, spiral imaging, and flow-encoding using either a constant slew rate or the more exact voltage-limited gradient models. Ultimately, these methods provide a time-optimal solution to many 2D and 3D gradient design problems in a sufficiently short time for interactive imaging.

Magnetic Resonance Imaging↗