bluuebunny/crossref_metadata_2025 huggingface dataset:
A Second Wind for T Cells
Authors: Adler Elizabeth M.
Published: December 2006

One of the mysteries of human immunodeficiency virus (HIV) infection is why the cellular immune response fails to clear the infection (see Rowland-Jones and Dong). Noting recent research implicating up-regulation of the inhibitory cell surface receptor programmed death 1 (PD-1) and production of functionally impaired "exhausted" virus-specific T cells in chronic infection of mice with lymphocytic choriomeningitis virus (LCMV), Day
et al
. investigated the role of PD-1 signaling in HIV infection. In people with chronic, untreated HIV infection, PD-1 expression was increased in CD8
+
T cells that specifically recognize HIV antigens. Increased PD-1 expression was associated with increased viral load and decreased CD4
+
T cell count. Antiretroviral therapy, which decreased viral load (and antigen exposure), led to a decrease in PD-1 expression. There was an inverse relation between PD-1 expression and the proliferative response of HIV-specific T cells to HIV peptides, indicating greater functional exhaustion. Intriguingly, incubation of peripheral blood mononuclear cells with blocking antibodies directed against PD-1 ligands enhanced both the proliferative response to HIV peptides and interferon-γ production. Similarly, increased PD-1 expression on CD4 T
+
cells was associated with increased viral load and decreased CD4
+
T cell count, and incubation with antibody against PD-1 ligand 1 enhanced proliferation in response to an HIV protein. Thus, the authors concluded that chronic HIV infection was associated with up-regulation of PD-1 on HIV-specific T cells, that this up-regulation was associated with impaired T cell function, and that blocking PD-1 activation might enhance the ability of T cells to control HIV. Trautmann
et al
. had similar findings and came to similar conclusions in a separate study.

C. L. Day, D. E. Kaufmann, P. Kiepiela, J. A. Brown, E. S. Moodley, S. Reddy, E. W. Mackey, J. D. Miller, A. J. Leslie, C. DePierres, Z. Mncube, J. Duraiswamy, B. Zhu, Q. Eichbaum, M. Altfeld, E. J. Wherry, H. M. Coovadia, P. J. R. Goulder, P. Klenerman, R. Ahmed, G. J. Freeman, B. D. Walker, PD-1 expression on HIV-specific T cells is associated with T-cell exhaustion and disease progression.
Nature
443
, 350-354 (2006).
[PubMed]

L. Trautmann, L. Janbazian, N. Chomont, E. A. Said, S. Gimmig, B. Bessette, M.-R. Boulassel, E. Delwart, H. Sepulveda, R. S Balderas, J.-P. Routy, E. K Haddad, R.-P. Sekaly, Upregulation of PD-1 expression on HIV-specific CD8
+
T cells leads to reversible immune dysfunction.
Nature Med.
, published online 20 August 2006 (doi:10.1038/nm1482).
[PubMed]

S. Rowland-Jones, T. Dong, Tired T cells turn around.
Nature
443
, 282-283 (2006).
[PubMed]
Disulfide Switch Alters Receptor Signals
Authors: Ray L. Bryan
Published: December 2006

Coagulation of the blood is regulated by a member of the cytokine receptor family known as tissue factor (TF). Tissue factor associates with the protease factor VIIa and leads to activation of a proteolytic cascade that results in cleavage of fibrinogen and blood coagulation. But the TF-VIIa complex also initiates signaling through the protease-activated receptor 2 (PAR2), which influences a range of biological processes, including inflammation, angiogenesis, and vascular function. Ahamed
et al
. now report that a disulfide bond between two cysteine residues on the extracellular portion of TF acts as a switch to promote one or the other of these two actions of TF--coagulation or cell signaling through PAR2. The authors used a set of antibodies that recognized distinct epitopes on TF and dose-response experiments to show that two distinct pools of TF regulated coagulation (measured as proteolytic generation of factor Xa) or PAR2 signaling [measured by monitoring phosphorylation of ERKs (extracellular signal–regulated kinases)]. Studies with mutant TF supported the authors’ suspicion that a conformational change in TF might result from formation or breakage of the Cys
186
-Cys
209
disulfide bond. Furthermore, TF was found to associate with the enzyme protein disulfide isomerase (PDI). Reduction of the disulfide bond by PDI appeared to suppress coagulation, but TF retained its signaling activity through PAR2. Conversely, an antibody that inhibited interaction of TF with PAR2 inhibited signaling but allowed TF to function in control of coagulation. Pharmacological inhibition of PDI inhibited signaling through PAR2 initiated by the TF-VIIa complex, but not activation of the coagulation cascade. The findings may have therapeutic implications in that they demonstrate that it is possible to inhibit signaling initiated by TF-VIIa without compromising regulation of coagulation.

J. Ahamed, H. H. Versteeg, M. Kerver, V. M. Chen, B. M. Mueller, P. J. Hogg, W. Ruf, Disulfide isomerization switches tissue factor from coagulation to cell signaling.
Proc. Natl. Acad. Sci.
U.S.A.
103
, 13932-13937 (2006).
[Abstract]
[Full Text]
From Myc Activation to Angiogenesis
Authors: Gough Nancy R.
Published: December 2006

Myc is encoded by an oncogene that is frequently activated in cancer. Myc is a basic helix-loop-helix leucine zipper transcription factor that integrates cell proliferation with changes in the local environment to accommodate that growth. In tumor growth, this frequently involves stimulation of angiogenesis. Shchors
et al
. used a transgenic mouse model in which
myc
expression was inducibly activated in the presence of the apoptosis inhibitor Bcl-X
L
in pancreatic β cells. Within 3 days of Myc expression, β cells proliferated as did endothelial cells, despite the fact that Myc activity and abundance were only increased in the β cells. When Myc expression was induced in isolated islets, a factor--which was determined by immunofluorescence and enzyme-linked immunosorbent assay (ELISA) to be vascular endothelial growth factor A (VEGF A)--was secreted into the medium. Application of this conditioned medium to human umbilical vein endothelial cells stimulated proliferation and tubule formation. Myc did not directly stimulate the transcription of VEGF A. Instead, using immunofluorescence analysis of islets from mice in which expression of Myc was induced, the authors showed that β cell Myc led to a redistribution of VEGF A from diffusely distributed throughout the islet to present in discrete foci. These foci also contained endothelial cells and engaged VEGF A–VEGFR2 (VEGF receptor 2) complexes. An increase in matrix metalloproteinase (MMP) activity was observed in the islets at the time of VEGF A redistribution; however, once again, Myc did not stimulate the expression of any MMP genes. The angiogenic effects of Myc appear to be the result of stimulation of the gene encoding interleukin-1β (IL-1β), because not only was this gene’s expression increased, neutralizing antibodies inhibited the release of VEGF A from cultured islets and reduced the redistribution of VEGF A in vivo. Thus, before the onset of tissue hypoxia, which is also a trigger for angiogenesis, Myc stimulates the production of the proinflammatory IL-1β, which stimulates MMP activity and thereby allows release of matrix-sequestered VEGF A and stimulates angiogenesis. These results help clarify the sequence of events associated with vascularization of tumors and suggest that interfering with IL-1β may be a useful tool in the battle against cancer progression.

K. Shchors, E. Shchors, F. Rostker, E. R. Lawlor, L. Brown-Swigart, G. I. Evan, The Myc-dependent angiogenic switch in tumors is mediated by interleukin 1β.
Genes Dev.
20
, 2527-2538 (2006).
[Abstract]
[Full Text]
Polarizing Neurons
Authors: Adler Elizabeth M.
Published: December 2006

Early in development, neurons form neurites; one neurite elongates to become an axon and the others then become dendrites (see Pinheiro and Gertler). But what "primes" that neurite to become the axon? Localized activation of the small guanosine triphosphatase (GTPase) Rac, which regulates the actin cytoskeleton and microtubule dynamics, has been implicated in axon formation, leading Watabe-Uchida
et al
. to search for upstream regulators involved in establishing neuronal polarity. A yeast two-hybrid screen of a human fetal cDNA brain library with a dominant-negative Rac1 mutant identified DOCK7 (dedicator of cytokinesis 7), one of a family of unconventional Rho family guanine

nucleotide exchange factors, as a binding partner. DOCK7 was highly expressed in rat brain and was most abundant during late embryonic and early postnatal development. In primary cultures of hippocampal neurons, DOCK7 was most abundant at the time axons appeared and was preferentially expressed in one of the early neurites and then in the developing axon. DOCK7 overexpression did not affect the total number of neurites but increased the number of axons; a mutant form of DOCK7 that did not activate Rac failed to induce additional axons (and sometimes prevented formation of any). DOCK7 knockdown with RNA interference blocked neuronal polarization and axon formation. Rac-dependent phosphorylation of Oncoprotein 18 (Op18 or stathmin) on serine-16 (Op18-S16-P) inhibits destabilization of microtubules by Op18. DOCK7 knockdown decreased Op18-S16-P in developing neurons, whereas DOCK7 overexpression enhanced Op18-S16-P. Op18-S16-P was enhanced in developing axons in vitro, and expression of a nonphosphorylatable mutant inhibited axon formation, as well as DOCK7-dependent induction of multiple axons. Thus, the authors propose that DOCK 7 regulates axon formation by means of Op18 regulation of microtubule dynamics.

M. Watabe-Uchida, K. A. John, J. A. Janas, S. E. Newey, L. Van Aelst, The Rac activator DOCK7 regulates neuronal polarity through local phosphorylation of stathmin/Op18.
Neuron
51
, 727-739 (2006).
[PubMed]

E. M. Pinheiro, F. B. Gertler, Nervous Rac: DOCK7 regulation of axon formation.
Neuron
51
, 674-676 (2006).
[PubMed]
Inhibition of PIP5K by Apoptotic Stresses
Authors: Gough Nancy R.
Published: December 2006

Peroxide or ultraviolet radiation triggered cell death and stimulated the translocation of a reporter of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P
2
] to the cytosol, indicating that PI(4,5)P
2
was depleted in the cells. When overexpressed in HeLa cells, murine phosphatidylinositol phosphate 5 kinase α (PIP5Kα, which is homologous to human PIP5Kβ) prevented the decrease in PI(4,5)P
2
abundance and increase in apoptosis caused by oxidative stress. Overexpression of PIP5Kα was associated with an increase in extracellular signal–regulated kinase 1 and 2 (ERK1/2) phosphorylation. Pharmacological inhibition of ERK activation sensitized cells to peroxide-induced apoptosis and prevented overexpressed PIP5Kα from increasing cell survival. Peroxide transiently inhibited the activity of PIP5K; however, peroxide triggered a sustained translocation (lasting hours) of a green fluorescent protein (GFP)-tagged PIP5Kα away from the plasma membrane to the cytosol, which would take the enzyme away from its substrate. Peroxide stimulated the tyrosine phosphorylation of PIP5Kα, and this was prevented if the Src family of kinases was inhibited. The authors suggest that oxidative stress or ultraviolet radiation activates Src, which leads to the tyrosine phosphorylation of PIP5Kα and translocation of the enzyme away from the plasma membrane and thereby prevents the regeneration of PI(4,5)P
2
, which is necessary for activation of survival signals mediated by the ERK pathway.

J. R. Halstead, J. van Rheenen, M. H. J. Snel, S. Meeuws, S. Mohammed, C. S. D’Santos, A. J. Heck, K. Jalink, N. Divecha, A role for PtdIns(4,5)
P
2
and PIP5Kα in regulating stress-induced apoptosis.
Curr. Biol.
16
, 1850-1856 (2006).
[Online Journal]
Tanning in the Dark?
Authors: Adler Elizabeth M.
Published: December 2006

Fair-skinned people who experience difficulty tanning often have functional disruptions of MC1R (melanocortin 1 receptor), the receptor for melanocyte-stimulating hormone (MSH), and also have increased susceptibility to skin cancer. D’Orazio
et al
. used a line of red/blonde-haired, pheomelanin-producing mice with an inactivating mutation of the MSH receptor (

Mc1r
e/e

) to explore the link between exposure to ultraviolet light (UV), MSH signaling, and tanning, as well as to UV-induced skin cancers. UV light elicited an increase in the mRNA encoding MSH in both primary human keratinocytes and the mouse PAM12 keratinocyte line; moreover, conditioned medium from UV-exposed PAM12 keratinocytes elicited a response in melanoma cells that was lost following absorption with an antibody to MSH. When exposed to UV, the ears of wild-type mice tanned, whereas those of

Mc1r
e/e

mice did not. MC1R activates adenosine 3′,5′-monophosphate (cAMP) signaling. In a line of mice that expressed

Mc1r
e/e

and that had (like humans but unlike wild-type mice) epidermal melanocytes in their truncal skin, topical treatment with the adenylate cyclase stimulator forskolin elicited eumelanin production and skin darkening. Furthermore, forskolin treatment protected against UV-induced "sunburn" and tumor production (mostly squamous cell carcinomas). Thus, the data suggest that small-molecule manipulation of MSH signaling could be used to influence skin pigmentation and might even be useful in preventing UV-induced skin damage and cancer.

J. A. D'Orazio, T. Nobuhisa, R. Cui, M. Arya, M. Spry, K. Wakamatsu, V. Igras, T. Kunisada, S. R. Granter, E. K. Nishimura, S. Ito, D. E. Fisher, Topical drug rescue strategy and skin protection based on the role of
Mc1r
in UV-induced tanning.
Nature
443
, 340-344 (2006).
[PubMed]
Beyond Self-Nonself for MHC
Authors: Hines Pamela J.
Published: December 2006

Proteins of the major histocompatibility complex class 1 (MHC1), which are important in identifying self and nonself tissue for the immune system, are also found in the brain. Syken
et al
. show that a receptor, PirB, to which the MHC1 proteins bind, is also found in neurons of the brain. In mice carrying a mutant PirB lacking its signal transduction capabilities, the overall structure of the brain remained normal. However, these mice showed greater than normal plasticity in the visual cortex. Thus, intercellular signaling through PirB seems to be critical for keeping visual plasticity within limits.

J. Syken, T. GrandPre, P. O. Kanold, C. J. Shatz, PirB restricts ocular-dominance plasticity in visual cortex.
Science
313
, 1795-1800 (2006).
[Abstract]
[Full Text]
Protein Pathways in Epilepsy
Authors: Hines Pamela J.
Published: December 2006

One cause of epilepsy is mutations in proteins that function in the brain. Fukata
et al
. identified the partners of a complex of proteins located at rat brain synapses. Of the various components, one (LGI1) seems to function as a ligand, one (ADAM22) as a receptor, and one (PSD-95) as a scaffolding anchor. LGI1 controls the strength of excitatory synapses. Both the ligand and the receptor of this complex are implicated by genetics and mutations as causing certain types of epilepsy.

Y. Fukata, H. Adesnik, T. Iwanaga, D. S. Bredt, R. A. Nicoll, M. Fukata, Epilepsy-related ligand/receptor complex LGI1 and ADAM22 regulate synaptic transmission.
Science
313
, 1792-1795 (2006).
[Abstract]
[Full Text]

S. H. Snyder, Adam finds an exciting mate.
Science
313
, 1744-1745 (2006).
[Summary]
[Full Text]
Social Experience and the Need to Sleep
Authors: Stern Peter
Published: December 2006

Sleep is widely observed in the animal kingdom and yet we still don’t know why it is beneficial. Studying
Drosophila
, Ganguly-Fitzgerald
et al
. developed a strategy for elucidating the mechanisms underlying the need to sleep. They observed that a rich social experience, versus an impoverished one, increased the duration of sleep, which in turn was promoted by processes that underlie learning and memory, such as dopamine and cyclic adenosine monophosphate signaling pathways. Mutations in 17 genes were found to disrupt experience-dependent changes in sleep.

I. Ganguly-Fitzgerald, J. Donlea, P. J. Shaw, Waking experience affects sleep need in
Drosophila
.
Science
313
, 1775-1781 (2006).
[Abstract]
[Full Text]
Focus Issue: From Genes to Tissues
Authors: Gough Nancy R.
Published: December 2006

Science
and
Science
’s STKE highlight the molecular mechanisms that control the development of complex organisms.
Science
emphasizes the evolution of the eye and heart and the Hox gene family, whereas articles at
Science
's STKE highlight the regulatory mechanisms by which gene expression profiles are established to allow complex structures to form.
Variations on a Theme: Hox and Wnt Combinatorial Regulation During Animal Development
Authors: Bondos Sarah
Published: December 2006

Shockingly few transcription factors and cell signaling pathways are utilized to pattern organs and to specify the fate of a seemingly endless variety of unique cell types during animal development. This dichotomy led to the hypothesis that each factor is used in multiple tissues and that a combinatorial code of factors determines cell fate or tissue identity in a unique fashion. Two recent papers describe temporal changes in the interplay between Hox transcription factors, which specify positional identity, and Wnt signaling, which provides spatial information and promotes asymmetric cell division. These changes guide cells through a series of discrete steps, leading to unique fates. Variations between these two studies highlight the diversifying potential of combinatorial regulation, in short, that the pathways through which these molecules interact can vary even between adjacent cells. Shared features include cross-regulatory interactions to redeploy patterning genes in a tissue-specific manner for organogenesis and coregulation of common downstream targets. Identification of additional combinatorial gene targets and elucidation of their underlying molecular mechanisms are important future tasks in developmental biology and the study of evolution.
MAPping Out Arteries and Veins
Authors: Lamont Ryan E. , Childs Sarah
Published: December 2006

Growing evidence suggests that a genetic program specifies the identity of arteries and veins before the onset of circulation. A signaling cascade involving sonic hedgehog (Shh), vascular endothelial growth factor (VEGF), the VEGF receptor 2 (VEGFR2), homeobox proteins Foxc1 and Foxc2, the Notch receptor, and the downstream transcription factor gridlock is required for expression of arterial markers, whereas only a single transcription factor, COUP-TFII (chicken ovalbumin upstream promoter–transcription factor II), has previously been implicated in maintaining venous fate. Recent work has now implicated two competing pathways downstream of VEGFR2 in arterial versus venous specification: Activation of the phospholipase C–γ (PLC-γ)–mitogen-activated protein kinase (MAPK) pathway acts in arterial specification, whereas the phosphoinositide 3-kinase (PI3K)–Akt pathway acts to allow a venous fate by inhibition of the PLC-γ–MAPK pathway. Here, we review this work and discuss how activation of the MAPK signaling cascade could stimulate an arterial fate.
Gene Control by Large Noncoding RNAs
Authors: Shamovsky Ilya , Nudler Evgeny
Published: December 2006

Large noncoding RNAs (lncRNAs) have emerged as key players in regulating various fundamental cellular processes. Recent reports identify a functional lncRNA, Evf-2, that operates during development to control the expression of specific homeodomain proteins, and they provide important insights into the mechanism of cooperation between a newly discovered nuclear receptor co-repressor protein (SLIRP) and steroid receptor activator RNA. Evf-2 is the first example of lncRNA directly involved in organogenesis in vertebrates.
Pruning a Dendritic Tree
Authors: Adler Elizabeth M.
Published: December 2006

During development, the dendritic arborization undergoes pruning to eliminate unnecessary or inappropriate processes. Noting that dendritic pruning of the
Drosophila
dendritic arborizing sensory neuron ddaC during metamorphosis resembled apoptosis in some respects (including fragmentation and clearance of cellular debris by phagocytes), Williams
et al
. looked to see whether components of the apoptotic machinery played a role. ddaC pruning was suppressed in flies lacking functional
Drosophila
Nedd2-like caspase (DRONC, which is the only initiator caspase required for apoptosis in flies) and when dominant-negative forms of DRONC were selectively expressed in ddaC. Overexpression of
Drosophila
inhibitor of apoptosis protein 1 (DIAP1), which inhibits DRONC, or of p35, which inhibits effector caspases, suppressed the removal of dendritic branches. Expression of HID (head involution defective) in ddaC, which antagonizes DIAP1 and is therefore proapoptotic, elicited cell death. A probe for caspase activity (consisting of the mouse CD8 extracellular and transmembrane domain, fused to a portion of the caspase substrate PARP fused to a fluorescent protein) revealed that caspase activity was confined to the dendrites of ddaC undergoing pruning, whereas HID expression elicited caspase activity throughout the cell. Experiments in which engulfment was suppressed suggested that caspase activation took place after dendritic branches had been severed. Thus, dendritic pruning of ddaC during
Drosophila
metamorphosis appears to depend on localized activation of caspases within dendrites.

D. W. Williams, S. Kondo, A. Krzyzanowska, Y. Hiromi, J. W. Truman, Local caspase activity directs engulfment of dendrites during pruning.
Nat. Neurosci.
9
, 1234-1236 (2006).
[PubMed]
TAO2 Directs TAK1 to JNK
Authors: Gough Nancy R.
Published: December 2006

Transforming growth factor β-activated kinase 1 (TAK1) is capable of stimulating both the c-Jun N-terminal kinase (JNK) pathway and the nuclear factor κB (NF-κB) pathway. HuangFu
et al
. show that in response to osmotic stress, TAK1 selectively activates JNK without activating NF-κB. After validating that osmotic stress or interleukin-1 (IL-1) both activated TAK1 in cultured 293 IL-1R1 cells (stably expressing the IL-1 receptor), the authors showed that only IL-1 stimulated both JNK phosphorylation and the DNA binding activity of NF-κB and degradation of inhibitor of NF-κB (IκB). TAK1-deficient cells that expressed a truncated form of TAK1 lacking the kinase domain (TAK1Δ/Δ) failed to activate JNK in response to osmotic stress, confirming the importance of the kinase activity of TAK1 in the response. A yeast two-hybrid screen identified TAO1 (thousand-and-one amino acid kinase 1) as a binding partner for TAK1, and coimmunoprecipitation experiments confirmed that both TAO1 and the related protein TAO2, which is known to participate in JNK signaling, interacted with TAK1. The interaction did not require the kinase activity of TAO2, because a catalytically inactive mutant of TAO2 also bound TAK1. Overexpression of activated TAK1 can stimulate NF-κB activity; however, when activated TAK1 and TAO2 or the catalytically inactive form of TAO2 were coexpressed, NF-κB activation was diminished. In contrast, coexpression of activated TAK1 and TAO2 augmented JNK activation. Overexpression of TAO2 also inhibited NF-κB activation in response to tumor necrosis factor (TNF), which is also mediated by TAK1. TAO2 did not interfere with kinase activity of TAK1; instead, TAO2 interfered with the interaction between TAK1 and IKK (IκB kinase), which is required for degradation of IκB and activation of NF-κB. Knockdown of TAO2 using RNA interference resulted in decreased JNK activation and a modest activation of NF-κB in response to osmotic stress. Thus, TAO2 has a kinase-independent function in controlling the signaling pathways activated by TAK1, thus allowing the cell to use the same kinase TAK1 to mediate different responses to different stimuli.

W.-C. HuangFu, E. Omori, S. Akira, K. Matsumoto, J. Ninomiya-Tsuji, Osmotic stress activates the TAK1-JNK pathway while blocking TAK1-mediated NF-κB activation: TAO2 regulates TAK1 pathways.
J. Biol. Chem.
281
, 28802-28810 (2006).
[Abstract]
[Full Text]
Stop to Start
Authors: Simpson Stephen
Published: December 2006

The T cell surface receptor CTLA-4 helps dampen immune responses, and deficiency in the protein can lead to uncontrolled immune activation and autoimmunity. This effect has been attributed to the loss of negative signals that down-regulate T cell activation. Schneider
et al
. (see the Perspective by Mustelin) tracked T cells as they interacted with activating dendritic cells in culture and in vivo. CTLA-4 appeared to stimulate roaming of T cells away from dendritic cells, which lessened the likelihood that the T cells would remain activated. This finding makes CTLA-4 a potentially important clinical target.

H. Schneider, J. Downey, A. Smith, B. H. Zinselmeyer, C. Rush, J. M. Brewer, B. Wei, N. Hogg, P. Garside, C. E. Rudd, Reversal of the TCR stop signal by CTLA-4.
Science
313
, 1972-1975 (2006).
[Abstract]
[Full Text]

T. Mustelin, Restless T cells sniff and go.
Science
313
, 1902-1903 (2006).
[Summary]
[Full Text]
Sweet Smell of Communication
Authors: Hines Pamela J.
Published: December 2006

The aromas put out by plants serve to draw in insect pollinators, but they also enable communication with other plants. Runyon
et al
., studying a parasitic plant that is also a noxious weed, find that the dodder plant responds to volatile emissions from tomato plants such that the seedling parasite can rapidly locate and latch onto a host plant. Wheat, which dodder generally disdains as a host, releases volatiles that include a seemingly repellent component. The function of volatile signals in this interaction between plants resembles the function of volatiles in signaling between insect herbivores and their plant fodder.

J. B. Runyon, M. C. Mescher, C. M. De Moraes, Volatile chemical cues guide host location and host selection by parasitic plants.
Science
313
, 1964-1967 (2006).
[Abstract]
[Full Text]
Mapping Biological Connectivity
Authors: Jasny Barbara R.
Published: December 2006

Comprehensive catalogs of biological information (such as sequence or protein structure data) can have enormous utility in biomedical research. Lamb
et al
. have extended this approach to create comprehensive catalogs of cellular states, as defined by RNA expression. The effects of 164 small molecules on the complete messenger RNA expression profiles were examined in established cell lines, with a primary focus on a breast cancer epithelial cell line. By comparing the genomic signature of drug candidates (the anticancer drug gedunin, estrogen, histone deacetylase, and phenothiazine antipyschotics) or a disease state (obesity, Alzheimer’s disease, and dexamethasone-resistant acute lymphoblastic leukemia) to this resource, it was possible to identify potential mechanisms of action, confirm previous applications of known drugs, and identify additional potential uses for known drugs.

J. Lamb, E. D. Crawford, D. Peck, J. W. Modell, I. C. Blat, M. J. Wrobel, J. Lerner, J.-P. Brunet, A. Subramanian, K. N. Ross, M. Reich, H. Hieronymus, G. Wei, S. A. Armstrong, S. J. Haggarty, P. A. Clemons, R. Wei, S. A. Carr, E. S. Lander, T. R. Golub, The connectivity map: Using gene-expression signatures to connect small molecules, genes, and disease.
Science
313
, 1929-1935 (2006).
[Abstract]
[Full Text]
Focus Issue: Exciting Times for Signaling in the Brain
Authors: Adler Elizabeth M.
Published: December 2006

This week’s issues of
Science
and
Science
’s STKE are devoted to topics in neuroscience and include articles that span the range of neuronal activity from that of the individual neuron to that of the whole brain. The
Science
Special Issue takes a look at computational models of neuronal function, whereas STKE casts on eye on excitatory signaling in the brain.
D-Serine Regulation of NMDA Receptor Activity
Authors: Wolosker Herman
Published: December 2006

TheN-Methyl-D-aspartate–type glutamate receptor (NMDAR) plays a key role in several important processes involving the nervous system, including brain development, synaptic plasticity, and learning. Unlike other neurotransmitter receptors, which are activated by individual neurotransmitters, activation of NMDARs requires the binding of a coagonist (D-serine or glycine) in addition to glutamate. Although previously considered an "unnatural" amino acid,D-serine is a key regulator of NMDAR activity and may be the main physiological ligand at the coagonist site.D-Serine is synthesized in the mammalian brain and is enriched in astrocytes, a class of glial cells that ensheath synapses in the brain. Astrocytes physiologically affect NMDAR neurotransmission by releasingD-serine, suggesting thatD-serine acts as a gliotransmitter. However, recent findings indicate thatD-serine signaling does not depend solely on glia, becauseD-serine and its biosynthetic enzyme are also present in substantial amounts in neurons. Here, we discuss these new findings, which begin to shed light on the relative roles of glia and neurons inD-serine signaling.
Tale of Two Two-Timing Proteins
Authors: Ray L. Bryan
Published: December 2006

Cells put many proteins to more than one use, including the transcription factor TFII-I. Caraveo
et al
. (see the Perspective by Park and Dolmetsch) found that TFII-I may inhibit calcium entry into cells by interacting with another protein that itself has dual roles in regulating cellular calcium concentrations--phospholipase C-γ (PLC-γ). PLC-γ promotes the generation of inositol 1,4,5-trisphosphate, a second messenger that causes calcium release from intracellular stores, and also interacts with the membrane calcium channel TRPC3 and promotes insertion of the channel into the plasma membrane. The interaction of TFII-I with PLC-γ appears to depend on TFII-I’s phosphorylation, which may keep PLC-γ from interacting with the TRPC3 channel and thereby limit calcium entry through the plasma membrane.

G. Caraveo, D. B. van Rossum, R. L. Patterson, S. H. Snyder, S. Desiderio, Action of TFII-I outside the nucleus as an inhibitor of agonist-induced calcium entry.
Science
314
, 122-125 (2006).
[Abstract]
[Full Text]

C. Y. Park, R. Dolmetsch, The double life of a transcription factor takes it outside the nucleus.
Science
314
, 64-65 (2006).
[Abstract]
[Full Text]
More Regulation for FOXO
Authors: Ray L. Bryan
Published: December 2006

The FOXO (Forkhead box O) transcription factors are implicated in control of stress responses, cell death, aging, and tumor suppression, so perhaps it is no surprise that they are subject to multiple layers of regulation. Key targets of protein kinase B, they are also regulated by acetylation (which appears to enhance or suppress transcriptional activity, depending on the site of acetylation) and polyubiquitination (the covalent addition of multiple ubiquitin polypeptides). Van der Horst
et al
. now report that FOXO4 is also regulated by monoubiquitination, which--unlike polyubiquitination, which often targets proteins for degradation--often has other signaling roles. The authors show that in human embryonic kidney 293T cells expressing tagged FOXO4 and ubiquitin molecules, oxidative stress brought about by incubation of cells with hydrogen peroxide caused increased monoubiquitination of FOXO4. A fluorescence complementation assay in which part of the yellow fluorescent protein was tacked on to ubiquitin and part onto FOXO4 revealed nuclear or perinuclear localization of the ubiquitinated protein (detected when the parts of the fluorescent protein come together). Analysis of a FOXO-responsive reporter gene showed that expression of a FOXO4-ubiquitin fusion protein (that mimics monoubiquitinated FOXO) increased transcriptional activation by FOXO4. A search for proteins associated with the deubiquitinating enzyme (DUB) USP7 (also called HAUSP, for herpes virus-associated ubiquitin-specific protease) independently turned up FOXO4. Overexpression of USP7 or depletion of the protein by RNA interference caused decreased or increased FOXO transcriptional activity, respectively. The authors propose that the regulation of FOXO4 by USP7 might provide a new therapeutic strategy against cancer to complement current efforts to antagonize signals from protein kinase B. Furthermore, they note that there is remarkable similarity in the regulatory mechanisms controlling FOXO4 with those regulating the p53 tumor suppressor protein, better understanding of which promises to shed light on mechanisms of aging in mammals. Huang and D’Andrea provide commentary.

A. van der Horst, A. M. M. de Vries-Smits, A. B. Brenkman, M. H. van Triest, N. van den Broek, F. Colland, M. M. Maurice, B. M. T. Burgering, FOXO4

transcriptional activity is regulated by monoubiquitination and USP7/HAUSP.
Nat. Cell Biol.
8
, 1064-1073 (2006).
[PubMed]

T. T. Huang, A. D. D’Andrea, HAUSP hunting the FOX(O).
Nat. Cell Biol.
8
, 1043-1045 (2006).
[PubMed]
A Mysterious Mechanism for Promoting Anion Conductance
Authors: Adler Elizabeth M.
Published: December 2006

Proteins in the chloride channel, calcium-activated (CLCA) family have been implicated as playing a role in diseases that involve dysfunction of epithelial secretion, such as asthma and cystic fibrosis, and have been shown to mediate a calcium-activated chloride conductance. Mundhenk
et al
. used immunoprecipitation with antibodies directed against either the N or tagged C terminus at different times after [
35
S]methionine labeling, as well as Western analysis, to investigate the processing and secretion of murine ClCA3 (mCLCA3) transiently transfected into COS-1 or human embryonic kidney (HEK) 293 cells. mCLCA3 is cleaved into N-terminal and C-terminal products, and the authors found that both cleavage products were secreted and that they coprecipitated from both cell lysates and cell culture medium. Both products were glycosylated. Confocal immunofluorescence analysis indicated that the N-terminal and C-terminal products colocalized in intracellular vesicles and that mCLCA3 fluorescently tagged at the C terminus colocalized with markers for the Golgi and the endoplasmic reticulum. Neither the N-terminal nor the C-terminal product was observed in association with the plasma membrane. Thus, the authors conclude that mCLCA3, which elicits a calcium-activated chloride conductance when expressed in HEK293 cells, does not itself encode a transmembrane anion channel but rather encodes secreted products that may act as signaling molecules to regulate anion channel function.

A second study indicated that another member of the same protein family, human CLCA2, probably does not itself form a channel either.

L. Mundhenk, M. Alfalah, R. C. Elble, B. U. Pauli, H. Y. Naim, A. D. Gruber, Both cleavage products of the mCLCA3 protein are secreted soluble proteins.
J. Biol. Chem.
281
, 30072-30080 (2006).
[Abstract]
[Full Text]

R. C. Elble, V. Walia, H.-C. Cheng, C. J. Connon, L. Mundhenk, A. D. Gruber, B. U. Pauli, The putative chloride channel hCLCA2 has a single C-terminal transmembrane segment.
J. Biol. Chem.
281
, 29448-29454 (2006).
[Abstract]
[Full Text]
Channeling Local Translation
Authors: Hurtley Stella M.
Published: December 2006

Local, activity-dependent changes in excitability are thought to play a role in various aspects of neuromodulation. Translation of dendritically localized messenger RNAs is one way for a neuron to modify its excitability and signal processing machinery at or near active synapses. Raab-Graham
et al
. used photoconvertible fluorophores to show that potassium channels are locally translated in dendrites. This local translation is regulated by
N
-methyl-
D
-aspartate receptor activation via the mammalian target of rapamycin/phosphatidylinositol 3-kinase signaling pathway.

K. F. Raab-Graham, P. C. G. Haddick, Y. N. Jan, L. Y. Jan, Activity- and mTOR-dependent suppression of Kv1.1 channel mRNA translation in dendrites.
Science
314
, 144-148 (2006).
[Abstract]
[Full Text]
New Substrates for Factor Inhibiting HIF
Authors: Gough Nancy R.
Published: December 2006

Factor inhibiting hypoxia-inducible factor (FIH) is an asparaginyl hydroxylase, and hydroxylation of Asn of HIF (hypoxia-inducible factor) by FIH disrupts the interaction of HIF with the transcriptional coactivators CBP/p300. FIH activity is inhibited during hypoxia. Cockman
et al
. performed a yeast two-hybrid screen for proteins that interacted with FIH and found and confirmed the interaction with three ankryrin repeat domain (ARD)-containing proteins. Other ARD-containing peptides were also found to be substrates for FIH-dependent Asn hydroxylation. The interaction with the p105 precursor of the p50 component of the nuclear factor κB (NF-κB) transcription factor and with IκBα were characterized further. Interactions between the endogenous proteins were demonstrated by coimmunoprecipitation, and the interaction of p105 with FIH required Asn
678
. In vitro assays showed that in the presence of p105 or IκBα, FIH activity was stimulated, and liquid chromatography/mass spectrometry confirmed that p105 and IκBα were hydroxylated in vivo. RNA interference experiments showed that hydroxylation was dependent on FIH and hydroxylation of IκBα was decreased by hypoxic conditions. Despite using several different experimental approaches, the authors failed to show a clear consequence of ARD hydroxylation on NF-κB activity. Thus, it remains to be determined whether Asn hydroxylation is serving a structural role or is a regulatory posttranslational modification that alters the activity or interactions of these newly defined substrates.

M. E. Cockman, D. E. Lancaster. I. P. Stolze, K. S. Hewitson, M. A. McDonough, M. L. Coleman, C. H. Coles, X. Yu, R. T. Hay, S. C. Ley, C. W. Pugh, N. J. Oldham, N. Masson, C. J. Schofield, P. J. Ratcliffe, Posttranslational hydroxylation of ankyrin repeats in IκB proteins by the hypoxia-inducible factor (HIF) asparaginyl hydroxylase, factor inhibiting HIF (FIH).
Proc. Natl. Acad. Sci. U.S.A.
103
, 14767-14772 (2006).
[Abstract]
[Full Text]
XIAP as a Positive Feedback Regulator of Caspase Activation
Authors: Gough Nancy R.
Published: December 2006

Inhibitor of apoptosis proteins (IAPs) are best known for their roles as inhibitors of caspases and thereby inhibitors of the cell death process known as apoptosis. Legewie
et al
. developed a mathematical model of the core intrinsic apoptotic process involving Apaf-1, caspase 9, caspase 3, and X-linked IAP (XIAP). The input into the model is increased abundance of cytochrome c, which activates Apaf-1e, and the output is the concentration of active caspase 3. The model is based on 16 kinetic parameters and 13 differential equations. Three models were tested: a wild-type model in which XIAP competitively interacts with caspase 3 and caspase 9, a model in the presence of a mutant caspase 9 that cannot be cleaved and activated by caspase 3, and a noncompetitive model in which XIAP noncompetitively interacted with both caspase 3 and caspase 9. In the wild-type model, as active Apaf-1 concentration increased, the time course with which active caspase 3 was produced decreased as expected. When the activation of caspase 3 was plotted against the concentration of active Apaf-1, a bistable and irreversible state was observed both in the wild-type model and in the caspase 9 mutant model (although the total concentration of active caspase 3 was less in the caspase 9 mutant model). This suggested that the positive feedback between caspase 9 and caspase 3 was not the only contributor to bistability in the system. Further analysis suggested that XIAP contributed a positive feedback into caspase 3 activation. Caspase 3 was proposed to sequester XIAP away from caspase 9 under conditions of strong stimulation, thereby allowing caspase 9 to become further activated and ultimately allowing caspase 3 to be activated. The requirements were that the interactions between XIAP and caspase 3 and caspase 9 were competitive, caspase 3 abundance exceeded that of XIAP, and XIAP abundance exceeded that of caspase 9. The bistability and irreversibility of all three models depended on the concentrations of both caspase 3 and caspase 9, with only the wild-type model showing irreversibility in the physiological concentrations of each caspase, indicating that both caspase 3-mediated feedback and XIAP-mediated feedback contribute to irreversible bistability under physiological conditions. Their model accounts for experimentally observed differences in cellular responses to apoptotic stimuli by showing that the all-or-none threshold of the system is influenced by the abundance of caspase 3, caspase 9, and XIAP. The authors suggest wet-lab experiments that could be used to verify the model proposed.

S. Legewie, N. Blüthgen, H. Herzel, Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability.
PLoS Comput. Biol.
2
, e120, 1061-1073 (2006).
[PubMed]
Keep It Moving
Authors: Simpson Stephen
Published: December 2006

The actin-based molecular motors of the myosin family are encoded by multiple genes. Mammals possess two genes encoding long-tailed "amoeboid" Myo1e and Myo1f forms. Kim
et al
. now find that Myo1f negatively regulates the activity of neutrophils, the immune cells that engulf and kill bacteria. Myo1f did not directly influence phagocytic activity or the intracellular oxidative burst in these cells that eventually kills bacteria. However, cells from mice lacking Myo1f had reduced motility and increased adhesion caused by exocytosis of integrin-containing granules upon neutrophil stimulation. Myo1f deficiency also led to increased susceptibility to bacterial infection. Thus, Myo1f regulates the host response to infection by ensuring mobility of phagocytic cells through the modulation of integrin-dependent adhesion.

S. V. Kim, W. Z. Mehal, X. Dong, V. Heinrich, M. Pypaert, I. Mellman, M. Dembo, M. S. Mooseker, D. Wu, R. A. Flavell, Modulation of cell adhesion and motility in the immune system by Myo1f.
Science
314
, 136-139 (2006).
[Abstract]
[Full Text]
VRACs CARVe a Path for Novel Mechanisms of Communication in the CNS
Authors: Mulligan Sean J. , MacVicar Brian A.
Published: December 2006

Because the brain is encased by the skull, the ability to control cell volume in the brain is crucial, and pathological conditions that disturb cell volume homeostasis may severely compromise neural function and survival. Astrocytes are the main cell type to show swelling in response to pathological conditions. More recently, a role for swelling-induced neurotransmitter release from astrocytes under nonpathological conditions has been reported. Astrocytes express a volume-regulated anion channel (VRAC) that is involved in volume homeostasis. In addition to transporting chloride, VRACs allow the efflux of chloride and amino acids such as taurine, glutamate, and aspartate. Glutamate and aspartate are potent activators of neuronal glutamate receptors. Therefore, this nonsynaptic form of cellular communication may modulate neuronal excitability and synaptic activity.
Osmosensing by Bacteria
Authors: Wood Janet M.
Published: December 2006

Osmosensors are proteins that sense environmental osmotic pressure. They mediate or direct osmoregulatory responses that allow cells to survive osmotic changes and extremes. Bacterial osmosensing transporters sense high external osmotic pressure and respond by mediating organic osmolyte uptake, hence cellular rehydration. Detailed studies of osmosensing transporters OpuA, BetP, and ProP suggest that they sense and respond to different osmotic pressure–dependent cellular properties. These studies also suggest that each protein has a cytoplasmic osmosensory or osmoregulatory domain, but that these domains differ in structure and function. It is not yet clear whether each transporter represents a distinct osmosensory mechanism or whether different research groups are approaching the same mechanism by way of different paths. Principles emerging from this research will apply to other osmosensors, including those that initiate signal transduction cascades in prokaryotes and eukaryotes.
Regulation and Function of IKK and IKK-Related Kinases
Authors: Häcker Hans , Karin Michael
Published: December 2006

Members of the nuclear factor kappa B (NF-κB) family of dimeric transcription factors (TFs) regulate expression of a large number of genes involved in immune responses, inflammation, cell survival, and cancer. NF-κB TFs are rapidly activated in response to various stimuli, including cytokines, infectious agents, and radiation-induced DNA double-strand breaks. In nonstimulated cells, some NF-κB TFs are bound to inhibitory IκB proteins and are thereby sequestered in the cytoplasm. Activation leads to phosphorylation of IκB proteins and their subsequent recognition by ubiquitinating enzymes. The resulting proteasomal degradation of IκB proteins liberates IκB-bound NF-κB TFs, which translocate to the nucleus to drive expression of target genes. Two protein kinases with a high degree of sequence similarity, IKKα and IKKβ, mediate phosphorylation of IκB proteins and represent a convergence point for most signal transduction pathways leading to NF-κB activation. Most of the IKKα and IKKβ molecules in the cell are part of IKK complexes that also contain a regulatory subunit called IKKγ or NEMO. Despite extensive sequence similarity, IKKα and IKKβ have largely distinct functions, due to their different substrate specificities and modes of regulation. IKKβ (and IKKγ) are essential for rapid NF-κB activation by proinflammatory signaling cascades, such as those triggered by tumor necrosis factor α (TNFα) or lipopolysaccharide (LPS). In contrast, IKKα functions in the activation of a specific form of NF-κB in response to a subset of TNF family members and may also serve to attenuate IKKβ-driven NF-κB activation. Moreover, IKKα is involved in keratinocyte differentiation, but this function is independent of its kinase activity. Several years ago, two protein kinases, one called IKKε or IKK-i and one variously named TBK1 (TANK-binding kinase), NAK (NF-κB–activated kinase), or T2K (TRAF2-associated kinase), were identified that exhibit structural similarity to IKKα and IKKβ. These protein kinases are important for the activation of interferon response factor 3 (IRF3) and IRF7, TFs that play key roles in the induction of type I interferon (IFN-I). Together, the IKKs and IKK-related kinases are instrumental for activation of the host defense system. This Review focuses on the functions of IKK and IKK-related kinases and the molecular mechanisms that regulate their activities.