We present MRiLab, a new comprehensive simulator for large-scale realistic MRI simulations on a regular PC equipped with a modern graphical processing unit (GPU). MRiLab combines realistic tissue ...modeling with numerical virtualization of an MRI system and scanning experiment to enable assessment of a broad range of MRI approaches including advanced quantitative MRI methods inferring microstructure on a sub-voxel level. A flexible representation of tissue microstructure is achieved in MRiLab by employing the generalized tissue model with multiple exchanging water and macromolecular proton pools rather than a system of independent proton isochromats typically used in previous simulators. The computational power needed for simulation of the biologically relevant tissue models in large 3D objects is gained using parallelized execution on GPU. Three simulated and one actual MRI experiments were performed to demonstrate the ability of the new simulator to accommodate a wide variety of voxel composition scenarios and demonstrate detrimental effects of simplified treatment of tissue micro-organization adapted in previous simulators. GPU execution allowed ~ 200× improvement in computational speed over standard CPU. As a cross-platform, open-source, extensible environment for customizing virtual MRI experiments, MRiLab streamlines the development of new MRI methods, especially those aiming to infer quantitatively tissue composition and microstructure.
Global cerebral ischemia in rodents is an established model in experimental research on cerebral ischemia which is characterized morphologically by a selective neuronal damage in the hippocampus, ...striatum and cortex. Using this model many studies have been performed to examine the pathophysiology of ischemic neuronal damage. Based upon these results it has been analysed whether substances which interact with the pathophysiological processes reduce the ischemic neuronal damage. Besides the morphological changes global ischemia leads to functional changes which can be assessed by behavioural studies. The Morris water maze examines the animals' abilities to learn, remember and go to a place in space only defined by its position relative to distal extramaze cues. In this test ischemic animals display a deficit in spatial learning as revealed by an increase in latency and in swim distance in the escape trials and a deficit in spatial memory as shown by reduced quadrant time and crossings over the former platform position during the probe trial. In several studies it could be demonstrated that neuroprotective strategies which reduce ischemic neuronal damage also attenuate or even completely prevent the ischemia-induced behavioural deficits in the water maze. Transplantation of fetal tissue which can also be used to achieve morphological recovery following global ischemia results in an amelioration of the ischemia-induced deficit. Thus, the water maze can clearly show that transplanted tissue can be functionally relevant. Data from the water maze seem to be a valuable completion to morphology which is especially important with respect to the relevance of experimental studies for clinical trials.
Abstract
Pupylation, a post-translational modification found in
Mycobacterium tuberculosis
and other Actinobacteria, involves the covalent attachment of prokaryotic ubiquitin-like protein (Pup) to ...lysines on target proteins by the ligase PafA (proteasome accessory factor A). Pupylated proteins, like ubiquitinated proteins in eukaryotes, are recruited for proteasomal degradation. Proteomic studies suggest that hundreds of potential pupylation targets are modified by the sole existing ligase PafA. This raises intriguing questions regarding the selectivity of this enzyme towards a diverse range of substrates. Here, we show that the availability of surface lysines alone is not sufficient for interaction between PafA and target proteins. By identifying the interacting residues at the pupylation site, we demonstrate that PafA recognizes authentic substrates via a structural recognition motif centered around exposed lysines. Through a combination of computational analysis, examination of available structures and pupylated proteomes, and biochemical experiments, we elucidate the mechanism by which PafA achieves recognition of a wide array of substrates while retaining selective protein turnover.
Focal brain lesions can lead to metabolic and structural changes in areas distant from but connected to the lesion site. After focal ischemic or excitotoxic lesions of the cortex and/or striatum, ...secondary changes have been observed in the thalamus, substantia nigra pars reticulata, hippocampus and spinal cord. In all these regions, inflammatory changes characterized by activation of microglia and astrocytes appear. In the thalamus, substantia nigra pars reticulata and hippocampus, an expression of proinflammatory cytokine like tumor necrosis factor-alpha and interleukin-1beta is induced. However, time course of expression and cellular localisation differ between these regions. Neuronal damage has consistently been observed in the thalamus, substantia nigra and spinal cord. It can be present in the hippocampus depending on the procedure of induction of focal cerebral ischemia. This secondary neuronal damage has been linked to antero- and retrograde degeneration. Anterograde degeneration is associated with somewhat later expression of cytokines, which is localised in neurons. In case of retrograde degeneration, the expression of cytokines is earlier and is localised in astrocytes. Pharmacological intervention aiming at reducing expression of tumor necrosis factor-alpha leads to reduction of secondary neuronal damage. These first results suggest that the inflammatory changes in remote areas might be involved in the pathogenesis of secondary neuronal damage.
Stop codon suppression using dedicated tRNA/aminoacyl-tRNA synthetase (aaRS) pairs allows for genetically encoded, site-specific incorporation of non-canonical amino acids (ncAAs) as chemical handles ...for protein labeling and modification. Here, we demonstrate that piggyBac-mediated genomic integration of archaeal pyrrolysine tRNA (tRNAPyl)/pyrrolysyl-tRNA synthetase (PylRS) or bacterial tRNA/aaRS pairs, using a modular plasmid design with multi-copy tRNA arrays, allows for homogeneous and efficient genetically encoded ncAA incorporation in diverse mammalian cell lines. We assess opportunities and limitations of using ncAAs for fluorescent labeling applications in stable cell lines. We explore suppression of ochre and opal stop codons and finally incorporate two distinct ncAAs with mutually orthogonal click chemistries for site-specific, dual-fluorophore labeling of a cell surface receptor on live mammalian cells.
Riboswitches are structured RNAs typically located in the 5' untranslated regions of bacterial mRNAs that bind metabolites and control gene expression. Most riboswitches sense one metabolite and ...function as simple genetic switches. However, we found that the 5' region of the Bacillus clausii metE messenger RNA includes two riboswitches that respond to S-adenosylmethionine and coenzyme B₁₂. This tandem arrangement yields a composite gene control system that functions as a two-input Boolean NOR logic gate. These findings and the discovery of additional tandem riboswitch architectures reveal how simple RNA elements can be assembled to make sophisticated genetic decisions without involving protein factors.
We applied a computational pipeline based on comparative genomics to bacteria, and identified 22 novel candidate RNA motifs. We predicted six to be riboswitches, which are mRNA elements that regulate ...gene expression on binding a specific metabolite. In separate studies, we confirmed that two of these are novel riboswitches. Three other riboswitch candidates are upstream of either a putative transporter gene in the order Lactobacillales, citric acid cycle genes in Burkholderiales or molybdenum cofactor biosynthesis genes in several phyla. The remaining riboswitch candidate, the widespread Genes for the Environment, for Membranes and for Motility (GEMM) motif, is associated with genes important for natural competence in Vibrio cholerae and the use of metal ions as electron acceptors in Geobacter sulfurreducens. Among the other motifs, one has a genetic distribution similar to a previously published candidate riboswitch, ykkC/yxkD, but has a different structure. We identified possible non-coding RNAs in five phyla, and several additional cis-regulatory RNAs, including one in ε-proteobacteria (upstream of purD, involved in purine biosynthesis), and one in Cyanobacteria (within an ATP synthase operon). These candidate RNAs add to the growing list of RNA motifs involved in multiple cellular processes, and suggest that many additional RNAs remain to be discovered.
Promoting a MOSAIC future in science Banerjee, Ruma; Block, Kirsten F.
Trends in biochemical sciences (Amsterdam. Regular ed.),
06/2024, Letnik:
49, Številka:
6
Journal Article
Recenzirano
Discoveries at the frontiers of science and finding solutions to pressing biomedical problems will be accelerated when talent, which is widely distributed, is better aligned with opportunities. ...Strategies to enhance a MOSAIC (Maximizing Opportunities for Scientific and Academic Independent Careers) professoriate and diversify the biomedical landscape are discussed.
Discoveries at the frontiers of science and finding solutions to pressing biomedical problems will be accelerated when talent, which is widely distributed, is better aligned with opportunities. Strategies to enhance a MOSAIC (Maximizing Opportunities for Scientific and Academic Independent Careers) professoriate and diversify the biomedical landscape are discussed.
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