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At least 1,351 records · Page 75Linked to original sources
PubMed2004

Evidence that human genes of modular proteins have retained significantly more ancestral introns than their fly or worm orthologues.

Comparison of the exon-intron structures of human, fly and worm orthologues of mosaic genes assembled from class 1-1 modules by exon-shuffling has revealed that human genes retained significantly more of the original inter-module introns than their protostome orthologues. It is suggested that the much higher rate of intron loss in the worm- and insect lineages than in the chordate lineage reflects their greater tendency for genome compaction.

Algorithms↗
PubMed2005

Synthetic modular systems--reverse engineering of signal transduction.

During the last decades, biology has decomposed cellular systems into genetic, functional and molecular networks. It has become evident that these networks consist of components with specific functions (e.g., proteins and genes). This has generated a considerable amount of knowledge and hypotheses concerning cellular organization. The idea discussed here is to test the extent of this knowledge by reconstructing, or reverse engineering, new synthetic biological systems from known components. We will discuss how integration of computational methods with proteomics and engineering concepts might lead us to a deeper and more abstract understanding of signal transduction systems. Designing and successfully introducing synthetic proteins into cellular pathways would provide us with a powerful research tool with many applications, such as development of biosensors, protein drugs and rewiring of biological pathways.

Animals↗
PubMed2005

Complications encountered while using thin-wire-hybrid-external fixation modular frames for fracture fixation. A retrospective clinical analysis and possible support for "Damage Control Orthopaedic Surgery".

One hundred ninety eight adult patients who had sustained long bone fractures were treated by external fixation from admission to bone healing and consolidation. Of these, 135 had sustained high-energy injuries, 39 of them had suffered multi-system injuries. Superficial pin track infection was the most common complication, occurring predominantly in pins located in the femur, upper tibia and upper humerus. There were no cases of deep infection or osteomyelitis. One patient with a femoral shaft fracture developed a DVT although he was on preventive low molecular weight heparin, i.e. sc Clexane 40 mg daily. There were no cases of PE or ARDS. External fixation systems are a minimal invasive surgical modality, which allow three-dimensional fracture fixation after closed or minimal open reduction. They require a good command of surgical anatomy, but provide an optimal preservation of the fracture's soft tissue envelope, the critical biological factor for new bone formation and fracture healing. Recent publications have suggested that in the critically ill patient, minimally invasive fracture fixation surgery may prevent the perpetuation of a reactive, life threatening inflammatory reaction (the "second hit") which may induce the development of multiple organ dysfunction (MODS).

Adult↗
PubMed2004

C1q and tumor necrosis factor superfamily: modularity and versatility.

C1q is the target recognition protein of the classical complement pathway and a major connecting link between innate and acquired immunity. As a charge pattern recognition molecule of innate immunity, C1q can engage a broad range of ligands via its globular (gC1q) domain and modulate immune cells, probably via its collagen region. The gC1q signature domain, also found in many non-complement proteins, has a compact jelly-roll beta-sandwich fold similar to that of the multifunctional tumor necrosis factor (TNF) ligand family. The members of this newly designated 'C1q and TNF superfamily' are involved in processes as diverse as host defense, inflammation, apoptosis, autoimmunity, cell differentiation, organogenesis, hibernation and insulin-resistant obesity. This review is an attempt to draw structural and functional parallels between the members of the C1q and TNF superfamily.

Amino Acid Sequence↗
PubMed2004

Modular structure in developmentally eliminated DNA in Tetrahymena may be a consequence of frequent insertions and deletions.

The work reported here describes insertion-deletion (Indel) polymorphisms in two internally eliminated sequences (IESs, that are deleted during development in Tetrahymena): a 1.8 kb Indel at one end of the 1.1 kb H1 IES and a 0.5 kb Indel inside the 1.4 kb calmodulin (C) IES. These two IESs are located in the proximity of the H1 histone and calmodulin genes, respectively, and are among the ten IESs that have been fully sequenced out of an estimated total of 6000. Three hundred base-pairs of the 1.8 kb H1 Indel are retained in the macronucleus. Both the +Indel and the -Indel variants of the H1 and C IESs that occur in different strains are eliminated during development. Thus, a drastic change involving over half of the deleted sequence and 300 bp of flanking sequence does not disable developmental elimination of the H1 IES, which may indicate a lack of requirement for specific sequences on the Indel side of the IES. The H1 Indel is a composite of three sequence elements: a unique segment and two other sections containing members of different repeat families. One of these, a 0.5 kb repetitive component, is 75% similar to another 0.5 kb sequence that constitutes the C Indel, a sequence present in the middle of the calmodulin IES in some strains, but not in others. Therefore, the C Indel sequence is likely to have been part of a mobile unit, even though it has no obvious features of a transposon. However, sequences similar to the C Indel are present in about 100 copies in the genome. The results suggest that IESs may consist, at least in part, of relatively short modules of repeated sequences that are the source of insertion-deletion polymorphisms among strains of Tetrahymena thermophila.

Animals↗
PubMed2004

Clustering of protein structural fragments reveals modular building block approach of nature.

Structures of peptide fragments drawn from a protein can potentially occupy a vast conformational continuum. We co-ordinatize this conformational space with the help of geometric invariants and demonstrate that the peptide conformations of the currently available protein structures are heavily biased in favor of a finite number of conformational types or structural building blocks. This is achieved by representing a peptides' backbone structure with geometric invariants and then clustering peptides based on closeness of the geometric invariants. This results in 12,903 clusters, of which 2207 are made up of peptides drawn from functionally and/or structurally related proteins. These are termed "functional" clusters and provide clues about potential functional sites. The rest of the clusters, including the largest few, are made up of peptides drawn from unrelated proteins and are termed "structural" clusters. The largest clusters are of regular secondary structures such as helices and beta strands as well as of beta hairpins. Several categories of helices and strands are discovered based on geometric differences. In addition to the known classes of loops, we discover several new classes, which will be useful in protein structure modeling. Our algorithm does not require assignment of secondary structure and, therefore, overcomes the limitations in loop classification due to ambiguity in secondary structure assignment at loop boundaries.

Algorithms↗
PubMed2004

The Escherichia coli twin-arginine translocation apparatus incorporates a distinct form of TatABC complex, spectrum of modular TatA complexes and minor TatAB complex.

The Tat system transports folded proteins across bacterial plasma and plant thylakoid membranes. To date, three key Tat subunits have been identified and mechanistic studies indicate the presence of two types of complex: a TatBC-containing substrate-binding unit and a separate TatA complex. Here, we used blue-native gel electrophoresis and affinity purification to study the nature of these complexes in Escherichia coli. Analysis of solubilized membrane shows that the bulk of TatB and essentially all of the TatC is found in a single 370kDa TatABC complex. TatABC was purified to homogeneity using an affinity tag on TatC and this complex runs apparently as an identical band. We conclude that this is the primary core complex, predicted to contain six or seven copies of TatBC together with a similar number of TatA subunits. However, the data indicate the presence of an additional form of Tat complex containing TatA and TatB, but not TatC; we speculate that this may be an assembly or disassembly intermediate of the translocator. The vast majority of TatA is found in separate complexes that migrate in blue-native gels as a striking ladder of bands with sizes ranging from under 100 kDa to over 500 kDa. Further analysis shows that the bands differ by an average of 34 kDa, indicating that TatA complexes are built largely, but possibly not exclusively, from modules of three or four TatA molecules. The range and nature of these complexes are similar in a TatC mutant that is totally inactive, indicating that the ladder of bands does not stem from ongoing translocation activity, and we show that purified TatA can self-assemble in vitro to form similar complexes. This spectrum of TatA complexes may provide the flexibility required to generate a translocon capable of transporting substrates of varying sizes across the plasma membrane in a folded state.

Arginine↗
PubMed2005

The energy landscape of modular repeat proteins: topology determines folding mechanism in the ankyrin family.

Proteins consisting of repeating amino acid motifs are abundant in all kingdoms of life, especially in higher eukaryotes. Repeat-containing proteins self-organize into elongated non-globular structures. Do the same general underlying principles that dictate the folding of globular domains apply also to these extended topologies? Using a simplified structure-based model capturing a perfectly funneled energy landscape, we surveyed the predicted mechanism of folding for ankyrin repeat containing proteins. The ankyrin family is one of the most extensively studied classes of non-globular folds. The model based only on native contacts reproduces most of the experimental observations on the folding of these proteins, including a folding mechanism that is reminiscent of a nucleation propagation growth. The confluence of simulation and experimental results suggests that the folding of non-globular proteins is accurately described by a funneled energy landscape, in which topology plays a determinant role in the folding mechanism.

Algorithms↗
PubMed2006

Modularity of the transcriptional response of protein complexes in yeast.

A comprehensive study is performed on the condition-dependent expression of genes coding for the components of hand curated multi-protein complexes of the yeast Saccharomyces cerevisiae, in order to identify coherent transcriptional modules within these complexes. Such modules are defined as groups of genes within complexes whose expression profiles under a common set of experimental conditions allow us to discriminate them from random sets of genes. Our analysis reveals that complexes such as the cytoplasmic ribosome, the proteasome and the respiration chain complexes previously characterized as "stable" or "permanent" represent transcriptional modules that are coherently up or down-regulated in many different conditions. Overall however, some level of coherent expression is detected only in 71 out of the total of 113 complexes with at least five different protein components that could be reliably analyzed. Of these, 26 behave as coherently expressed transcriptional modules encompassing all the components of the complex. In another 15, at least half of the components make up such modules and in ten, few or no modules are detected. In an additional 20 complexes coherent expression is detected, but in too few conditions to enable reliable module detection. Interestingly, the transcriptional modules, when detected, often correspond to one or more known sub-complexes with specific functions. Furthermore, detected modules are generally consistent with transcriptional modules identified on the basis of predicted cis-regulatory sequence motifs. Also, groups of genes shared between complexes that carry out related functions tend to be part of overlapping transcriptional modules identified in these complexes. Together these findings suggest that transcriptional modules may represent basic functional and evolutionary building blocs of protein complexes.

Cluster Analysis↗
PubMed2006

Cyclops: new modular software suite for cryo-EM.

Cyclops is a new computer program designed as a graphical front-end that allows easy control and interaction with tasks and programs for 3D reconstruction of biological complexes using cryo-electron microscopy. Cyclops' current plug-ins are designed for automated particle picking and include two new algorithms, automated carbon masking and quaternion based rotation space sampling, which are also presented here. Additional plug-ins are in the pipeline. Cyclops allows straightforward organization and visualization of all data and tasks and allows both interactive and batch-wise processing. Furthermore, it was designed for straightforward implementation in grid architectures. As a front-end to a collection of programs it provides a common interface to these programs, thus enhancing the usability of the suite and the productivity of the user.

Algorithms↗
PubMed2005

Modular transcutaneous functional electrical stimulation system.

A new multipurpose programmable transcutaneous electric stimulator, Compex Motion, was developed to allow users to design various custom-made neuroprostheses, neurological assessment devices, muscle exercise systems, and experimental setups for physiological studies. Compex Motion can generate any arbitrary stimulation sequence, which can be controlled or regulated in real-time using any external sensor or laboratory equipment. Compex Motion originated from the existing Compex 2 electric stimulator, manufactured by a Swiss based company, Compex SA. The Compex Motion stimulator represents a further evolution and expansion of the ETHZ-ParaCare functional electrical stimulation system. This stimulator provides all the advanced functional electrical stimulation (FES) application and control features and can be easily incorporated into any standard rehabilitation program. Compex Motion has successfully been applied as a neuroprosthesis for walking, reaching and grasping in more than 100 stroke and spinal cord injured patients. This system has also been used to strengthen muscles and to investigate muscle properties in able-bodied subjects. Compex Motion is a multipurpose FES system specially designed to promote sharing and exchanging of stimulation protocols, sensors, and user interfaces. To the best of our knowledge an FES system that has similar capabilities does not exist yet.

Adult↗
PubMed2004

A new modular protein of Cryptosporidium parvum, with ricin B and LCCL domains, expressed in the sporozoite invasive stage.

The recombinant SA35 peptide has been described as an antigenic portion of a larger Cryptosporidium parvum protein. We identified and characterized the encoding Cpa135 gene and the entire protein, Cpa135. The Cpa135 gene was found to consist of a single exon of 4671 bp, and the mRNA transcribed in the sporozoites was identified. The predicted 1556 amino-acid protein showed the presence of domains which are widely conserved also in other unrelated phylogenetic groups (i.e. a ricin B and a LCCL motif). Comparison of Cpa135 sequence with genomic and protein databases revealed many related genes in other apicomplexan species and high homology with CCP2 protein from Plasmodium yoelii and Plasmodium berghei. The Cpa135 protein was identified and localized by using a monoclonal antibody (Mab) directed against the SA35 antigen (anti-SA35). In oocyst-sporozoite lysate, the anti-SA35 MAb recognized a 135 kDa protein that forms a protein complex larger than 200 kDa, which is mediated by disulfide bridges. Cpa135 synthesis was up-regulated during the excystation process. After host-cell invasion, Cpa135 gene expression was undetectable up to 48 h, whereas mRNA synthesis was newly observed at 72 h post-infection. The Cpa135 protein was localized in the apical complex, and it was found to be secreted by sporozoites during their gliding. Cpa135 persisted during the intracellular stages of the parasite, and it defined the boundaries of the parasitophorous vacuole in the infected cells. The unique array of domains and the homology with other apicomplexan proteins indicate that the Cpa135 protein is representative of a new family of proteins.

Amino Acid Motifs↗
PubMed2004

Neural responses to Mooney images reveal a modular representation of faces in human visual cortex.

The way in which information about objects is represented in visual cortex remains controversial. One model of human object recognition poses that information is processed in modules, highly specialised for different categories of objects; an opposing model appeals to a distributed representation across a large network of visual areas. We addressed this debate by monitoring activity in face- and object-selective areas while human subjects viewed ambiguous face stimuli (Mooney faces). The measured neural response in the face-selective region of the fusiform gyrus was greater when subjects reported seeing a face than when they perceived the image as a collection of blobs. In contrast, there was no difference in magnetic resonance response between face and no-face perceived events in either the face-selective voxels of the superior temporal sulcus or the object-selective voxels of the parahippocampal gyrus and lateral occipital complex. These results challenge the concept that neural representation of faces is distributed and overlapping and suggest that the fusiform gyrus is tightly linked to the awareness of faces.

Adult↗
PubMed2005

Hemispheric asymmetry, modular variability and age-related changes in the human entorhinal cortex.

The verrucae areae entorhinalis (VAE) are a characteristic feature of the human brain that occupy the anterior and posterolateral parts of the parahippocampal gyri and correspond to the islands of layer II neurons. We analyzed VAE in 60 neurologically normal subjects ranging from 23 to 85 years of age using a casting method. In 10 of these subjects the total number of neurons in the entorhinal islands was estimated stereologically using the optical fractionator. The number and surface area of VAE were higher in the left hemisphere compared with the right, and this leftward asymmetry was highly significant. Regression analysis showed a negative correlation between average VAE area and age in both hemispheres, representing a rate loss of about 800 microm2 per year. The estimated number of neurons obtained with the optical fractionator showed no significant difference between the left and the right hemisphere (468,000+/-144,000 vs. 405,000+/-117,000). There was a highly significant negative correlation between neuron numbers and age in both sides. In addition, clusters of small, undifferentiated layer II neurons ('heterotopias') were frequently observed in the rostral part of the entorhinal cortex in young and elderly adults. Layer II entorhinal neurons are among the first to show neurofibrillary changes during normal aging. The present data confirm the occurrence of age-related neuron loss in the entorhinal cortex. Considering the consistent projections from ipsilateral auditory association areas that, together with Broca's motor-speech area (Brodmann areas 44 and 45), show leftward asymmetry from early infancy (such as Brodmann area 22, planum temporale, and area 52 in the long insular gyrus), we speculate that functional lateralization of the human entorhinal cortex may be associated with specialization for memory processing related to language. Due to the dependence of hippocampal formation on entorhinal projections, this finding is also consistent with the greater capacity of the left hippocampus for verbal episodic memory.

Adult↗
PubMed2006

The structure of a ketoreductase determines the organization of the beta-carbon processing enzymes of modular polyketide synthases.

The structure of the ketoreductase (KR) from the first module of the erythromycin synthase with NADPH bound was solved to 1.79 A resolution. The 51 kDa domain has two subdomains, each similar to a short-chain dehydrogenase/reductase (SDR) monomer. One subdomain has a truncated Rossmann fold and serves a purely structural role stabilizing the other subdomain, which catalyzes the reduction of the beta-carbonyl of a polyketide and possibly the epimerization of an alpha-substituent. The structure enabled us to define the domain boundaries of KR, the dehydratase (DH), and the enoylreductase (ER). It also constrains the three-dimensional organization of these domains within a module, revealing that KR does not make dimeric contacts across the 2-fold axis of the module. The quaternary structure elucidates how substrates are shuttled between the active sites of polyketide synthases (PKSs), as well as related fatty acid synthases (FASs), and suggests how domains can be swapped to make hybrid synthases that produce novel polyketides.

Alcohol Oxidoreductases↗
PubMed2004

Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.

As reconstructed biochemical reaction networks continue to grow in size and scope, there is a growing need to describe the functional modules within them. Such modules facilitate the study of biological processes by deconstructing complex biological networks into conceptually simple entities. The definition of network modules is often based on intuitive reasoning. As an alternative, methods are being developed for defining biochemical network modules in an unbiased fashion. These unbiased network modules are mathematically derived from the structure of the whole network under consideration.

Animals↗
PubMed2006

Beyond faces and modularity: the power of an expertise framework.

Studies of perceptual expertise typically ask whether the mechanisms underlying face recognition are domain specific or domain general. This debate has so dominated the literature that it has masked the more general usefulness of the expertise framework for studying the phenomenon of category specialization. Here we argue that the value of an expertise framework is not solely dependent on its relevance to face recognition. Beyond offering an alternative to domain-specific accounts of face specialization in terms of interactions between experience, task demands, and neural biases, expertise studies reveal principles of perceptual learning that apply to many different domains and forms of expertise. As such the expertise framework provides a unique window onto the functional plasticity of the mind and brain.

Animals↗
PubMed2005

Modular cloning in plant cells.

New plant genes are being discovered at a rapid pace. Yet, in most cases, their precise function remains elusive. The recent advent of recombinational cloning techniques has significantly improved our ability to investigate gene functions systematically. For example, proteins fused with diverse fluorescent tags can be expressed at will using versatile cloning cassettes. In addition, novel binary T-DNA vectors are now available to assemble multiple DNA fragments simultaneously, which greatly facilitate plant cell and protein engineering.

Cloning, Molecular↗