Gene/Protein Disease Symptom Drug Enzyme Compound
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We describe the arrangement of white muscle fibers and tendinous myoseptal structures and the relation of these structures to each other in order to provide an anatomical framework for discussions and experimental research on fish swimming mechanics. For the three major craniate groups, the petromyzontids, myxinids and gnathostomes, we identify three conditions that differ remarkably. Myxinids are characterized by asymmetrical myosepta with long cones. Within a single myoseptum these are connected by collagenous fibers that are almost oriented longitudinally. Distinct tendons are absent in myxinid myosepta. Petromyzontid myosepta lack cones and distinct myoseptal tendons, whereas gnathostomes bear cones and distinct tendinous structures: the lateral band, epineural (epipleural) tendon and myhabdoid tendon. Myoseptal fibers of petromyzontids and myoseptal tendons of gnathostome myosepta are firmly anchored in the skin. Myxinids lack firm myoseptal-skin-connections. Their muscular arrangement is neither comparable to that of petromyzontids nor to that of gnathostomes. The latter two bear archlike arrangements of muscle fibers spanning several segments that are hypothesized to play a role during bending. In gnathostomes, archlike helical muscle fiber arrangements (HMFAs) are present that span the length of several body segments and are multiply intersected by myosepta. Hence, a series of tendinous lateral bands of myosepta is embedded in HMFAs. The posterodorsally oriented HMFAs are underlain by posteroventrally oriented crossing muscle fibers (CMFs). Bending may be generated by contraction of the muscle fibers belonging to an HMFA and the simultaneous counteraction of CMFs. Moving caudally, this anterior muscle fiber arrangement gradually changes, eventually becoming the posterior muscle fiber arrangement. This pattern suggests that the function of the myomeres will also change. Three additional putative roles of myoseptal tendons can be deduced from their relations to white muscle fibers in gnathostomes (and in part in petromyzontids): (1) Posterior transmission of anteriorly generated muscular forces via lateral bands and/or myorhabdoid tendons. These tendons are more robust posteriorly. Anterior and posterior cones appear to play an important role in force transmission. (2) Pulling on collagen fibers of the skin via lateral bands and myorhabdoid tendons, suggesting a transmission of muscular forces that puts the skin into tension. (3) Resisting radial expansion of contracting muscle fibers by epineural (epipleural) tendons. By the latter two mechanisms modulation of body stiffness is likely to be achieved.
Comp Biochem Physiol A Mol Integr Physiol 2002 Dec
PMID:Spatial arrangement of white muscle fibers and myoseptal tendons in fishes. 1248 90

RNA binding proteins often contain multiple arginine glycine repeats, a sequence that is frequently methylated by protein arginine methyltransferases. The role of this posttranslational modification in the life cycle of RNA binding proteins is not well understood. Herein, we report that Sam68, a heteronuclear ribonucleoprotein K homology domain containing RNA binding protein, associates with and is methylated in vivo by the protein arginine N-methyltransferase 1 (PRMT1). Sam68 contains asymmetrical dimethylarginines near its proline motif P3 as assessed by using a novel asymmetrical dimethylarginine-specific antibody and mass spectrometry. Deletion of the methylation sites and the use of methylase inhibitors resulted in Sam68 accumulation in the cytoplasm. Sam68 was also detected in the cytoplasm of PRMT1-deficient embryonic stem cells. Although the cellular function of Sam68 is unknown, it has been shown to export unspliced human immunodeficiency virus RNAs. Cells treated with methylase inhibitors prevented the ability of Sam68 to export unspliced human immunodeficiency virus RNAs. Other K homology domain RNA binding proteins, including SLM-1, SLM-2, QKI-5, GRP33, and heteronuclear ribonucleoprotein K were also methylated in vivo. These findings demonstrate that RNA binding proteins are in vivo substrates for PRMT1, and their methylation is essential for their proper localization and function.
Mol Biol Cell 2003 Jan
PMID:Sam68 RNA binding protein is an in vivo substrate for protein arginine N-methyltransferase 1. 1252 43

The gross, light, and electron microscopic anatomies of the porcine intrinsic cardiac nervous system were investigated in 26 pigs to facilitate functional studies in this model. Gross anatomy: Numerous ganglia and interconnecting nerves (ganglionated plexuses) were found to be concentrated in epicardial fat in five atrial and six ventricular regions. The five atrial ganglionated plexuses identified were (1) the ventral right atrial, (2) the right vena cava-right atrial, (3) the dorsal atrial, (4) the interatrial septal, and (5) the left superior vena cava-left atrial ones. Six ventricular ganglionated plexuses were identified in close proximity to the (1) roots of the aorta and pulmonary artery (craniomedial), extending along the left main coronary artery to the (2) ventral interventricular and (3) circumflex coronary arteries. (4) A ganglionated plexus was identified around the origin of the dorsal interventricular coronary artery, as well as the (5) right main and (6) right marginal coronary arteries. Isolated neurons were identified scattered throughout the cranial interventricular septum. Microscopic anatomy: Approximately 3,000 neuronal somata were estimated to compose this intrinsic cardiac nervous system. Some ganglia contained more than 100 neurons. Neuronal somata had dimensions of roughly 33.1 (short axis) by 46.3 (long axis) microm. Most were multipolar, a small population of unipolar neurons being identified in atrial and ventricular tissues. At the electron microscopic level, asymmetrical axodendritic synapses with small clear, round vesicles were identified, some containing large dense-cored vesicles. In summary, porcine intrinsic cardiac neurons are concentrated in 11 distinct atrial and ventricular ganglionated plexuses. These extensive plexuses, along with fewer scattered neurons, display varied neuronal morphology and synaptology that represent the anatomical substrate for complex information processing within the intrinsic cardiac component of the porcine cardiac neuronal hierarchy. These anatomical data provide a framework for physiological analyses of the porcine intrinsic cardiac nervous system.
Anat Rec A Discov Mol Cell Evol Biol 2003 Mar
PMID:Porcine intrinsic cardiac ganglia. 1255 41

Photodynamic therapy (PDT) is a minimally invasive treatment that can be employed in many human diseases including prostate cancer. PDT for prostate cancer depends on the sequestration of a photosensitizing drug within the glandular tissue. The photosensitizer is subsequently activated by light (usually from a laser) and the active drug destroys tissue. Since prostate cancer is a multifocal disease, PDT must ablate the glandular prostate completely. This will depend on the precise placement of light sources in the prostate and delivery of a therapeutic light dose to the entire gland. Also, sources of light and their spatial distribution must be tailored to each individual patient. The uniform, therapeutic light distribution can be achieved by interstitial light irradiation. In this case, the light is delivered by diffusers placed within the substance of the prostate parallel to the urethra at a distance optimized to deliver adequate levels of light and to create the desired photodynamic effect. To help achieve the uniform light distribution throughout the prostate we have developed a computer program that can determine treatment effects. The program predicts the best set of parameters and the position of light diffusers in space, and displays them in graphical or in numerical form assuming a fixed attenuation coefficient. The two parameters of greatest importance in the computer simulation are attenuation coefficient and critical fluence. Both depend on the concentration of active drug within the prostate gland. It is necessary to know the nature of the spatial distribution of photosensitizer within the prostate to execute computer modeling of PDT with high precision. We found that the concentration of SnET2 is heterogeneous in nature, and is higher in the proximity of the glandular capsule. It is clear therefore that any future attempts of computerized modeling of this procedure must take into consideration the uneven sequestration of photosensitizer and the consequential asymmetrical necrosis of the prostate.
Int J Mol Med 2003 Mar
PMID:Spatial distribution of liposome encapsulated tin etiopurpurin dichloride (SnET2) in the canine prostate: implications for computer simulation of photodynamic therapy. 1257 28

The conformational preferences of cyclosophoroheptadecaose (Cys-A), which is a member of a class of cyclic (1 --> 2)-beta-D-glucan, were characterized by molecular dynamics simulations. Simulated annealing and constant temperature molecular dynamics simulations were performed on the Cys-A. The simulations produced various types of compact and asymmetrical conformations of Cys-A. Excellent agreement was found between experimental data and corresponding values predicted by molecular modeling. Most glycosidic linkages were concentrated in the lowest energy region of phi-psi energy map, and the values of radius of gyration (R(G)) and the nuclear Overhauser effect (NOE) distance data derived from our simulations were finely consistent with the reported experimental values. This result will also give novel insights for the molecular complexation mechanism of Cys-A with various guest chemicals.
J Comput Aided Mol Des
PMID:Molecular dynamics simulation of cyclosophoroheptadecaose (Cys-A). 1260 53

Using airway microdissection and three-dimensional confocal microscopy techniques in combination with the immunomarkers protein gene product (PGP) 9.5 and calcitonin gene-related peptide (CGRP), we defined the distribution of small afferent nerves fibers and all nerves throughout the intrapulmonary airways, along with the distribution of airway neuroendocrine cells and neuroepithelial bodies. We found (i) the presence of CGRP-and PGP 9.5-positive structures along the entire intrapulmonary airway tree of adult rats, (ii) decreasing nerve density from more proximal to more distal generations of conducting airways, (iii) the presence of nerve fibers in terminal bronchioles, (iv) the asymmetrical distribution of nerves within a single generation of intrapulmonary airway with regard to associated vessels, (v) the frequent interchange of single nerve fibers across epithelial and sub-epithelial compartments without termination, and (vi) a definably intimate relationship between afferent nerves and neuroepithelial bodies (NEBs) (i.e., 58% of NEBs studied were observed to have nerve fibers coursing through them, indicating direct connections). We conclude that the distribution of nervous elements (nerve fibers and neuroendocrine cells) within the intrapulmonary airways is highly heterogeneous, varying between airway levels and locally within a specific airway level.
Am J Respir Cell Mol Biol 2003 May
PMID:The three-dimensional distribution of nerves along the entire intrapulmonary airway tree of the adult rat and the anatomical relationship between nerves and neuroepithelial bodies. 1270 15

The body of a Japanese flounder (Paralichthys olivaceus) changes from a symmetrical to an asymmetrical form during metamorphosis. To obtain detailed information on the mechanisms of the migration of the right eye to the left side, soft and hard tissues in the head of larval flounders were examined using transmission electron microscopy (TEM). Retrorbital vesicles (Rvs) are pairs of sac-like structures under the eyes. It has been suggested that the asymmetrical development of Rvs, with the right (blind) one being bigger than the left, is the driving force behind eye migration. The present study revealed that the ultrastructure of the Rv sheath is quite similar to that of a lymphatic capillary. Thus, it is possible that the Rv is a part of the lymph system, and is probably related to the secondary vascular system in teleosts. If we assume that the Rv sheath has a high permeability to liquid, similar to lymphatic capillaries, it is not plausible that the active expansion of the Rv pushes the eyeball. On the other hand, the pseudomesial bar (Pb) is a bone that is unique to flounders and is present only on the right (blind) side. At the beginning of eye migration, an aggregation of fibroblast-like cells is observed in the dermis under the right eye, where the Pb will subsequently be formed. These cells have a well-developed rough endoplasmic reticulum (rER) and mitochondria, and are probably responsible for formation of the thick layers of collagen fibrils around them. Since it is unlikely that the active expansion of the Rv causes eye migration, the role played by the Pb and its rudiment becomes more significant in right eye migration in the Japanese flounder becomes more significant.
Anat Rec A Discov Mol Cell Evol Biol 2003 Jul
PMID:Fine structure of soft and hard tissues involved in eye migration in metamorphosing Japanese flounder (Paralichthys olivaceus). 1280 50

The antibody-binding site is formed as a result of the association between VH and VL domains. Several studies have shown that this association plays an important role in the mechanism of antigen-antibody interaction (Stanfield et al. Structure 1: 83-93, 1993). Considering this, we propose that variations in the VH-VL association are part of the diversification strategy of the antibody repertoires. Previously, a model of association for VH-VL domains based on geometrical characteristics of the packing at the interface was developed by Chothia et al. (J. Mol. Biol. 186: 61-663, 1985). This model includes a common association form for antibodies and a three-layer structure for the interface. In the present work, a complementary model is introduced to account for the general geometrical restrictions of the VH-VL interface, and particular arrangements related to the chemical properties or the side-chain orientations of participating residues. Groups of residues assume common side-chain orientations, which are apparently related to particular functions of different interface zones. Analyses of amino acid usage and network are in agreement with the side-chain orientation patterns. Based on these observations, a three-zone model has evolved to illuminate geometrical and functional restrictions acting over the VH-VL interface. Additionally, this study has revealed the asymmetrical relationships between VH and VL residues important for the association of the two domains.
J Mol Recognit
PMID:An improved model of association for VH-VL immunoglobulin domains: asymmetries between VH and VL in the packing of some interface residues. 1283 65

A DNA sequence-dependent nucleosome structural and dynamic polymorphism was recently uncovered through topoisomerase I relaxation of mononucleosomes on two homologous approximately 350-370 bp DNA minicircle series, one originating from pBR322, the other from the 5S nucleosome positioning sequence. Whereas both pBR and 5S nucleosomes had access to the closed, negatively crossed conformation, only the pBR nucleosome had access to the positively crossed conformation. Simulation suggested this discrepancy was the result of a reorientation of entry/exit DNAs, itself proposed to be the consequence of specific DNA untwistings occurring in pBR nucleosome where H2B N-terminal tails pass between the two gyres. The present work investigates the behavior of the same two nucleosomes after binding of linker histone H5, its globular domain, GH5, and engineered H5 C-tail deletion mutants. Nucleosome access to the open uncrossed conformation was suppressed and, more surprisingly, the ability of 5S nucleosome to positively cross was largely restored. This, together with the paradoxical observation of a less extensive crossing in the negative conformation with GH5 than without, favored an asymmetrical location of the globular domain in interaction with the central gyre and only entry (or exit) DNA, and raised the possibility of the domain physical rotation as a mechanism assisting nucleosome fluctuation from one conformation to the other. Moreover, both negative and positive conformations showed a high degree of loop conformational flexibility in the presence of the full-length H5 C-tail, which the simulation suggested to reflect the unique feature of the resulting stem to bring entry/exit DNAs in contact and parallel. The results point to the stem being a fundamental structural motif directing chromatin higher order folding, as well as a major player in its dynamics.
J Mol Biol 2003 Aug 29
PMID:Linker histone-dependent organization and dynamics of nucleosome entry/exit DNAs. 1292 39

Box C/D small ribonucleoprotein particles (sRNPs) are archaeal homologs of small nucleolar ribonucleoprotein particles (snoRNPs) in eukaryotes that are responsible for site specific 2'-O-methylation of ribosomal and transfer RNAs. The function of box C/D sRNPs is characterized by step-wise assembly of three core proteins around a box C/D RNA that include fibrillarin, Nop5p, and L7Ae. The most distinct structural feature in all box C/D RNAs is the presence of two conserved box C/D motifs accompanied by often a single, and sometimes two, antisense elements located immediately upstream of either the D or D' box. Despite this asymmetric distribution of antisense elements, the bipartite feature of the box C/D motifs appears to be in pleasing agreement with a recently reported three-dimensional structure of the core protein complex between fibrillarin and Nop5p. This investigates functional implications of the symmetric features both in box C/D RNAs and in the fibrillarin-Nop5p complex. Site-directed mutagenesis was employed to generate box C/D RNAs lacking one of the two box C/D motifs and a mutant fibrillarin-Nop5p complex deficient in self-association. The ability of the mutated components to assemble and to direct methyl transfer reactions was assessed by gel mobility-shift, analytical ultracentrifugation, and in vitro catalysis studies. The results presented here suggest that, while a box C/D sRNP is capable of asymmetrical assembly, the symmetries in both the box C/D RNA and in the fibrillarin-Nop5p complex are required for efficient catalysis. These findings underscore the importance of functional assembly in methyl transfer reactions.
J Mol Biol 2003 Oct 17
PMID:Functional requirement for symmetric assembly of archaeal box C/D small ribonucleoprotein particles. 1452 17


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