bluuebunny/crossref_metadata_2025 huggingface dataset:
Mutations Affecting the MA Portion of the v-Abl Protein Reveal a Conserved Role of Gag in Abelson Murine Leukemia Virus (MLV) and Moloney MLV
Authors: Yi Chae-ryun , Rosenberg Naomi
Published: March 2008

Abelson murine leukemia virus (Ab-MLV) arose from a recombination between
gag
sequences in Moloney MLV (Mo-MLV) and the c-
abl
proto-oncogene. The v-Abl oncoprotein encoded by Ab-MLV contains MA, p12, and a portion of CA sequences derived from the
gag
gene of Mo-MLV. Previous studies indicated that alteration of MA sequences affects the biology of Mo-MLV and Ab-MLV. To understand the role of these sequences in Ab-MLV transformation more fully, alanine substitution mutants that affect Mo-MLV replication were examined in the context of Ab-MLV. Mutations affecting Mo-MLV replication decreased transformation, while alanine mutations in residues dispensable for Mo-MLV replication did not. The altered v-Abl proteins displayed aberrant subcellular localization that correlated to transformation defects. Immunofluorescent analyses suggested that aberrant trafficking of the altered proteins and improper interaction with components of the cytoskeleton were involved in the phenotype. Similar defects in localization were observed when the Gag moiety containing these mutations was expressed in the absence of
abl
-derived sequences. These results indicate that MA sequences within the Gag moiety of the v-Abl protein contribute to proper localization by playing a dominant role in trafficking of the v-Abl molecule.
Comparison of Cellular Ribonucleoprotein Complexes Associated with the APOBEC3F and APOBEC3G Antiviral Proteins
Authors: Gallois-Montbrun Sarah , Holmes Rebecca K. , Swanson Chad M. , Fernández-Ocaña Mireia , Byers Helen L. , Ward Malcolm A. , Malim Michael H.
Published: March 2008

The human apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3F (APOBEC3F [A3F]) and A3G proteins are effective inhibitors of infection by various retroelements and share ∼50% amino acid sequence identity. We therefore undertook comparative analyses of the protein and RNA compositions of A3F- and A3G-associated ribonucleoprotein complexes (RNPs). Like A3G, A3F is found associated with a complex array of cytoplasmic RNPs and can accumulate in RNA-rich cytoplasmic microdomains known as mRNA processing bodies or stress granules. While A3F RNPs display greater resistance to disruption by RNase digestion, the major protein difference is the absence of the Ro60 and La autoantigens. Consistent with this, A3F RNPs also lack a number of small polymerase III RNAs, including the RoRNP-associated Y RNAs, as well as 7SL RNA. Alu RNA is, however, present in A3F and A3G RNPs, and both proteins suppress Alu element retrotransposition. Thus, we define a number of subtle differences between the RNPs associated with A3F and A3G and speculate that these contribute to functional differences that have been described for these proteins.
Plasma Membrane Microdomains Containing Vesicular Stomatitis Virus M Protein Are Separate from Microdomains Containing G Protein and Nucleocapsids
Authors: Swinteck B. Dancho , Lyles Douglas S.
Published: March 2008

Immunogold electron microscopy and analysis were used to determine the organization of the major structural proteins of vesicular stomatitis virus (VSV) during virus assembly. We determined that matrix protein (M protein) partitions into plasma membrane microdomains in VSV-infected cells as well as in transfected cells expressing M protein. The sizes of the M-protein-containing microdomains outside the virus budding sites (50 to 100 nm) were smaller than those at sites of virus budding (approximately 560 nm). Glycoprotein (G protein) and M protein microdomains were not colocalized in the plasma membrane outside the virus budding sites, nor was M protein colocalized with microdomains containing the host protein CD4, which efficiently forms pseudotypes with VSV envelopes. These results suggest that separate membrane microdomains containing either viral or host proteins cluster or merge to form virus budding sites. We also determined whether G protein or M protein was colocalized with VSV nucleocapsid protein (N protein) outside the budding sites. Viral nucleocapsids were observed to cluster in regions of the cytoplasm close to the plasma membrane. Membrane-associated N protein was colocalized with G protein in regions of plasma membrane of approximately 600 nm. In contrast to the case for G protein, M protein was not colocalized with these areas of nucleocapsid accumulation. These results suggest a new model of virus assembly in which an interaction of VSV nucleocapsids with G-protein-containing microdomains is a precursor to the formation of viral budding sites.
Upregulation of the TLR3 Pathway by Kaposi's Sarcoma-Associated Herpesvirus during Primary Infection
Authors: West John , Damania Blossom
Published: March 2008

Kaposi's sarcoma-associated herpesvirus (KSHV) is associated with several different human malignancies, including Kaposi's sarcoma, primary effusion lymphoma, and multicentric Castleman's disease. KSHV establishes lifelong latency in the host and modulates the host immune response. Innate immunity is critical for controlling de novo viral infection. Toll-like receptors (TLRs) are key components of the innate immune system, and they serve as pathogen recognition receptors that stimulate the host antiviral response. In particular, TLR3 has been implicated in RNA virus recognition. Currently, there is no information regarding how KSHV infection modulates any TLR pathway. We report the first evidence that KSHV upregulates TLR3 expression in human monocytes during primary infection. This is also the first demonstration of a human DNA tumor virus upregulating TLR3, a TLR that thus far has been associated with the recognition of RNA viruses. We found that KSHV upregulates the TLR3 pathway and induces TLR3-specific cytokines and chemokines, including beta 1 interferon (IFN-β1) and CXCL10 (IP-10). Small interfering RNAs directed against TLR3 greatly reduced the ability of KSHV to upregulate IFN-β1 and CXCL10 upon infection.
Proteomics Analysis Unravels the Functional Repertoire of Coronavirus Nonstructural Protein 3
Authors: Neuman Benjamin W. , Joseph Jeremiah S. , Saikatendu Kumar S. , Serrano Pedro , Chatterjee Amarnath , Johnson Margaret A. , Liao Lujian , Klaus Joseph P. , Yates John R. , Wüthrich Kurt , Stevens Raymond C. , Buchmeier Michael J. , Kuhn Peter
Published: March 2008

Severe acute respiratory syndrome (SARS) coronavirus infection and growth are dependent on initiating signaling and enzyme actions upon viral entry into the host cell. Proteins packaged during virus assembly may subsequently form the first line of attack and host manipulation upon infection. A complete characterization of virion components is therefore important to understanding the dynamics of early stages of infection. Mass spectrometry and kinase profiling techniques identified nearly 200 incorporated host and viral proteins. We used published interaction data to identify hubs of connectivity with potential significance for virion formation. Surprisingly, the hub with the most potential connections was not the viral M protein but the nonstructural protein 3 (nsp3), which is one of the novel virion components identified by mass spectrometry. Based on new experimental data and a bioinformatics analysis across the
Coronaviridae
, we propose a higher-resolution functional domain architecture for nsp3 that determines the interaction capacity of this protein. Using recombinant protein domains expressed in
Escherichia coli
, we identified two additional RNA-binding domains of nsp3. One of these domains is located within the previously described SARS-unique domain, and there is a nucleic acid chaperone-like domain located immediately downstream of the papain-like proteinase domain. We also identified a novel cysteine-coordinated metal ion-binding domain. Analyses of interdomain interactions and provisional functional annotation of the remaining, so-far-uncharacterized domains are presented. Overall, the ensemble of data surveyed here paint a more complete picture of nsp3 as a conserved component of the viral protein processing machinery, which is intimately associated with viral RNA in its role as a virion component.
Surface Loop Dynamics in Adeno-Associated Virus Capsid Assembly
Authors: DiPrimio Nina , Asokan Aravind , Govindasamy Lakshmanan , Agbandje-McKenna Mavis , Samulski R. Jude
Published: March 2008

The HI loop is a prominent domain on the adeno-associated virus (AAV) capsid surface that extends from each viral protein (VP) subunit overlapping the neighboring fivefold VP. Despite the highly conserved nature of the residues at the fivefold pore, the HI loops surrounding this critical region vary significantly in amino acid sequence between the AAV serotypes. In order to understand the role of this unique capsid domain, we ablated side chain interactions between the HI loop and the underlying EF loop in the neighboring VP subunit by generating a collection of deletion, insertion, and substitution mutants. A mutant lacking the HI loop was unable to assemble particles, while a substitution mutant (10 glycine residues) assembled particles but was unable to package viral genomes. Substitution mutants carrying corresponding regions from AAV1, AAV4, AAV5, and AAV8 yielded (i) particles with titers and infectivity identical to those of AAV2 (AAV2 HI1 and HI8), (ii) particles with a decreased virus titer (1 log) but normal infectivity (HI4), and (iii) particles that synthesized VPs but were unable to assemble into intact capsids (HI5). AAV5 HI is shorter than all other HI loops by one amino acid. Replacing the missing residue (threonine) in AAV2 HI5 resulted in a moderate particle assembly rescue. In addition, we replaced the HI loop with peptides varying in length and amino acid sequence. This region tolerated seven-amino-acid peptide substitutions unless they spanned a conserved phenylalanine at amino acid position 661. Mutation of this highly conserved phenylalanine to a glycine resulted in a modest decrease in virus titer but a substantial decrease (1 log order) in infectivity. Subsequently, confocal studies revealed that AAV2 F661G is incapable of efficiently completing a key step in the infectious pathway nuclear entry, hinting at a possible perturbation of VP1 phospholipase activity. Molecular modeling studies with the F661G mutant suggest that disruption of interactions between F661 and an underlying P373 residue in the EF loop of the neighboring subunit might adversely affect incorporation of the VP1 subunit at the fivefold axis. Western blot analysis confirmed inefficient incorporation of VP1, as well as a proteolytically processed VP1 subunit that could account for the markedly reduced infectivity. In summary, our studies show that the HI loop, while flexible in amino acid sequence, is critical for AAV capsid assembly, proper VP1 subunit incorporation, and viral genome packaging, all of which implies a potential role for this unique surface domain in viral infectivity.
Contribution of CD8+T Cells to Containment of Viral Replication and Emergence of Mutations inMamu-A*01-Restricted Epitopes in Simian Immunodeficiency Virus-Infected Rhesus Monkeys
Authors: Kim Eun-Young , Veazey Ronald S. , Zahn Roland , McEvers Kimberly J. , Baumeister Susanne H. C. , Foster Gabriel J. , Rett Melisa D. , Newberg Michael H. , Kuroda Marcelo J. , Rieber E. Peter , Piatak Michael , Lifson Jeffrey D. , Letvin Norman L. , Wolinsky Steven M. , Schmitz Jörn E.
Published: March 2008

Here, we investigated the containment of virus replication in simian immunodeficiency virus (SIV) infection by CD8+lymphocytes. Escape mutations inMamu-A*01epitopes appeared first in SIV Tat TL8 and then in SIV Gag p11C. The appearance of escape mutations in SIV Gag p11C was coincident with compensatory changes outside of the epitope. Eliminating CD8+lymphocytes from rhesus monkeys during primary infection resulted in more rapid disease progression that was associated with preservation of canonical epitopes. These results confirm the importance of cytotoxic T cells in controlling viremia and the constraint on epitope sequences that require compensatory changes to go to fixation.
Very rare aetiology of giant popliteal pseudoaneurysm: anterior cruciate ligament surgery
Authors: Kanko M , Buluc L , Yavuz S , Muezzinoglu S , Berki T
Published: March 2008

There are various causes of the formation of arterial pseudoaneurysms, including trauma, surgical procedures, infection and iatrogenic injuries. A popliteal aneurysm was detected in a patient with pain and discomfort in his leg. The patient had a history of knee surgery. The aneurysm was treated surgically. Aneurysms following penetrating arterial injury resulting from surgical intervention requiring the use of surgical devices is one of the possible traumatic causes.
Severe asthma: approach and management
Authors: Reddy R C
Published: March 2008

Management of severe asthma remains a significant challenge. Patients with this condition do not respond adequately to inhaled corticosteroids and bronchodilators, forcing a search for alternative strategies. The clinician's initial priority is to firmly establish the diagnosis of severe asthma, as many conditions can mimic and/or aggravate this disease. Once the diagnosis is confirmed and confounding variables addressed, a variety of pharmacological and non-pharmacological approaches must be considered. Continuous use of oral corticosteroids carries a risk of significant adverse effects. Leukotriene modifiers and antibodies to IgE are effective for some patients but not for many others. Alternative anti-inflammatory drugs and novel or unconventional modalities may also be used. Although severe asthma remains a clinical dilemma, a rational diagnostic and therapeutic strategy can be used to improve patient outcomes.
An update on cardioembolic stroke
Authors: Weir N U
Published: March 2008

About one-fifth of all ischaemic strokes are cardioembolic. Recent years have seen considerable progress in our understanding of atrial fibrillation, the most important cause of cardioembolism, and evidence-based treatment strategies have emerged. Progress in relation to other cardioembolic disorders has been more limited and here stroke prevention strategies remain less certain and subject to debate. This article briefly reviews the methods currently used to identify and investigate cardioembolic stroke and then provides an update on stroke prevention in relation to atrial fibrillation, valvular heart disease, patent foramen ovale and left ventricular dysfunction (after myocardial infarction and chronic failure).
Mechanism and Regulation of Class Switch Recombination
Authors: Stavnezer Janet , Guikema Jeroen E.J. , Schrader Carol E.
Published: March 2008

Antibody class switching occurs in mature B cells in response to antigen stimulation and costimulatory signals. It occurs by a unique type of intrachromosomal deletional recombination within special G-rich tandem repeated DNA sequences [called switch, or S, regions located upstream of each of the heavy chain constant (CH) region genes, except Cδ]. The recombination is initiated by the B cell–specific activation-induced cytidine deaminase (AID), which deaminates cytosines in both the donor and acceptor S regions. AID activity converts several dC bases to dU bases in each S region, and the dU bases are then excised by the uracil DNA glycosylase UNG; the resulting abasic sites are nicked by apurinic/apyrimidinic endonuclease (APE). AID attacks both strands of transcriptionally active S regions, but how transcription promotes AID targeting is not entirely clear. Mismatch repair proteins are then involved in converting the resulting single-strand DNA breaks to double-strand breaks with DNA ends appropriate for end-joining recombination. Proteins required for the subsequent S-S recombination include DNA-PK, ATM, Mre11-Rad50-Nbs1, γH2AX, 53BP1, Mdc1, and XRCC4-ligase IV. These proteins are important for faithful joining of S regions, and in their absence aberrant recombination and chromosomal translocations involving S regions occur.
Differentiation-dependent changes in the membrane properties of fiber cells isolated from the rat lens
Authors: Webb Kevin F. , Donaldson Paul J.
Published: March 2008

Impedance measurements in whole lenses showed that lens fiber cells possess different permeability properties to the epithelial cells from which they differentiate. To confirm these observations at the cellular level, we analyzed the membrane properties of fiber cells isolated in the presence of the nonselective cation channel inhibitor Gd3+. Isolated fiber cells were viable in physiological [Ca2+] and exhibited a range of lengths that reflected their stage of differentiation. Analysis of a large population of fiber cells revealed a subgroup of cells whose conductivity matched values measured in the whole lens ( 1 ). In this group of cells, membrane resistance, conductivity, and reversal potential all varied with cell length, suggesting that the process of differentiation is associated with a change in the membrane properties of fiber cells. Using pharmacology and ion substitution experiments, we showed that newly differentiated fiber cells (<150 μm) contained variable combinations of Ba2+-and tetraethylammonium-sensitive K+ currents. Longer fiber cells (150–650 μm) were dominated by a lyotropic anion conductance, which also appears to plays a role in the intact lens. Longer cells also exhibited a low-level, nonselective conductance that was eliminated by the replacement of extracellular Na+ with N-methyl-d-glucamine, indicating that the lens contains both Gd3+-sensitive and -insensitive nonselective cation conductances. Fiber cell differentiation is therefore associated with a shift in membrane permeability from a dominant K+ conductance(s) toward larger contributions from anion and nonselective cation conductances as fiber cells elongate.
IL-4 and IL-13 upregulate ornithine decarboxylase expression by PI3K and MAP kinase pathways in vascular smooth muscle cells
Authors: Wei Liu Hua , Yang Yang , Wu Guoyao , Ignarro Louis J.
Published: March 2008

Ornithine decarboxylase (ODC) is the first and rate-controlling enzyme in the synthesis of polyamines, which are essential for normal cell growth. We have previously demonstrated that IL-4 and IL-13 can stimulate rat aortic smooth muscle cell (RASMC) proliferation. The objective of this study was to determine whether IL-4 and IL-13 induce cell proliferation by upregulating ODC expression in RASMC. The results revealed that incubation of RASMC with IL-4 and IL-13 for 24 h caused four- to fivefold induction of ODC catalytic activity. The increased ODC catalytic activity was attributed to the increased expression of ODC mRNA. Moreover, these observations were paralleled by increased production of polyamines. We further investigated the signal transduction pathways responsible for ODC induction by IL-4 and IL-13. The data illustrated that PD-98059, a MEK (MAPK kinase) inhibitor, LY-294002, a phosphatidylinositol 3-kinase (PI3K) inhibitor, and H-89, a protein kinase A (PKA) inhibitor, substantially decreased the induction of ODC catalytic activity and ODC mRNA expression induced by IL-4 and IL-13, suggesting positive regulation of the ODC gene by ERK, PI3K, and PKA pathways. Interestingly, dexamethasone, a known inhibitor of cell proliferation, completely abrogated the response of RASMC to IL-4 and IL-13. Furthermore, the inhibition of ODC by these inhibitors led to the reduced production of polyamines and decreased DNA synthesis as monitored by [3H]thymidine incorporation. Our data indicate that upregulation of ODC by IL-4 and IL-13 might play an important role in the pathophysiology of vascular disorders characterized by excessive smooth muscle growth.
IK1 channel activity contributes to cisplatin sensitivity of human epidermoid cancer cells
Authors: Lee Elbert L. , Hasegawa Yuichi , Shimizu Takahiro , Okada Yasunobu
Published: March 2008

Cisplatin, a platinum-based drug, is an important weapon against many types of cancer. It induces apoptosis by forming adducts with DNA, although many aspects of its mechanism of action remain to be clarified. Previously, we found a role for the volume-sensitive, outwardly rectifying Cl− channel in cisplatin-induced apoptosis. To investigate the possibility that cation channels also have a role in the cellular response to cisplatin, we examined the activity of cation channels in cisplatin-sensitive KB-3-1 (KB) epidermoid cancer cells by the whole cell patch-clamp method. A cation channel in KB cells, activated by hypotonic stress, was identified as the Ca2+-activated, intermediate-conductance K+ (IK1) channel on the basis of its requirement for intracellular Ca2+, its blockage by the blockers clotrimazole and triarylmethane-34, and its suppression by a dominant-negative construct. Activity of this channel was not observed in KCP-4 cells, a cisplatin-resistant cell line derived from KB cells, and its molecular expression, observed by semiquantitative RT-PCR and immunostaining, appeared much reduced. Cell volume measurements confirmed a physiological role for the IK1 channel as a component of the volume-regulatory machinery in KB cells. A possible role of the IK1 channel in cisplatin-induced apoptosis was investigated. It was found that clotrimazole and triarylmethane-34 inhibited a cisplatin-induced decrease in cell viability and increase in caspase-3/7 activity, whereas 1-ethyl-2-benzimidazolinone, an activator of the channel, had the opposite effect. Thus IK1 channel activity appears to mediate, at least in part, the response of KB cells to cisplatin treatment.
Elucidation of the signaling network of COX-2 induction in sheared chondrocytes: COX-2 is induced via a Rac/MEKK1/MKK7/JNK2/c-Jun-C/EBPβ-dependent pathway
Authors: Healy Zachary R. , Zhu Fei , Stull Joshua D. , Konstantopoulos Konstantinos
Published: March 2008

Shear stress is a pathophysiologically relevant mechanical signal in cartilage biology and tissue engineering. Cyclooxygenase-2 (COX-2) is a pivotal proinflammatory enzyme, which is induced by mechanical loading-derived shear stress in chondrocytes. In the present study, we investigated the transcriptional machinery and signaling pathway regulating shear-induced COX-2 expression in human chondrocytic cells. Deletion and mutation analyses of the human cox-2 promoter reveal that the CCAAT/enhancer-binding protein (C/EBP) and activator protein-1 (AP-1) predominantly contribute to the shear-induced cox-2 promoter activity. Supershift assays disclose that C/EBPβ, but not C/EBPα or C/EBPδ, binds to the C/EBP site, whereas c-Jun binds to AP-1. Individual gene knockdown experiments demonstrate the direct regulation of C/EBPβ expression by c-Jun, and the critical roles of both c-Jun and C/EBPβ in shear-induced COX-2 synthesis. Our studies also indicate that Rac and, to a lesser extent, Cdc42 transactivate MEKK1, which is, in turn, responsible for activation of mitogen-activated protein kinase kinase 7 (MKK7). MKK7 regulates c-Jun NH2-terminal kinase 2 activation, which, in turn, triggers the phosphorylation of c-Jun that controls shear-mediated COX-2 upregulation in chondrocytes. Reconstructing the signaling network regulating shear-induced COX-2 expression and inflammation may provide insights to optimize conditions for culturing artificial cartilage in bioreactors and for developing therapeutic interventions for arthritic disorders.
Insulin increases the activity of mesangial BK channels through MAPK signaling
Authors: Foutz Ruth M. , Grimm P. Richard , Sansom Steven C.
Published: March 2008

Glomerular hyperfiltration and mesangial expansion have been described in mouse models of a hyperinsulinemic early stage of type 2 diabetes mellitus (DM). Large-conductance Ca2+-activated K+channels (BK) have been linked to relaxation of human mesangial cells (MC) and may contribute to MC expansion and hyperfiltration. We hypothesized that high insulin levels increase BK activity in MC by increasing the number and/or open probability ( Po) of BK in the plasma membrane. With the use of the patch-clamp technique, BK activity was analyzed in cultured MC exposed to normal insulin (1 nM) and high insulin (100 nM) for a 48-h period. The mean Poand the percentage of patches (cell attached) with detected BK increased by 100% in the insulin-treated cells. Real-time PCR revealed that insulin increased mRNA of BK-α. Western blot revealed an insulin-stimulated increase in BK-α from both total cellular and plasma membrane protein fractions. The mitogen-activated protein kinase (MAPK) inhibitors PD-098059 and U-0126 attenuated the insulin-induced increase in BK-α expression. PD-098059 inhibited insulin-stimulated phosphorylation of extracellular signal-regulated kinase 1/2 in MC. An insulin-stimulated increase also was found for total cellular BK-β1, the accessory subunit of BK in MC. A similar increase in BK-α mRNA and protein was evoked by an insulin-like growth factor I analog. Glomeruli, isolated from hyperinsulinemic early stage type 2 DM mice, exhibited increased BK-α mRNA by real-time PCR and protein by immunohistochemical staining and Western blot. These results indicate that insulin activates BK in the plasma membrane of MC and stimulates, via MAPK, an increase in cellular and plasma membrane BK-α.
Aldosterone and TGF-β1synergistically increase PAI-1 and decrease matrix degradation in rat renal mesangial and fibroblast cells
Authors: Huang Wei , Xu Chen , Kahng Kyoung W. , Noble Nancy A. , Border Wayne A. , Huang Yufeng
Published: March 2008

Aldosterone is thought to modulate renal fibrosis, in part, through increasing plasminogen activator inhibitor type 1 (PAI-1), a major inhibitor of ECM degradation. The present study investigated aldosterone effects on PAI-1 and transforming growth factor (TGF)-β1and asked whether PAI-1 effects were TGF-β mediated and whether aldosterone and TGF-β1acted synergistically to increase PAI-1 and decrease ECM degradation. Rat mesangial cells (MCs) and fibroblast cells [normal rat kidney (NRK)-49F] were used.3H-labeled ECM was produced by MCs. The effect of aldosterone and TGF-β on ECM degradation by newly plated MCs or NRK-49F was measured by the release of3H into medium. Aldosterone markedly increased PAI-1 mRNA and protein in both cell types, increases completely blocked by spironolactone and partially blocked by TGF-β neutralizing antibody. Adding both aldosterone and TGF-β1produced PAI-1 mRNA and protein increases higher than the sum of increases seen with either compound alone. Aldosterone or TGF-β1alone inhibited matrix degradation by 39 and 49% in MCs and 21 and 23% in NRK-49F, respectively. When both compounds were added, matrix degradation was further decreased by 93% in MCs and 61% in NRK-49F. The results indicate that aldosterone-induced PAI-1 increases are partially mediated by TGF-β1and lead to decreased ECM degradation. While aldosterone alone induced TGF-β1weakly, aldosterone and TGF-β1added together produced dramatic synergistic effects on PAI-1 production and subsequent ECM accumulation. Thus the elevated aldosterone induced by renin-angiotensin-aldosterone system activation may amplify renin-angiotensin-aldosterone system profibrotic actions.
Label-retaining cells of the bladder: candidate urothelial stem cells
Authors: Kurzrock Eric A. , Lieu Deborah K. , deGraffenried Lea A. , Chan Camie W. , Isseroff Roslyn R.
Published: March 2008

Adult tissue stem cells replicate infrequently, retaining DNA nucleotide label (BrdU) for much longer periods than mature, dividing cells in which the label is diluted during a chase period. Those “label-retaining cells” (LRCs) have been identified as the tissue stem cells in skin, cornea, intestine, and prostate. However, in the urinary tract uroepithelial stem cells have not yet been identified. In this study, BrdU administration identified urothelial LRCs in the rat bladder with 9% of the epithelial basal cells retaining BrdU label 1 yr after its administration. Markers for stem cells in other tissues, Bcl, p63, cytokeratin 14, and β1 integrin, were immunolocalized in the basal bladder epithelium in or near urothelial LRCs, but not uniquely limited to these cells. Flow cytometry demonstrated that urothelial LRCs were small, had low granularity, and were uniquely β4 integrin bright. Urothelium from long-term labeled bladders was cultured and LRCs were found to be significantly more clonogenic and proliferative, characteristics of stem cells, than unlabeled urothelial cells. Thus, this work demonstrates that LRCs in the bladder localize to the basal layer, are small, low granularity, uniquely β4 integrin rich, slowly cycling and demonstrate superior clonogenic and proliferative ability compared with unlabeled epithelial cells. We propose that LRCs represent putative urothelial stem cells.
Reversal of a Distractor Effect on Saccade Target Selection After Superior Colliculus Inactivation
Authors: McPeek Robert M.
Published: March 2008

Recent evidence indicates that inactivation of the primate superior colliculus (SC) results in an increase in saccade target-selection errors. The pattern of errors suggests that a winner-take-all competition selects the saccade goal and that SC inactivation perturbs this process by biasing the competition against stimuli in the inactivated field. To investigate this idea, the difficulty of target selection was manipulated in a color-oddity search task by varying the number of homogeneous distractors in the search array. Previous studies have shown that target selection is easier when a greater number of homogeneous distractors is present, due to perceptual grouping of the distractors. These results were replicated when testing with the SC intact. Surprisingly, during SC inactivation, this normal trend was reversed: target-selection performance declined significantly with more distractors, resulting in a greater proportion of errant saccades to distractors. Examination of the saccade endpoints indicates that after SC inactivation, many errant saccades were directed to distractors adjacent to the target. This pattern of results suggests that the salience signal used by the SC for target selection is relatively broad in spatial scope. As a result, when the area of the SC representing the target location is inactivated, distractors near the target are at a competitive advantage relative to more distant distractors and, consequently, are selected more often as the saccade goal. This contributes to the trend of worse performance with more distractors due to the greater proximity of distractors to the target.
Crosstalk Between Vascular Endothelial Growth Factor, Notch, and Transforming Growth Factor-β in Vascular Morphogenesis
Authors: Holderfield Matthew T. , Hughes Christopher C.W.
Published: March 2008

Vascular morphogenesis encompasses a temporally regulated set of morphological changes that endothelial cells undergo to generate a network of interconnected tubules. Such a complex process inevitably involves multiple cell signaling pathways that must be tightly coordinated in time and space. The formation of a new capillary involves endothelial cell activation, migration, alignment, proliferation, tube formation, branching, anastomosis, and maturation of intercellular junctions and the surrounding basement membrane. Each of these stages is either known or suspected to fall under the influence of the vascular endothelial growth factor, notch, and transforming growth factor-β/bone morphogenetic protein signaling pathways. Vascular endothelial growth factor is essential for initiation of angiogenic sprouting, and also regulates migration of capillary tip cells, proliferation of trunk cells, and gene expression in both. Notch has been implicated in the regulation of cell fate decisions in the vasculature, especially the choice between arterial and venular endothelial cells, and between tip and trunk cell phenotype. Transforming growth factor-β regulates cell migration and proliferation, as well as matrix synthesis. In this review, we emphasize how crosstalk between these pathways is essential for proper patterning of the vasculature and offer a transcriptional oscillator model to explain how these pathways might interact to generate new tip cells during retinal angiogenesis.
Neural Mechanisms, Temporal Dynamics, and Individual Differences in Interference Control
Authors: Forstmann Birte U. , van den Wildenberg Wery P. M. , Ridderinkhof K. Richard
Published: March 2008

Functional magnetic resonance imaging (fMRI) methods may help in understanding processes of response capture and response inhibition in conflict tasks, such as the Simon task. However, data-driven approaches thus far have not yielded consistent insights into these processes. Here, a theory-driven approach is introduced that capitalizes on individual differences in the processes of central interest. Based on the so-called activation-suppression model, specific behavioral parameters for each individual derived from reaction time (RT) distribution analysis were computed and entered into model-based fMRI analyses. These parameters correspond closely to the processes of inappropriate location-driven response activation (capture) and the subsequent inhibition of this activation as detailed by the model. Data from 24 participants revealed activation in the pre-supplementary motor area, which covaried with the RT distribution measure of response capture. Activation in the right inferior frontal cortex was found to covary with the RT distribution measure of response inhibition. These results, which are consistent against the backdrop of the larger literature on cognitive control, could have been derived neither from the standard data-driven fMRI approach, nor from inspecting overall mean RT alone.
Estimating Topographic Blocking Using a Froude Number When the Static Stability Is Nonuniform
Authors: Reinecke Patrick A. , Durran Dale R.
Published: March 2008

A parameter widely used to predict topographic flow blocking is the nondimensional mountain height or, synonymously, the inverse Froude number. Predictions using this parameter are based on the morphology of flows with uniform upstream static stability and wind speed, which rarely occur in the real world. The appropriateness of applying this theory in the presence of nontrivial background stability is therefore investigated using a numerical model. Two methods were considered to estimate the low-level stability, averaging the Brunt–Väisälä frequency below the crest and using the bulk change in θ between the ground and crest level.

No single best method emerged for estimating the upstream static stability and thereby mapping the simulations with inversions onto the set of solutions with constant stratification. Instead, the best method depended on the application at hand. To predict the onset of flow stagnation, averaging the low-level stability worked best, while to predict low-level flow diversion the bulk estimate of low-level stability was most appropriate. These results are consistent across a range of inversion thicknesses and strengths. In addition, it is shown that variations in static stability above the mountain crest have little impact on flow blocking.
The IMPROVE-1 Storm of 1–2 February 2001. Part IV: Precipitation Enhancement across the Melting Layer
Authors: Woods Christopher P. , Locatelli John D. , Stoelinga Mark T.
Published: March 2008

Previous model simulations indicate that in stratiform precipitation, the precipitation rate can increase by 7% in the melting layer through direct condensation onto melting snow and the resultant cooled rain. In the present study, a model simulation of stratiform precipitation in a wide cold frontal rainband indicates that the precipitation rate can also increase by 5% in the melting layer through accretion, by melting snow and rain, of additional cloud water produced by the latent cooling of the ambient air associated with melting snow. The contribution of the combined processes, and therefore the additional precipitation gained through the latent cooling of melting snow within the melting layer, may contribute as much as 10% to the precipitation rate in stratiform precipitation.
Unimodality of Wave Amplitude in the Northern Hemisphere
Authors: Ambaum Maarten H. P.
Published: March 2008

A novel statistic for local wave amplitude of the 500-hPa geopotential height field is introduced. The statistic uses a Hilbert transform to define a longitudinal wave envelope and dynamical latitude weighting to define the latitudes of interest. Here it is used to detect the existence, or otherwise, of multimodality in its distribution function. The empirical distribution function for the 1960–2000 period is close to a Weibull distribution with shape parameters between 2 and 3. There is substantial interdecadal variability but no apparent local multimodality or bimodality.

The zonally averaged wave amplitude, akin to the more usual wave amplitude index, is close to being normally distributed. This is consistent with the central limit theorem, which applies to the construction of the wave amplitude index. For the period 1960–70 it is found that there is apparent bimodality in this index. However, the different amplitudes are realized at different longitudes, so there is no bimodality at any single longitude.

As a corollary, it is found that many commonly used statistics to detect multimodality in atmospheric fields potentially satisfy the assumptions underlying the central limit theorem and therefore can only show approximately normal distributions. The author concludes that these techniques may therefore be suboptimal to detect any multimodality.
An Enhanced Moisture Convergence–Evaporation Feedback Mechanism for MJO Air–Sea Interaction
Authors: Marshall Andrew G. , Alves Oscar , Hendon Harry H.
Published: March 2008

Simulations using an atmospheric model forced with observed SST climatology and the same atmospheric model coupled to a slab-ocean model are used to investigate the role of air–sea interaction on the dynamics of the MJO. Slab-ocean coupling improved the MJO in Australia’s Bureau of Meteorology atmospheric model over the Indo-Pacific warm pool by reducing its period from 70–100 to 45–70 days, thereby showing better agreement with the 30–80-day observed oscillation.

Air–sea coupling improves the MJO by increasing the moisture flux in the lower troposphere prior to the passage of active convection, which acts to promote convection and precipitation on the eastern flank of the main convective center. This process is triggered by an increase in surface evaporation over positive SST anomalies ahead of the MJO convection, which are driven by the enhanced shortwave radiation in the region of suppressed convection. This in turn generates enhanced convergence into the region, which supports evaporation–wind feedback in the presence of weak background westerly winds. A subsequent increase in low-level moisture convergence acts to further moisten the lower troposphere in advance of large-scale convection in a region of reduced atmospheric pressure. This destabilizing mechanism is referred to as enhanced moisture convergence–evaporation feedback (EMCEF) and is utilized to understand the role of air–sea coupling on the observed MJO. The EMCEF mechanism also reconciles traditionally opposing ideas on the roles of frictional wave–conditional instability of the second kind (CISK) and wind–evaporation feedback. These results support the idea that the MJO is primarily an atmospheric phenomenon, with air–sea interaction improving upon, but not critical for, its existence in the model.
Vertical-Mode Decompositions of 2-Day Waves and the Madden–Julian Oscillation
Authors: Haertel Patrick T. , Kiladis George N. , Denno Andrew , Rickenbach Thomas M.
Published: March 2008

Vertical structures of 2-day waves and the Madden–Julian oscillation (MJO) are projected onto vertical normal modes for a quiescent tropical troposphere. Three modes capture the gross tropospheric structure of 2-day waves, while only two modes are needed to represent most of the baroclinic structure of the MJO. Deep circulations that project onto the first baroclinic mode are associated with deep cumulonimbus and stratiform rainfall. Shallow circulations that project onto higher wavenumber modes are associated with precipitating shallow cumulus and congestus and stratiform rainfall. For both disturbances the horizontal divergence contributed by shallow modes is an important factor in the column-integrated moist enthalpy budget. These modes converge moist static energy for a time prior to when deep circulations export moist static energy. These results highlight the importance of properly representing the effects of shallow cumulus, congestus, and stratiform precipitation in theories of convectively coupled waves and in atmospheric models.
Subsiding Shells around Shallow Cumulus Clouds
Authors: Heus Thijs , Jonker Harm J. J.
Published: March 2008

In this study large-eddy simulations (LES) are used to gain more knowledge on the shell of subsiding air that is frequently observed around cumulus clouds. First, a detailed comparison between observational and numerical results is presented to better validate LES as a tool for studies of microscale phenomena. It is found that horizontal cloud profiles of vertical velocity, humidity, and temperature are in good agreement with observations. They show features similar to the observations, including the presence of the shell of descending air around the cloud. Second, the availability of the complete 3D dataset in LES has been exploited to examine the role of lateral mixing in the exchange of cloud and environmental air. The origin of the subsiding shell is examined by analyzing the individual terms of the vertical momentum equation. Buoyancy is found to be the driving force for this shell, and it is counteracted by the pressure-gradient force. This shows that evaporative cooling at the cloud edge, induced by lateral mixing of cloudy and environmental air, is the responsible mechanism behind the descending shell. For all clouds, and especially the smaller ones, the negative mass flux generated by the subsiding shell is significant. This suggests an important role for lateral mixing throughout the entire cloud layer. The role of the shell in these processes is further explored and described in a conceptual three-layer model of the cloud.
Modeling Supersaturation and Subgrid-Scale Mixing with Two-Moment Bulk Warm Microphysics
Authors: Morrison Hugh , Grabowski Wojciech W.
Published: March 2008

This paper describes further developments of a two-moment warm rain bulk microphysics scheme suitable for addressing the indirect impact of atmospheric aerosols on ice-free clouds in large-eddy simulation (LES) models. The emphasis is on the prediction of supersaturation, activation of cloud droplets, and the representation of microphysical transformations during parameterized turbulent mixing. A comprehensive approach is proposed that is capable of simulating droplet activation at the cloud base, in the cloud interior due to increasing updraft strength, and at the lateral edges due to entrainment. Such an approach requires high spatial resolution to capture maximum supersaturation at cloud base as well as to resolve entraining eddies that lead to additional activation above the cloud base. This approach can be used as a benchmark for developing and testing schemes suitable for lower spatial resolutions.

A novel approach for predicting the supersaturation field is proposed, with an emphasis on its application in an Eulerian framework. This approach produces consistency among the thermodynamic variables and mitigates the problem of spurious cloud-edge supersaturation noted in the past. A new subgrid scheme is also developed to treat microphysical transformations during turbulent entrainment and mixing. This scheme is designed to be as flexible as possible, allowing for the entire range of mixing scenarios from homogeneous to extremely inhomogeneous.

The above developments are applied in 2D simulations of moist convection for an idealized rising thermal, assuming either pristine or polluted aerosol conditions. The mixing scenario has a substantial impact on the cloud microphysical and optical properties. As expected, extremely inhomogeneous mixing results in substantially smaller mean droplet number concentration, larger effective radius, and smaller cloud optical depth compared to the run with homogeneous mixing. The subgrid mixing of cloud condensation nuclei (CCN) and formation of CCN from evaporated droplets during extremely inhomogeneous mixing are relatively less important for this case.
A Moisture-Stratiform Instability for Convectively Coupled Waves
Authors: Kuang Zhiming
Published: March 2008

A simple model of two vertical modes is constructed and analyzed to reveal the basic instability mechanisms of convectively coupled waves. The main novelty of this model is a convective parameterization based on the quasi-equilibrium concept and simplified for a model of two vertical modes. It hypothesizes 1) the approximate invariance of the difference between saturation moist static energy in the lower half of the troposphere and moist static energy in the subcloud layer, regardless of free troposphere humidity, and 2) that variations in the depth of convection are determined by moisture-deficit variations in the midtroposphere. Physical arguments for such a treatment are presented. For realistic model parameters chosen based on cloud system resolving model simulations (CSRMs) of an earlier study, the model produces unstable waves at wavelengths and with structures that compare well with the CSRM simulations and observations.

A moisture–stratiform instability and a direct–stratiform instability are identified as the main instability mechanisms in the model. The former relies on the effect of midtroposphere humidity on the depth of convection. The latter relies on the climatological mean convective heating profile being top heavy, and it is identified to be the same as the stratiform instability mechanism proposed by B. E. Mapes. The moisture–stratiform instability appears to be the main instability mechanism for the convectively coupled wave development in the CSRM simulations. The finite response time of convection has a damping effect on the waves that is stronger at high wavenumbers. The net moistening effect of the second-mode convective heating also damps the waves, but more strongly at low wavenumbers. These effects help to shape the growth rate curve so that the most unstable waves are of a few thousand kilometers in scale.