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Identification and subcellular localization of the soybean copper P1B-ATPase GmHMA8 transporter.

We have identified a copper P(1B)-ATPase transporter in soybean (Glycine max), named as GmHMA8, homologue to cyanobacterial PacS and Arabidopsis thaliana AtHMA8 (PAA2) transporters. A novel specific polyclonal anti-GmHMA8 antibody raised against a synthetic peptide reacted with a protein of an apparent mass of around 180-200 kDa in chloroplast and thylakoid membrane preparations isolated from soybean cell suspensions. Immunoblot analysis with this antibody also showed a band with similar apparent molecular mass in chloroplasts from Lotus corniculatus. Immunofluorescence labelling with the anti-GmHMA8 antibody and double immunofluorescence labelling with anti-GmHMA8 and anti-RuBisCo antibodies revealed the localization of the GmHMA8 transporter within the chloroplast organelle. Furthermore, the precise ultrastructural distribution of GmHMA8 within the chloroplast subcompartments was demonstrated by using electron microscopy immunogold labelling. The GmHMA8 copper transporter from soybean was localized in the thylakoid membranes showing a heterogeneous distribution in small clusters.

Amino Acid Sequence↗

Quantitative measurement of leakage volume and permeability in gliomas, meningiomas and brain metastases with dynamic contrast-enhanced MRI.

The spatial properties and function of the tumor vasculature differ with the tumor type and grade. T1-weighted dynamic contrast-enhanced imaging technique enables the simultaneous quantification of some functional parameters of the vasculature. These are the fractional contrast-enhancing volumes of the tissue compartments (blood volume and leakage/extravascular extracellular volume) and the exchange parameters (perfusion and permeability). The relatively long monitoring duration of 12 min used here made it necessary to divide the extravascular extracellular compartment into two subcompartments, a slowly and a fast enhancing one with different permeabilities. Forty-one gliomas (WHO grades II-IV), six meningiomas and eight distant metastases were investigated. It was shown that the technique noninvasively provides information for separating different tumor types and characterizing their microenvironment. Fast permeability describes vessel permeability and was significantly increased in meningiomas as compared with intra-axial tumors. The corresponding volume of the fast enhancing compartment was significantly increased in meningiomas compared to all gliomas taken together. Slow permeability describes diffusion within the extravascular extracellular space and was significantly reduced in low-grade gliomas, indicating short diffusion distances. The slowly enhancing extravascular extracellular space was found to be increased in high-grade gliomas and distant metastases. Blood volume differed significantly among some tumor entities and glioma grades. Perfusion was shown to increase linearly with blood volume for volumes of up to 20%, flattening out thereafter. The scatter plots of extravascular extracellular volume and blood volume were shown to differ among the tumor entities.

Adolescent↗

Combined MEG/EEG analysis of the interictal spike complex in mesial temporal lobe epilepsy.

We studied the functional organization of the interictal spike complex in 30 patients with mesial temporal lobe epilepsy (MTLE) using combined magnetoencephalography (MEG)/electroencephalography (EEG) recordings. Spikes could be recorded in 14 patients (47%) during the 2- to 3-h MEG/EEG recording session. The MEG and EEG spikes were subjected to separate dipole analyses; the MEG spike dipole localizations were superimposed on MRI scans. All spike dipoles could be localized to the temporal lobe with a clear preponderance in the medial region. Based on dipole orientations in MEG, patients could be classified into two groups: patients with anterior medial vertical (AMV) dipoles, suggesting epileptic activity in the mediobasal temporal lobe and patients with anterior medial horizontal (AMH) dipoles, indicating involvement of the temporal pole and the anterior parts of the lateral temporal lobe. Whereas patients with AMV dipoles had strictly unitemporal interictal and ictal EEG changes during prolonged video-EEG monitoring, 50% of patients with AMH dipoles showed evidence of bitemporal affection on interictal and ictal EEG. Nine patients underwent epilepsy surgery so far. Whereas all five patients with AMV dipoles became completely seizure-free postoperatively (Class Ia), two out of four patients with AMH dipoles experienced persistent auras (Class Ib). This difference, however, was not statistically significant. We therefore conclude that combined MEG/EEG dipole modeling can identify subcompartments of the temporal lobe involved in epileptic activity and may be helpful to differentiate between subtypes of mesial temporal lobe epilepsy noninvasively.

Adult↗

Oldies but goldies: searching for Christmas trees within the nucleolar architecture.

The nucleolus is the prominent nuclear organelle in which the biogenesis of ribosomal RNA and ribosomes takes place. Understanding of the molecular processes in the nucleolus is rapidly expanding; however, opinions and results on the precise localization of active ribosomal genes - in either of two nucleolar subcompartments, fibrillar centers and dense fibrillar components - are still divided. This review discusses the difficulties in studying the nucleolar structure using microscopy, and provides an overview of the published data, critically examining their relevance to the controversy. Additionally, evidence showing that the dense fibrillar components encompass the Christmas tree structures is discussed and ways to reconcile the controversy are proposed.

Animals↗

Nuclear tumor suppressors in space and time.

Numerous studies have identified key binding partners and functional activities of nuclear tumor-suppressor proteins such as the retinoblastoma protein, p53 and BRCA1. Historically, less attention has been given to the subnuclear locations of these proteins. Here, we describe several recent studies that promote the view that regulated association with subcompartments of the nucleus is inherent to tumor-suppressor function.

Animals↗

Regulated compartmentalization of the putative DEAD-box helicase MDDX28 within the mitochondria in COS-1 cells.

We recently cloned a putative DEAD-box helicase MDDX28 and found that it was localized to the nuclei and mitochondria of COS-1 cells. The mitochondrial localization of MDDX28 is largely diffuse. We have, however, used immunofluorescence and immunogold cytochemistry to show that the MDDX28 protein is localized in a distinct mitochondrial subcompartment in 5-10% of COS-1 cells. This proportion increases to approximately 35% after treatment with ethidium bromide, suggesting upregulation following transcription inhibition. To our knowledge, this is the first example of protein relocation in the mitochondria caused by transcription inhibition. The mitochondrial subcompartmentation of MDDX28 was negatively affected by mutations in a RNA-binding domain and three basic domains previously shown to be important in transcription-dependent intranuclear localization. Furthermore, immunogold cytochemistry and fractionation of rat liver indicated that the protein is a part of an RNA-protein (RNP) complex interacting peripherally with the mitochondrial inner membrane. Our results reveal new principles for regulation of protein localization in the mitochondria and suggest parallels between the function of the MDDX28 protein in the nucleus and mitochondria.

Animals↗

Nuclear RNAs confined to a reticular compartment between chromosome territories.

RNA polymerase II transcripts are confined to nuclear compartments. A detailed analysis of the nuclear topology of RNA from individual genes was performed for transcripts from the marker gene coding for chloramphenicol acetyltransferase, expressed at a high level from the HTLV-1 LTR promoter. The construct was transfected into A293 cells where the RNA was organized as an extensive reticular network. We also studied the RNA distribution from combinations of neighboring HIV and bacterial resistance genes that co-integrated within the genome of COS-7 cells-revealing spherical or track-like accumulations of RNA that were extensively branched. There were many nuclei with distinct but overlapping RNA accumulations. Since the coding genes localized at the overlapping points, the RNAs are synthesized at a common region and diverge. The correlation between the frequency of the separation of the transcripts and the physical distance of the respective genes suggests a subcompartmentalization in the microenvironment of genes on the basis of geometric parameters. Thus, the more distant the genes are on the same chromosome, the more likely they are confined to separated subcompartments of an extensive reticular system. Co-delineation of the RNA transcripts with Cajal bodies and chromosome territories indicated the organization of nuclear RNA transcripts in a reticular interchromosome domain compartment.

Animals↗

Tvp38, Tvp23, Tvp18 and Tvp15: novel membrane proteins in the Tlg2-containing Golgi/endosome compartments of Saccharomyces cerevisiae.

Four previously uncharacterized proteins (Tvp38, Tvp23, Tvp18 and Tvp15) were found in Tlg2-containing membrane by proteomic analysis of immunoisolated Golgi subcompartments of Saccharomyces cerevisiae (Inadome et al., Mol. Cell. Biol., 25 (2005) 7696-7710). Immunofluorescence double staining of HA-tagged Tvp proteins and myc-tagged tSNAREs supported that these proteins mainly localize in the Tlg2-containing compartments. Conserved sequences of Tvp38, Tvp23 and Tvp18 are found in higher eukaryotes, but these homologues have not been characterized yet. All Tvp proteins were nonessential for growth under laboratory conditions. Immunoprecipitation of Tvp proteins indicated that Tvp23, Tvp18 and Tvp15 are in an interactive network with Yip1-family proteins, Yip4 and Yip5. They may collectively assist in the effective maintenance/function of the late Golgi/endosomal compartments. Disruptions of tvp15 and tvp23 showed synthetic aggravation with ypt6 or ric1 null mutation. Processing of carboxypeptidase Y and alkaline phosphatase in tvp disruptants occurred as in the wild type.

Adaptor Proteins, Signal Transducing↗

Highly tissue substructure-specific effects of human papilloma virus in mucosa of HIV-infected patients revealed by laser-dissection microscopy-assisted gene expression profiling.

Human papilloma virus (HPV) causes focal infections of epithelial layers in skin and mucosa. HIV-infected patients on highly active antiretroviral therapy (HAART) appear to be at increased risk of developing HPV-induced oral warts. To identify the mechanisms that allow long-term infection of oral epithelial cells in these patients, we used a combination of laser-dissection microscopy (LDM) and highly sensitive and quantitative, non-biased, two-step multiplex real-time RT-PCR to study pathogen-induced alterations of specific tissue subcompartments. Expression of 166 genes was compared in three distinct epithelial and subepithelial compartments isolated from biopsies of normal mucosa from HIV-infected and non-infected patients and of HPV32-induced oral warts from HIV-infected patients. In contrast to the underlying HIV infection and/or HAART, which did not significantly elaborate tissue substructure-specific effects, changes in oral warts were strongly tissue substructure-specific. HPV 32 seems to establish infection by selectively enhancing epithelial cell growth and differentiation in the stratum spinosum and to evade the immune system by actively suppressing inflammatory responses in adjacent underlying tissues. With this highly sensitive and quantitative method tissue-specific expression of hundreds of genes can be studied simultaneously in a few cells. Because of its large dynamic measurement range it could also become a method of choice to confirm and better quantify results obtained by microarray analysis.

Adult↗

Prostate stem cell compartments: expression of the cell cycle inhibitor p27Kip1 in normal, hyperplastic, and neoplastic cells.

The stem cells of rapidly renewing tissues give rise to transiently proliferating cells, which in turn give rise to postmitotic terminally differentiated cells. Although the existence of a transiently proliferating compartment has been proposed for the prostate, little molecular anatomical evidence for its presence has been obtained to date. We used down-regulation of the cyclin-dependent kinase inhibitor p27Kip1 to identify cells capable of entering the proliferative phase of the cell cycle and, therefore, competent to fulfill the role of the transiently proliferating compartment. We examined the expression of p27Kip1 in relation to its role in the development of prostatic carcinoma. Formalin-fixed paraffin-embedded specimens from matched samples of normal-appearing prostate tissue, benign prostatic hyperplasia, high-grade prostatic intraepithelial neoplasia, primary adenocarcinomas, and pelvic lymph node metastases were evaluated by comparative immunohistochemistry against p27Kip1. In normal-appearing prostate epithelium, moderate to strong nuclear staining of p27Kip1 was present in greater than 85% of the terminally differentiated secretory cells. The normal basal cell compartment, believed to contain prostatic stem cells, showed distinctive p27Kip1 expression; acini in epithelial benign prostatic hyperplasia tissue contained more p27Kip1-negative basal cells than acini from non-benign prostatic hyperplasia tissue. A third layer of cells was identified that was sandwiched between the basal cells and the luminal cells, and this layer was consistently p27Kip1 negative. This intermediate layer was accentuated in the periurethral region, as well as in prostate tissue that had been subjected to prior combined androgen blockade. We hypothesize that, on appropriate additional mitogenic stimulation, cells in this layer, and other p27Kip1-negative basal cells, are competent for rapid entry into the cell cycle. Consistent with the fact that cancer cells are capable of cell division, all cases of high-grade prostatic intraepithelial neoplasia and invasive carcinoma also showed down-regulation of p27Kip1 as compared with the surrounding normal-appearing secretory cells. In pelvic lymph node metastases, p27Kip1 expression was also reduced. In summary, our results suggest that lack of nuclear p27Kip1 protein may delineate a potential transiently proliferating subcompartment within the basal cell compartment of the human prostate. In addition, these studies support the hypothesis that reduced expression of p27Kip1 removes a block to the cell cycle in human prostate epithelial cells and that dysregulation of p27Kip1 protein levels may be a critical early event in the development of prostatic neoplasia.

Adenocarcinoma↗

What fuels polypeptide translocation? An energetical view on mitochondrial protein sorting.

Protein sorting into mitochondria is achieved by the concerted action of at least four translocation complexes. Vectorial transport of polypeptide chains by these complexes requires different driving forces. In particular, Deltapsi, matrix adenosine triphosphate and the free energy of the binding to other protein components are used in series to achieve sorting of proteins to the various mitochondrial subcompartments. The processes providing the translocation energy are presented in this review and their impact for protein sorting into and within mitochondria is discussed.

Adenosine Triphosphatases↗

Identification and characterization of a novel murine multigene family containing a PHD-finger-like motif.

The genes Phf5a and Phf5b-ps are the first two members of a novel murine multigene family that is highly conserved during evolution and belongs to the superfamily of PHD-finger genes. The Phf5 gene family contains an active locus on mouse chromosome 15, region E and several processed pseudogenes on different chromosomes. The active locus, Phf5a, is expressed ubiquitously in pre- and postnatal murine tissues and encodes a protein of 110 amino acids. The protein is localized in the nucleus in a non-homogenous pattern as the nucleolar subcompartment is almost free of Phf5a. The molecular and biological functions of Phf5a are unknown up-to-date, but the systematic deletion of its yeast homolog is lethal, pointing out that the protein is required for cell viability. Interpretation of our data and review of the literature suggest both basic and essential cellular functions of the Phf5a protein, possibly acting as a chromatin-associated protein.

3T3 Cells↗

Electron tomography of frozen-hydrated isolated triad junctions.

Cryoelectron microscopy and tomography have been applied for the first time to isolated, frozen-hydrated skeletal muscle triad junctions (triads) and terminal cisternae (TC) vesicles derived from sarcoplasmic reticulum. Isolated triads were selected on the basis of their appearance as two spherical TC vesicles attached to opposite sides of a flattened vesicle derived from a transverse tubule (TT). Foot structures (ryanodine receptors) were resolved within the gap between the TC vesicles and TT vesicles, and some residual ordering of the receptors into arrays was apparent. Organized dense layers, apparently containing the calcium-binding protein calsequestrin, were found in the lumen of TC vesicles underlying the foot structures. The lamellar regions did not directly contact the sarcoplasmic reticulum membrane, thereby creating an approximately 5-nm-thick zone that potentially constitutes a subcompartment for achieving locally elevated [Ca(2+) ] in the immediate vicinity of the Ca(2+)-conducting ryanodine receptors. The lumen of the TT vesicles contained globular mass densities of unknown origin, some of which form cross-bridges that may be responsible for the flattened appearance of the transverse tubules when viewed in cross-section. The spatial relationships among the TT membrane, ryanodine receptors, and calsequestrin-containing assemblage are revealed under conditions that do not use dehydration, heavy-metal staining, or chemical fixation, thus exemplifying the potential of cryoelectron microscopy and tomography to reveal structural detail of complex subcellular structures.

Animals↗

Axonal projections and synapses from the supratrigeminal region to hypoglossal motoneurons in the rat.

Neural circuits from the supratrigeminal region (Vsup) to the hypoglossal motor nucleus were studied in rats using anterograde and retrograde neuroanatomical tracing methodologies. Iontophoretic injection of 10% biotinylated dextran amine (BDA) unilaterally into the Vsup anterogradely labeled axons and axon terminals bilaterally in the hypoglossal nucleus (XII) as well as other regions of the brainstem. In the ipsilateral XII, the highest density of BDA labeling was found in the dorsal compartment and the ventromedial subcompartment of the ventral compartment, where BDA labeling formed a dense, patchy distribution. Microinjection of 20% horseradish peroxidase (HRP) ipsilaterally or bilaterally into the tongue resulted in retrograde labeling of XII motoneurons confined to the dorsal and ventral compartments of the hypoglossal motor nucleus. Under light microscopical examination, BDA-labeled terminals were observed closely apposing the somata and primary dendrites of HRP-labeled hypoglossal motoneurons. Two hundred and sixty-five of these BDA-labeled terminals were examined at the ultrastructural level. One hundred and twelve BDA-labeled axon terminals were observed synapsing with either the somata (39%, 44/112) or the large or medium-size dendrites (61%, 68/112) of retrogradely labeled hypoglossal motoneurons. Axon terminals containing spherical vesicles (S-type) formed asymmetric synapses with HRP-labeled hypoglossal motoneuron dendrites. In contrast to this, F(F)-type axon terminals, containing flattened vesicles, formed symmetric synapses with both the somata and dendrites of HRP-labeled hypoglossal motoneurons with a preponderance of the contacts on their somata. Axon terminals containing pleomorphic vesicles (F(P)-type) were noted forming both symmetric and asymmetric synapses with HRP-labeled hypoglossal motoneuron somata and dendrites. The present study provides anatomical evidence of neuronal projections and synaptic connections from the supratrigeminal region to hypoglossal motoneurons. These data suggest that the supratrigeminal region, as one of the premotor neuronal pools of the hypoglossal nucleus, may coordinate and modulate the activity of tongue muscles during oral motor behaviors.

Animals↗

Light and electron microscopic observations of a direct projection from mesencephalic trigeminal nucleus neurons to hypoglossal motoneurons in the rat.

A direct projection from rat mesencephalic trigeminal nucleus (Vme) neurons to the hypoglossal nucleus (XII) motoneurons was studied using a double labeling method of anterogradely biotinylated dextran amine (BDA) tracing combined with retrogradely horseradish peroxidase (HRP) transport at both light and electron microscopic levels. BDA was iontophoresed unilaterally into the caudal Vme, and 7 days later HRP was injected into the ipsilateral tongue to label hypoglossal motoneurons. The BDA-labeled fibers were seen descended along Probst' tract and were traced to the caudal medulla. In this course, the fibers gave off axon collaterals bearing varicosities in the trigeminal motor nucleus (Vmo), the parvicellular reticular formation (PCRt), the dorsomedial portions of the subnuclei of oralis (Vodm) and interpolaris (Vidm) and in the XII ipsilaterally. The labeling of terminals was most dense in the PCRt at the levels of caudal pons and rostral medulla, which displayed a "dumbbell-shaped" form in the transverse planes. In the XII, labeled terminals were distributed mainly in the dorsal compartment of the nucleus. One hundred sixty-eight appositions made by BDA-labeled terminals on HRP-labeled motoneurons were seen in the dorsal compartment (71%) and in the lateral subcompartment (24%) of the ventral XII. Under electron microscopy BDA-labeled boutons containing clear, spherical synaptic vesicles were found to form synaptic contacts with the somata and dendrites of hypoglossal motoneurons with asymmetric specializations. The present study provides new evidence that the trigeminal proprioceptive afferent neurons terminate in the XII and make synaptic contacts with their motoneurons.

Animals↗

Localization of translational components at the ultramicroscopic level at postsynaptic sites of the rat brain.

We investigated the localization of components of translational machinery and their regulators in the postsynaptic region. We examined several components, especially those involved in translational regulation: components of (1) MAPK-Mnk-eIF4E, (2) PI3-kinase-PDK-Akt/PKB-FRAP/mTOR-PHAS/4EBP, (3) p70S6K-S6 ribosomal protein and (4) eEF2 kinase/CaMKIII-eEF2 pathways. Western blotting detected all the components examined in the synaptic fractions, and their differential localization to the synaptic subcompartments: initiation or elongation factors, except for eIF5, were detected predominantly in the dendritic lipid raft fraction, which contained ER marker proteins. In contrast, most of their regulatory kinases were distributed to both the postsynaptic density (PSD) and the dendritic lipid raft fractions, or enriched in the former fraction. Localization of eIF4E at synaptic sites was further examined immunohistochemically at the electron microscopic level. The eIF-4E-immunoreactivity was localized to the postsynaptic sites, especially to the microvesicle-like structures underneath the postsynaptic membrane in the spine, some of which were localized in close proximity to PSD. These results suggest that the postsynaptic local translational system, in at least four major regulatory pathways, is similar to those in the perinuclear one, and that it takes place, at least partly, immediately beneath the postsynaptic membrane. The results also suggest the presence of ER-associated type of translational machinery at the postsynaptic sites.

Animals↗

Calretinin and calbindin-D28k in dopaminergic neurons of the rat midbrain: a triple-labeling immunohistochemical study.

We used triple-labeling immunohistochemistry in rat midbrain sections to identify dopaminergic neurons that contain either one or both of the calcium-binding proteins, calretinin (CR) and calbindin-D28k (CB). Midbrain dopaminergic neurons were immunohistochemically labeled for tyrosine hydroxylase (TH), CR, and CB. In the substantia nigra pars compacta (SNC), TH+/CR+/CB+ cells were clustered in two regions: the dorsal tier of the rostral SNC and the medial part of the intermediate SNC. The ventral tier of the rostral SNC mainly comprised both TH+/CR+/CB- and TH+/CR-/CB- cells. The lateral part of the intermediate SNC and the caudal SNC primarily consisted of TH+/CR-/CB- cells. Throughout the extent of the SNC, approximately half of the TH+ neurons were stained for neither CR nor CB, while the remaining TH+ populations were labeled for CR and/or CB. Throughout the ventral tegmental area, TH+/CR+/CB+ cells, TH+/CR+/CB- cells, TH+/CR-/CB+ cells, and TH+/CR-/CB- cells were found generally scattered, though the TH+/CR-/CB- cells were dominant in number. In the substantia nigra pars lateralis, interfascicular nucleus, and caudal linear nucleus, more than half of the TH+ cells were stained for both CR and CB. In the retrorubral field, two-thirds of the TH+ neurons contained neither protein. The present findings suggest that the SNC can be divided into subcompartments based on the distribution of dopaminergic neurons that contain calcium-binding proteins. Furthermore, because CR and CB likely contribute to calcium homeostasis by buffering intracellular calcium concentrations, midbrain dopaminergic neurons containing one or both of these calcium-binding proteins may have a higher calcium-buffering capacity than those lacking the two proteins.

Animals↗

The kinetics of V-J joining throughout 3.5 megabases of the mouse Ig kappa locus fit a constrained diffusion model of nuclear organization.

To gain insight into the nuclear organization of the mouse Ig kappa locus and how it may relate to the formation of synapses during recombination, we have studied the kinetics of rearrangement of different V kappa gene families to J kappa gene segments in the pre-B cell line, 103bcl2. Remarkably, V kappa gene families separated by more than 3.5 Mb from J kappa gene segments rearranged with nearly identical kinetics to those as close as 18 kb to J kappa gene segments. These results fit a model of nuclear organization in which the entire V kappa J kappa region resides within a single nuclear subcompartment and is capable of exhibiting multiple reversible contacts through diffusion and Brownian motion.

Animals↗