bluuebunny/crossref_metadata_2025 huggingface dataset:
Slowing Tumor Growth with a One-Two Punch
Authors: Kiberstis Paula A.
Published: December 2007

Drugs that inhibit receptor tyrosine kinases (RTKs) have emerged as promising anti-cancer therapies in clinical trials, but certain solid tumors such as glioblastoma multiforme (GBM) respond poorly to them. Work by Stommel
et al
. may help explain why GBM, an aggressive form of brain cancer, is so refractory to this class of drugs, which are typically administered as single agents. Glioblastoma cells display concomitant activation of multiple RTKs, all of which stimulate the phosphatidylinositol 3-kinase (PI3K) signaling pathway, a critical driver of cell growth. In preclinical models, combinations of agents targeting multiple RTKs were more powerful than single agents in inhibiting the PI3K pathway and slowing tumor cell growth. These results suggest a potential strategy for optimizing the efficacy of RTK inhibitors in GBM, an idea that can now be tested in clinical trials.

J. M. Stommel, A. C. Kimmelman, H. Ying, R. Nabioullin, A. H. Ponugoti, R. Wiedemeyer, A. H. Stegh, J. E. Bradner, K. L. Ligon, C. Brennan, L. Chin, R. A. DePinho, Coactivation of receptor tyrosine kinases affects the response of tumor cells to targeted therapies.
Science
318
, 287-290 (2007).
[Abstract]
[Full Text]
MicroRNAs Strike a Balance
Authors: Purnell Beverly A.
Published: December 2007

Hundreds of microRNAs (miRNAs) are thought to repress thousands of target messenger RNAs (mRNAs), but it has been difficult to study the interaction between individual miRNA-mRNA pairs. Choi
et al
. developed a way to block the interaction between a miRNA and specific target sites. Antisense morpholino oligonucleotides complementary to miRNA binding sites could protect specific mRNAs from miRNA-mediated repression. Applying this technology during zebrafish embryogenesis, they found that the miRNA miR-430 inhibits an antagonist and an agonist of the Nodal signaling pathway. Loss of repression led to an imbalance of signaling and abnormal development.

W.-Y. Choi, A. J. Giraldez, A. F. Schier, Target protectors reveal dampening and balancing of Nodal agonist and antagonist by miR-430.
Science
318
, 271-274 (2007).
[Abstract]
[Full Text]
Signaling Between Symbiotic Partners
Authors: Hines Pamela J.
Published: December 2007

Plants and certain fungi of the soil work together in a symbiotic mycorrhizal relationship that involves 80% of land plant species. Drissner
et al
. have now identified a molecular signal that mediates the relationships between these large and small partners. Using the gene that encodes an orthophosphate transporter known to be engaged in symbiotic transactions, the authors found that phospholipid extracts from plant-fungal symbioses could activate transcription of the target gene from potato. Further studies with cultured tomato cells and mass spectrometry indicated the key signaling compound to be lysophosphatidylcholine (LPC).

D. Drissner, G. Kunze, N. Callewaert, P. Gehrig, M. Tamasloukht, T. Boller, G. Felix, N. Amrhein, M. Bucher, Lyso-phosphatidylcholine is a signal in the arbuscular mycorrhizal symbiosis.
Science
318
, 265-268 (2007).
[Abstract]
[Full Text]
Chronoregulation by Asparagine Deamidation
Authors: Weintraub Steven J. , Deverman Benjamin E.
Published: December 2007

Every asparagine in every protein undergoes nonenzymatic deamidation to aspartate or isoaspartate at a rate determined by the surrounding protein structure and cellular environment. Under physiologic conditions, the deamidation half-life of individual asparagines in proteins is proposed to range from less than a day to several centuries. More than 200 proteins have been shown to undergo deamidation to a meaningful degree, and modeling predicts that hundreds more undergo deamidation at rates that have the potential to be of biological consequence. Because deamidation converts an asparagine into an aspartate or isoaspartate, it introduces a negative charge into a protein and results in the isomerization of a residue. Therefore, deamidation has the potential to change protein function. Additionally, deamidation is thought to render some proteins more susceptible to degradation. In most instances in which asparagine deamidation has been identified in vivo, it is involved in pathology. Hence, deamidation has been viewed primarily as a form of protein damage. However, the pervasiveness and evolutionary persistence of these unstable asparagines suggest that they may have a beneficial role. Notably, the change of even a single neighboring amino acid can have a marked effect on the rate of deamidation of an asparagine. Therefore, the underlying rate of deamidation of any asparagine is genetically programmable. This characteristic, combined with the wide range of deamidation rates that can be programmed, imparts to asparagines the potential to serve as molecular timers that regulate protein function and stability.
Interferon’s New Weapon
Authors: Foley John F.
Published: December 2007

MicroRNAs (miRNAs) are small noncoding RNAs that inhibit the expression of target genes by promoting mRNA degradation or inhibiting mRNA translation. In plants and invertebrates, miRNAs are involved in the innate immune response to viruses, but it was not known whether they performed a similar function in mammals. Type I interferons such as interferon-β (IFN-β) are antiviral cytokines that are crucial to host defense against virus infection, and Pedersen
et al
. investigated whether miRNAs might play a role in this response. The authors used microarrays to identify about 30 miRNAs with altered abundance in an IFN-β-treated compared with untreated human hepatoma-derived cell line (Huh7). The sequences of eight of these miRNAs showed complementarities with the hepatitis C virus (HCV) RNA genome. The abundance of miR-122, a liver-specific miRNA that is essential for HCV replication, was decreased in IFN-β-treated Huh7 cells compared with untreated cells. The authors transfected a modified Huh7 cell line that contained an autonomously replicating HCV genome with synthetic miRNA mimics of the IFN-β-induced HCV-specific miRNAs and found that HCV replication (as assessed by quantitative measurement of HCV RNA) was reduced by five of these miRNAs compared with that in control miRNA-transfected cells. Transfection of HCV-containing Huh7 cells with a mixture of inhibitors of these same five miRNAs attenuated the ability of IFN-β to inhibit HCV replication. The addition of synthetic miR-122 further interfered with IFN-β-mediated inhibition of HCV replication. Together, these data show that miRNAs contribute to the antiviral effects of IFN-β, highlighting a new component to host defense mechanisms against viruses.

I. M. Pedersen, G. Cheng, S. Wieland, S. Volinia, C. M. Croce, F. V. Chisari, M. David, Interferon modulation of cellular microRNAs as an antiviral mechanism.
Nature
449
, 919-922 (2007).
[PubMed]
Targeting Acetyl-CoA Carboxylase to Stay Lean
Authors: Ray L. Bryan
Published: December 2007

Acetyl-CoA carboxylase (ACC) regulates synthesis and oxidation of fatty acids, and mice lacking the ACC2 isoform are leaner than wild-type animals. Choi
et al
. further characterized whole-body energy metabolism and insulin sensitivity of
Acc2
–/–
mice and obtained results supporting the possibility of ACC2 inhibitors as agents to treat obesity and type 2 diabetes. By monitoring activity of the animals, food consumption, and energy expenditure, the authors showed that
Acc2
–/–
animals ate more food than did wild-type animals but were still leaner than the control animals. The
Acc2
–/–
animals were also resistant to obesity brought on by eating a diet high in fats. These effects could be explained by the increase in energy expenditure that was observed in the knockout animals. Although oxidation of fats and of carbohydrates have been thought to be mutually exclusive (thus providing an explanation for insulin resistance observed in animals with excess fatty acids), Choi
et al
. found that oxidation of both fats and carbohydrates was increased in the
Acc2
–/–
animals. Insulin responsiveness was also enhanced in the knockout animals. Resistance to insulin that occurs with fat accumulation is thought to result from accumulation of diacylglycerol in muscle and liver and consequent activation of protein kinase C (PKC) θ and PKCε in muscle and liver, respectively. In the
Acc2
–/–
mice, enhanced sensitivity to insulin was associated with decreased activity of the PKC enzymes. ACC2 is not a particularly easy target for development of therapeutics in that the ACC1 isoform is required for viability during embryogenesis. Nevertheless, the authors propose, the properties of the
Acc2
–/–
animals show that patients with common diseases like diabetes and obesity could be helped by continued efforts to develop a specific inhibitor for ACC2.

C. S. Choi, D. B. Savage, L. Abu-Elheiga, Z.-X. Liu, S. Kim, A. Kulkarni, A. Distefano, Y.-J. Hwang, R. M. Reznick, R. Codella, D. Zhang, G. W. Cline, S. J. Wakil, G. I. Shulman, Continuous fat oxidation in acetyl-CoA carboxylase 2 knockout mice increases total energy expenditure, reduces fat mass, and improves insulin sensitivity.
Proc. Natl. Acad. Sci. U.S.A
.
104
, 16480-16485 (2007).
[Abstract]
[Full Text]
Clocks in the Corals
Authors: Purnell Beverly A.
Published: December 2007

Moonlight triggers the synchronized spawning of reef-building corals; however, the mechanism underlying detection of moonlight by these animals is largely unknown. Levy
et al.
now demonstrate the presence of ancient blue-light-sensing photoreceptors, cryptochromes, in the reef-building coral
Acropora millepora
(phylum Cnidaria). Cryptochromes regulate entrainment of the circadian clock of higher animals and plants. Expression of two coral
cryptochrome
genes,
cry1
and
cry2
, was rhythmic under a light-dark cycle but not in constant darkness. Expression of
cry2
varied with the full moon. This work suggests that cryptochromes not only function in the circadian clock of plants and higher animals but also may trigger the synchronized spawning of the Great Barrier Reef.

O. Levy, L. Appelbaum, W. Leggat, Y. Gothlif, D. C. Hayward, D. J. Miller, O. Hoegh-Guldberg, Light-responsive cryptochromes from a simple multicellular animal, the coral
Acropora millepora.
Science
318
, 467-470 (2007).
[Abstract]
[Full Text]
Off with the Methyl Marks
Authors: Riddihough Guy
Published: December 2007

The methylation of histones, proteins that make up the bulk of chromatin in eukaryotes, plays a critical role in the epigenetic regulation of gene expression. Although the enzymes that put this mark onto chromatin are well known, the class of enzymes that take it off again, the Jumonji C (JmjC) family of demethylases, are a more recent discovery (see the Perspective by Rivenbark and Strahl). Although several JmjC lysine demethylases are known, no JmjC protein has been identified that can remove methyl groups from arginine residues in histones. Chang
et al
. now report the discovery of an enzyme, JMJD6, that demethylates histone H3 at arginine 2 and histone H4 at arginine 3, marks that are likely a critical part of the "histone code" that modulates chromatin function. Di- and trimethylation of histone H3 on lysine 27 (H3K27me2-3) are exclusively repressing signals and are implicated in X chromosome inactivation, imprinting, stem cell maintenance, circadian rhythms, and cancer. The enzyme that places the marks has been known, and now Lee
et al
. have identified the human enzyme, UTX (ubiquitously transcribed mouse X chromosome gene), a JmjC-domain-containing protein (similar to other demethylase enzymes), responsible for removing the H3K27me2-3 marks and promoting the activation of gene expression.

B. Chang, Y. Chen, Y. Zhao, R. K. Bruick, JMJD6 is a histone arginine demethylase.
Science
318
, 444-447 (2007).
[Abstract]
[Full Text]

M. G. Lee, R. Villa, P. Trojer, J. Norman, K.-P. Yan, D. Reinberg, L. Di Croce, R. Shiekhattar, Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination.
Science
318
, 447-450 (2007).
[Abstract]
[Full Text]

A. G. Rivenbark, B. D. Strahl, Unlocking cell fate.
Science
318
, 403-404 (2007).
[Summary]
[Full Text]
Neurons or Glia? Can SHP2 Know It All?
Authors: Coskun Volkan , Zhao Jing , Sun Yi E.
Published: December 2007

Normal development of the nervous system relies on the spatially and temporally well-controlled differentiation of neurons and glia. Here, we discuss the intra- and extracellular molecular mechanisms that underlie the sequential genesis of neurons and glia, emphasizing recent studies describing the role of a signaling molecule, the tyrosine phosphatase SHP2, in normal brain development. Activation of SHP2 simultaneously enhances downstream activation of the MEK-ERK pathway, which subsequently promotes neurogenesis, while inhibiting the JAK-STAT pathway, which is critical for astroglial differentiation. Mutations in SHP2 that increase its tyrosine phosphatase activity cause a mental retardation–related disorder, Noonan syndrome. An imbalance in neurogenesis versus gliogenesis due to SHP2 mutations may contribute to Noonan syndrome.
Alchemy in the Soup: Transforming Metabolic Signals to Excitability
Authors: Nichols Colin G.
Published: December 2007

The intersection of cell metabolism with electrical signaling links the environment and cell function over time scales ranging from milliseconds to lifetimes. In responding to cellular metabolites, adenosine triphosphate (ATP)–sensitive potassium (K
ATP
) channels are an important component of this intersection. Recent studies have begun to delineate the roles of K
ATP
channels in multiple tissues and the far-reaching consequences of aberrant K
ATP
channel activity and disturbed sensing of cell metabolism.
Need ADP to See
Authors: Foley John F.
Published: December 2007

Ectonucleoside triphosphate diphosphohydrolase 2 (E-NTPDase2) is a membrane-bound ectoenzyme that converts adenosine triphosphate (ATP) into adenosine diphosphate (ADP). In investigating roles for E-NTPDase2 in development, Massé
et al
. injected E-NTPDase2 mRNA into one side of a developing
Xenopus
laevis
embryo and found ectopic eyelike structures on the injected side that were histologically characteristic of normal eyes.
Pax6
,
Rx1
, and
Six3
encode eye-field transcription factors (EFTFs) that are responsible for eye development. Using in situ hybridization, the authors found that overexpression of E-NTPDase2 in injected embryos increased the expression of these EFTF genes. Knockdown of E-NTPDase2 by injection with a specific antisense morpholino oligonucleotide (MO) resulted in reduced expression of
Pax6
compared with that in control MO-injected embryos, and knockdown of the ADP receptor P2Y1 had a synergistic effect on EFTF gene expression. Knockdown of both E-NTPDase2 and P2Y1 resulted in embryos with very small eyes, or even lacking an eye, on the injected side. Using a biosensor for ATP, transient production of ATP was detected in the anterior, but not posterior, neural plate at a time consistent with eye-field development; however, the cells responsible for releasing the ATP remain unknown. A P2Y1 antagonist blocked the effects of overexpression of E-NTPDase2, and a P2Y1 agonist rescued the effects of injection of an E-NTPDase2 MO. In humans, mutations in chromosome 9, where the gene locus of E-NTPDase2 is located, are associated with eye defects such as microphthalmia. This study suggests a mechanism whereby ADP signaling initiates development of the eye.

K. Massé, S. Bhamra, R. Eason, N. Dale, E. A. Jones, Purine-mediated signalling triggers eye development.
Nature
449
, 1058-1062 (2007).
[PubMed]
Providing a Calcium Source
Authors: Adler Elizabeth M.
Published: December 2007

Gliomas--highly migratory brain malignancies derived from glia--express an unusual splice variant of BK channels (large conductance potassium channels independently activated by depolarization and calcium) whose activity may support migration of these diffusely infiltrating tumors. Noting that gliomas are not excitable and that global increases in intracellular calcium concentration ([Ca
2+
]
i
) of sufficient magnitude to activate BK channels would be expected to influence numerous other Ca
2+
-dependent processes, Weaver
et al
. investigated the possibility that activation of glioma BK channels might depend on a nearby Ca
2+
source. Immunofluorescence analysis of two glioma cell lines revealed that BK channels localized with lipid raft markers in "hot spots" at the protruding edges of cells. Furthermore, Western analysis of fractionated cell lysates indicated that BK channels were associated with a lipid raft fraction defined by the presence of caveolin-1. Treatment of U251 cells with methyl-β-cyclodextrin to disrupt lipid rafts led to BK channel redistribution and rapidly decreased whole-cell BK currents. This reduction in BK current was not associated with channel internalization, nor was it associated with a loss of BK channel sensitivity to a global increase in [Ca
2+
]
i
. Pharmacological analysis indicated that inositol 1,4,5-trisphosphate receptors (IP
3
Rs), which were present in BK-containing hot spots and lipid raft fractions but did not coimmunoprecipitate with BK channels, provided the calcium source for BK activation. Thus, the authors propose that the localization of BK channels to lipid rafts allows IP
3
-mediated signaling pathways to activate BK channels and suggest that disruption of such pathways may provide a novel approach to inhibiting glioma migration.

A. K. Weaver, M. L. Olsen, M. B. McFerrin, H. Sontheimer, BK channels are linked to inositol 1,4,5-triphosphate receptors via lipid rafts.
J. Biol. Chem.
282
, 31558-31568 (2007).
[Abstract]
[Full Text]
Plant-Pathogen Arms Race
Authors: Zahn Laura M.
Published: December 2007

Plants recognize pathogens through immune-like receptors, which activate a resistance response. In turn, pathogens have evolved means to modify plant signaling pathways to avoid triggering the resistance response. Kay
et al.
and Römer
et al.
tackle the molecular mechanisms underlying this evolutionary arms race between plants and pathogens. The bacterial type III effector protein, AvrBs3, functions as a pathogenicity factor in susceptible host plants, which lack a resistance gene known as
Bs3
, by acting as a transcriptional activator. In contrast, plants carrying Bs3 recognize the AvrBs3 protein and activate the resistance gene
Bs3
, which simulates the plant resistance pathway.

P. Römer, S. Hahn, T. Jordan, T. Strauß, U. Bonas, T. Lahaye, Plant pathogen recognition mediated by promoter activation of the pepper
Bs3
resistance gene.
Science
318
, 645-648 (2007).
[Abstract]
[Full Text]

S. Kay, S. Hahn, E. Marois, G. Hause, U. Bonas, A bacterial effector acts as a plant transcription factor and induces a cell size regulator.
Science
318
, 648-651 (2007).
[Abstract]
[Full Text]
Neurotrophic Factors and Parkinson’s Disease: The Emergence of a New Player?
Authors: Dauer William
Published: December 2007

The administration of neurotrophic factors is a potential approach to the therapy of neurodegenerative disorders such as Parkinson’s disease. However, issues relating to compound delivery and potential side effects have limited the clinical application of this treatment strategy. The identification of CDNF and MANF, which constitute a new class of neurotrophic factors active against dopaminergic neurons, may provide new hope for therapeutic approaches to neurodegenerative disorders based on neurotrophic factors or downstream components of their signaling pathways.
Meeting Report: Zinc Signals 2007—Expanding Roles of the Free Zinc Ion in BiologyA Report on the 8th Annual Institute of Zinc In Biology: Zinc Signals Meeting, Cook’s Branch Ranch, Woodlands, Texas, June 1 to 4, 2007.
Authors: Frederickson Cathleen , Frederickson Christopher J. , Maret Wolfgang , Sandstead Harold , Giblin Leonard , Thompson Richard
Published: December 2007

One hundred years after Camille Delezenne was nominated for the Nobel Prize for his work on zinc-secreting salivary and pancreatic cells, the Institute of Zinc in Biology sponsored its eighth annual Zinc Signals conference. Convened in a pristine nature conservancy, the meeting was focused on cells that secrete zinc signals, such as neurons, prostatic cells, pancreatic cells, photoreceptors, and others and on the myriad extracellular receptors that respond to these zinc signals.
A New Angiogenesis Inhibitor
Authors: Adler Elizabeth M.
Published: December 2007

Although antibodies directed against vascular endothelial growth factor (αVEGF) can prolong life when given to individuals with certain cancers in conjunction with chemotherapy, inhibition of VEGF signaling can elicit adverse effects and also stimulate the production of alternative angiogenic mechanisms in tumors (see Jain and Xu). Noting that placental growth factor [PIGF, a member of the VEGF family that binds VEGF receptor 1 (VEGFR-1)] is not required for normal development and maintenance of the vasculature but has been implicated in pathological angiogenesis, Fischer
et al
. investigated the effect on tumors of an antibody directed against PIGF (αPIGF). αPIGF inhibited the growth or metastasis or both of various tumors in mice, some of which were resistant to inhibition of VEGFR signaling. Furthermore, αPIGF enhanced inhibition of tumor growth by the chemotherapeutic agents gemcitabine and cyclophosphamide, as well as the anticancer effects of an antibody directed against VEGFR-2 (αVEGFR-2). αPIGF inhibited tumor angiogenesis and lymphangiogenesis, as well as tumor recruitment of proangiogenic macrophages. αPIGF failed to increase the expression of several proangiogenic genes stimulated by αVEGFR-2, and it neither mimicked nor enhanced αVEGFR-2-dependent side effects. Indeed, pregnant mice treated with αPIGF delivered litters of healthy pups. Thus, the authors hope that αPIGF might represent a useful addition to the current anticancer armamentarium.

C. Fischer, B. Jonckx, M. Mazzone, S. Zacchigna, S. Loges, L. Pattarini, E. Chorianopoulos, L. Liesenborghs, M. Koch, M. De Mol, M. Autiero, S. Wyns, S. Plaisance, L. Moons, N. van Rooijen, M. Giacca, J.-M. Stassen, M. Dewerchin, D. Collen, P. Carmeliet, Anti-PIGF inhibits growth of VEGF(R)-inhibitor-resistant tumors without affecting healthy vessels.
Cell
131
, 463-475 (2007).
[PubMed]

R. K. Jain, L. Xu, αPlGF: A new kid on the antiangiogenesis block.
Cell
131
, 443-445 (2007).
[PubMed]
Modulating Intraorganelle Communication
Authors: Adler Elizabeth M.
Published: December 2007

The endoplasmic reticulum (ER) releases calcium signals to the mitochondria through inositol 1,4,5-trisphosphate receptors (IP
3
Rs) located at contacts known as mitochondrion-associated ER membrane (MAM). ER calcium can also influence protein folding by ER chaperones, many of which are calcium-binding proteins up-regulated in response to ER stress (such as calcium depletion). Hayashi and Su found that, in CHO cells, the sigma-1 receptor (Sig-1R, an ER protein implicated in neuroplasticity and neuroprotection) was apposed to mitochondria. Fractionation analysis revealed that Sig-1R was enriched in the MAM fraction, as were several calcium-binding chaperones, including BiP [the immunoglobulin heavy chain-binding protein, also known as glucose-regulated protein 78 (GRP78)]. Sig-1R coimmunoprecipitated with BiP, an association that depended on calcium; ER calcium depletion led to dissociation of Sig-1R from BiP, as did several psychotropic drugs and steroids that act as Sig-1R ligands. Sig-1R acted as a chaperone in vitro, and in calcium-free medium--but not medium containing calcium--the chaperone effects of Sig-1R and BiP were additive. Calcium depletion (through IP
3
R activation or pharmacological manipulation) promoted the association of Sig-1R with type 3 IP
3
Rs (IP
3
R3); although the Sig-1R ligand (+)pentazocine did not itself stimulate association between Sig-1R and IP
3
R3, it prolonged their association in response to calcium depletion. Sig-1Rs inhibited the IP
3
-dependent degradation of IP
3
R3 and modulated calcium signaling to the mitochondria. Various ER stressors stimulated an increase in Sig-1R mRNA and protein and, eventually, its redistribution throughout the ER. Thus, the authors propose that Sig-1Rs represent a ligand- and calcium-modulated ER chaperone that acts to regulate ER-mitochondrial signaling.

T. Hayashi, T.-P. Su, Sigma-1 receptor chaperones at the ER-mitochondrion interface regulate Ca
2+
signaling and cell survival.
Cell
131
, 596-610 (2007).
[PubMed]
Shifting Receptor Sensitivities
Authors: Ray L. Bryan
Published: December 2007

AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptors mediate excitatory responses to neurotransmitters in the brain and in other neurons of the central nervous system. Menuz
et al
. report that the presence or absence of auxiliary AMPA receptor subunits has a dramatic effect on the pharmacological properties of these receptors. The compound CNQX (6-cyano-7-nitroquinoxaline-2,3-dione) generally acts as a competitive antagonist of AMPA receptors. However, in receptor complexes in which one of the auxiliary subunits known as TARPS (for transmembrane AMPA receptor regulatory proteins) is present, CNQX actually functions as a partial agonist of the receptor. The presence of the extra subunit may help couple conformational changes in the receptor ligand-binding domains to opening of the receptor ion channel.

K. Menuz, R. M. Stroud, R. A. Nicoll, F. A. Hays, TARP auxiliary subunits switch AMPA receptor antagonists into partial agonists.
Science
318
, 815-817 (2007).
[Abstract]
[Full Text]
Of Life and Limb
Authors: Hines Pamela J.
Published: December 2007

The ability of amphibians to regenerate an amputated limb represents a developmental flexibility largely lost for humans. The regeneration process in amphibians depends on interactions with the nerve supply. Kumar
et al
. (see the Perspective by Stocum) have now identified a secreted protein growth factor expressed in the nerves and epidermis of newts during limb regeneration that can serve to support regeneration even when the nerve supply is removed.

A. Kumar, J. W. Godwin, P. B. Gates, A. A. Garza-Garcia, J. P. Brockes, Molecular basis for the nerve dependence of limb regeneration in an adult vertebrate.
Science
318
, 772-777 (2007).
[Abstract]
[Full Text]

D. L. Stocum, Acceptable nAGging.
Science
318
, 754-755 (2007).
[Summary]
[Full Text]
Dynamic Developmental Gene Regulation
Authors: Purnell Beverly A.
Published: December 2007

Gene regulatory networks control metazoan development and determine which transcription factors will regulate which regulatory genes. However, development is a dynamic process that is driven by continuous change in time and space. Smith
et al
. now show how a network subcircuit controls a circular pattern of regulatory gene expression that sweeps outward from the vegetal pole of the sea urchin embryo and extinguishes its own activity in the more central regions to establish a dynamic regulatory pattern of gene expression.

J. Smith, C. Theodoris, E. H. Davidson, A gene regulatory network subcircuit drives a dynamic pattern of gene expression.
Science
318
, 794-797 (2007).
[Abstract]
[Full Text]
Shifting from Spreading to Retraction
Authors: Adler Elizabeth M.
Published: December 2007

Integrin signaling has been implicated in both cell spreading (mediated through the small GTP-binding proteins Rac and cdc42) and cell retraction (mediated through RhoA). However, the mechanism whereby integrin temporally regulates these opposing processes--which must be coordinated in cell migration and wound repair--has been unclear. Noting that calpain cleavage of the cytoplasmic domain of integrin β
3
is inhibited by tyrosine phosphorylation at Y
759
, Flevaris
et al
. expressed a phosphorylation-mimicking integrin β
3
mutant in Chinese hamster ovary (CHO) cells, along with the wild-type integrin α
IIb
subunit, to investigate the role of calpain cleavage in integrin signaling. After determining that this R760E mutant was in fact resistant to calpain cleavage when expressed in CHO cells adherent to fibrinogen, the authors showed that cell-mediated clot retraction was inhibited with the R760E mutant cells, whereas cell spreading on fibrinogen was enhanced. In contrast, a deletion mutant that mimicked calpain cleavage exhibited defective cell spreading. RhoA was activated in cells with cleaved integrin β
3
, and pharmacological analysis indicated that defective spreading in the deletion mutant depended on activation of RhoA and Rho-dependent kinase (ROCK)-mediated retraction. A combination of pharmacological analysis and investigation of a dominant-negative c-Src mutant revealed that integrin β
3
-dependent c-Src signaling inhibited RhoA activation, thereby promoting cell spreading; integrin β
3
cleavage disrupted its binding to c-Src, thereby relieving its inhibition of RhoA and stimulating retraction. Thus, the authors propose that the phosphorylation-regulated cleavage of the integrin β
3
cytoplasmic domain by calpain switches the integrin β
3
signal to promote retraction instead of spreading.

P. Flevaris, A. Stojanovic, H. Gong, A. Chishti, E. Welch, X. Du, A molecular switch that controls cell spreading and retraction.
J. Cell Biol.
179
, 553-565 (2007).
[Abstract]
[Full Text]
Arcadlin Signals Internalization
Authors: Gough Nancy R.
Published: December 2007

The abundance of the cell adhesion molecule N-cadherin is one factor that contributes to dendritic spine plasticity. When N-cadherin activity is compromised, spine number is decreased. Yasuda
et al
. found that conditions that stimulate excitatory synapses, such as maximal electroconvulsive seizure in mice or application of glutamate or agents that elevate the concentration of adenosine 3′,5′-monophosphate (cAMP) to cultured hippocampal neurons, increased the abundance of arcadlin, a protocadherin protein that was recruited to excitatory dendrites. Furthermore, arcadlin coimmunoprecipitated with N-cadherin from rat hippocampi after stimulation, as well as from transfected cultured cells. Cultured cells transfected with arcadlin and N-cadherin exhibited diminished homophilic adhesiveness. Stimulated hippocampal cultures exhibited decreased abundance of N-cadherin at the cell surface (based on a surface biotinylation assay and immunofluorescent analysis). In neurons cultured from
acad
–/–
mice, increases in cAMP concentration did not decrease N-cadherin surface abundance. A yeast two-hybrid screen identified a kinase that the authors named TAO2β, which appears to be an alternative splice variant of TAO2, as a protein that interacted with arcadlin. This interaction was confirmed by coimmunoprecipitation of the two proteins from hippocampi of mice after maximal electroconvulsive seizure and in colocalization studies in transfected cells. TAO2 is a mitogen-activated protein kinase kinase kinase (MAPKKK), and when transfected cells or primary cultures of rat hippocampal neurons were treated with the arcadlin extracellular domain (Acad-EC) to ligate the arcadlin proteins, phosphorylated mitogen-activated protein kinase kinase 3 (MEK3) and p38 MAPK were detected, suggesting that TAO2β is also a p38 MAPKKK. The abundance of arcadlin at the cell surface, as well as that of N-cadherin, was decreased in response to Acad-EC through a mechanism that required TAO2β and p38 activity. TAO2 could not substitute for TAO2β in triggering arcadlin endocytosis, yet endocytosis required p38, suggesting a possible feedback mechanism depending on TAO2β. Indeed, in vitro phosphorylation assays confirmed that TAO2β was a substrate for p38, and, in cells transfected with mutants that lacked the phosphorylation site, the importance of this phosphorylation for triggering endocytosis of arcadlin was confirmed. Finally, the increase in spine density seen in cultured neurons from
acad
–/–
mice was reversed by knockdown of N-cadherin. Thus, arcadlin appears to link the endocytosis of N-cadherin to excitatory stimuli through a MAPK pathway.

S. Yasuda, H. Tanaka, H. Sugiura, K. Okamura, T. Sakaguchi, U. Tran, T. Takemiya, A. Mizoguchi, Y. Yagita, T. Sakurai, E. M. De Robertis, Activity-induced protocadherin arcadlin regulates dendritic spine number by triggering N-cadherin endocytosis via TAO2β and p38 MAP kinases.
Neuron
56
, 456-471 (2007).
[PubMed]
Life and Death Decisions
Authors: Hurtley Stella M.
Published: December 2007

How do cells determine whether to live or die after exposure to stressors that cause misfolding of intracellular proteins? Lin
et al
. find that the IRE1 signaling branch of the unfolded protein response plays a key role in promoting cell survival after protein misfolding in the endoplasmic reticulum (ER). Human cells shut off IRE1 signaling after prolonged ER protein misfolding in order to enhance cell survival.

J. H. Lin, H. Li, D. Yasumura, H. R. Cohen, C. Zhang, B. Panning, K. M. Shokat, M. M. LaVail, P. Walter, IRE1 signaling affects cell fate during the unfolded protein response.
Science
318
, 944-949 (2007).
[Abstract]
[Full Text]
STAT5A as a Tumor Suppressor
Authors: Foley John F.
Published: December 2007

The tyrosine kinase anaplastic lymphoma kinase (ALK) is normally found in neural cells, but chromosomal translocations involving
ALK
and the nucleophosmin gene,
NPM1
, occur in T cell lymphomas (NPM1-ALK
+
TCLs). Zhang
et al
. investigated a role for signal transducer and activator of transcription 5A (STAT5A) in the transformation of NPM1-ALK
+
TCLs. Western blotting showed the presence of STAT5A in T cells from healthy donors, but not in NPM1-ALK
+
TCLs and T cell lines. STAT5A mRNA was not detectable in NPM1-ALK
+
T cell lines as measured by reverse transcription polymerase chain reaction (RT-PCR) assays. DNA sequencing revealed the methylation of almost all of the CpG sites in the
STAT5A
promoter of NPM1-ALK
+
TCL cells obtained from patients, but no methylation in T cells from healthy donors. DNA methylation of gene promoters inhibits their transcription. Chromatin immunoprecipitation (ChIP) assays showed that SP1, an activator of
STAT5A
transcription, could not bind to the methylated
STAT5A
promoter in NPM1-ALK
+
T cells. Treatment of NPM1-ALK
+
T cells with the DNA methyltransferase inhibitor 5′-aza-2′-deoxycytidine (5′-aza) led to a time-dependent increase in the expression of
STAT5A
and the abundance of STAT5A protein. This was associated with a gradual decrease in the abundance of NPM1-ALK protein. Electrophoretic mobility shift assays showed that STAT5A bound directly to the enhancer region of
NPM1-ALK
. Transfection of an NPM1-ALK
+
T cell line with a small inhibitor RNA specific for NPM1-ALK resulted in the induction of
STAT5A
expression. Finally, treatment of NPM1-ALK
+
T cells with 5′-aza suppressed their growth in vitro. These results suggest that STAT5A acts as a tumor suppressor and that inhibiting ALK activity, which would prevent the silencing of
STAT5A
, might be therapeutically beneficial.

Q. Zhang, H. Y. Wang, X. Liu, M. A. Wasik, STAT5A is epigenetically silenced by the tyrosine kinase NPM1-ALK and acts as a tumor suppressor by reciprocally inhibiting NPM1-ALK expression.
Nat
.
Med
.
13
, 1341-1348 (2007).
[PubMed]
Flow-Induced Asymmetry
Authors: Gough Nancy R.
Published: December 2007

Mammalian embryos initially develop symmetrically; then, in response to Nodal signaling and the action of the transcription factor Pitx2, organ asymmetry occurs. For example, during embryonic development, two blood vessels on the right side--the right sixth branchial arch artery and the dorsal aorta--undergo complete regression, resulting in the formation of the asymmetrical aortic arch and the pulmonary trunk (see Snider and Conway). Yashiro
et al
. determined that although Pitx2 activity was required for regression of the sixth branchial arch artery, which is the first vessel to regress, expression of this gene was not required in the artery itself. Instead, Pitx2 was required for a morphological change, the formation of a spiral structure of the myocardial left outflow tract, a structure through which blood leaves the heart. In animals in which the outflow tract did not spiral, regression of neither the right sixth branchial arch artery nor the right dorsal aorta occurred. Echocardiography showed that after the formation of the spiral structure, the blood flow to the right side vessels destined for regression was reduced, whereas blood flow to the left side vessels was greater than before the morphological change. Furthermore, this change in blood flow was lost in embryos with a promoter-mutated
Pitx2
(Pitx
ΔASE/ΔASE
), which also lacked a spiral form to the outflow tract and had persistent right vessels. To confirm that decreased blood flow was the signal for regression, the authors ligated the left sixth branchial arch artery prior to the formation of the spiral structure by the outflow tract and found that the left-side vessels (sixth branchial arch artery and dorsal aorta) regressed and the right, unligated vessels persisted. In the persistent left vessels in wild-type animals, there was increased expression of the gene encoding platelet-derived growth factor-A (PDGF-A) and increased phosphorylation of vascular endothelial growth factor receptor 2 (VEGFR2) compared with that in the right vessels after the morphological change. Again, this difference was lost in the Pitx
ΔASE/ΔASE
embryos. Simultaneous pharmacological inhibition of PDGFR and VEGFR triggered bilateral loss of the sixth branchial arch arteries. Thus, the authors suggest that the Nodal-Pitx2 pathway triggers a morphological change that increases blood flow on the left side and decreases blood flow on the right side, producing an asymmetric signal of growth factor signaling, allowing the side with the higher blood flow to survive and the side with less to regress.

P. Snider, S. J. Conway, The power of blood.
Nature
450
, 180-181 (2007).
[PubMed]

K. Yashiro, H. Shiratori, H. Hamada, Haemodynamics determined by a genetic programme govern asymmetric development of the aortic arch.
Nature
450
, 285-288 (2007).
[PubMed]
Good Vibrations?
Authors: Adler Elizabeth M.
Published: December 2007

The beneficial effects of exercise on obesity--and associated conditions such as diabetes--are widely thought to depend on increased metabolic expenditure and are thus expected to correlate with how strenuous and long-lasting a particular physical activity is. Noting that daily exposure to brief periods of high-frequency, low-intensity mechanical signals is anabolic for bone and muscle and that adipocytes, osteoblasts, and myocytes all derive from a common progenitor (the mesenchymal stem cell), Rubin
et al
. investigated the effects of low-magnitude mechanical signals (LMMS) on adipogenesis. After several months’ exposure to a high-frequency mechanical stimulus of lower magnitude than would be incurred by walking (15 minutes 5 days a week of whole-body vibration on an oscillating platform), the fat volume of the torsos of LMMS mice was reduced about 27% relative to that of control mice. This difference, which could not be attributed to changes in food intake, was accompanied by a decrease in liver nonesterified free fatty acid and triglyceride content (both risk factors for type II diabetes). Flow cytometry analysis of mice that had received transplants of green fluorescent protein (GFP)-labeled bone marrow cells indicated that a smaller fraction of marrow-derived mesenchymal stem cells had differentiated into adipocytes in mice subjected for 6 weeks to LMMS. Thus, the authors conclude that brief exposure to high-frequency LMMS can decrease adiposity, at least in part by influencing the generation of adipocytes from mesenchymal stem cells, and speculate that these findings may lead to nonpharmacologic interventions against obesity that do not require prolonged and strenuous physical activity.

C. T. Rubin, E. Capilla, Y. K. Luu, B. Busa, H. Crawford, D. J. Nolan, V. Mittal, C. J. Rosen, J. E. Pessin, S. Judex, Adipogenesis is inhibited by brief, daily exposure to high-frequency, extremely low-magnitude mechanical signals.
Proc. Natl. Acad. Sci. U.S.A.
104
, 17879-17884 (2007).
[Abstract]
[Full Text]
LPS and Liver Fibrosis
Authors: Foley John F.
Published: December 2007

Fibrosis, the production of scar tissue, occurs as a result of tissue damage and is associated with inflammation. In the liver, fibrosis is due to Kupffer cells (liver macrophages), which produce transforming growth factor-β (TGF-β), a primary inducer of liver fibrosis, and hepatic stellate cells (HSCs), which differentiate into extracellular matrix-producing myofibroblasts. Because of accompanying stress on the gut wall, liver injury is associated with the increased abundance, in the liver and blood, of the bacterial product lipopolysaccharide (LPS), a ligand for Toll-like receptor 4 (TLR4), so Seki
et al
. (see the commentary by Friedman) compared liver fibrosis in wild-type and TLR4-mutant mice following liver injury. Immunohistochemical analysis showed that TLR4-mutant mice had less fibrosis than did wild-type mice. Both Kupffer cells and HSCs express TLR4 on their cell surface. In wild-type mice whose Kupffer cells (but not HSCs) were depleted, fibrosis after injury was similar in mice that received bone marrow transplantations from either TLR4-mutant or wild-type mice, indicating that LPS activation of HSCs (but not Kupffer cells) was important for fibrosis. LPS treatment of HSCs isolated from Coll-GFP reporter mice [in which the green fluorescent protein (GFP) gene is controlled by the
collagen-α1
promoter] did not induce GFP production or myofibroblast differentiation but sensitized them to TGF-β treatment. DNA microarray analysis showed that
Bambi
(encoding bone morphogenetic protein and activin membrane-bound inhibitor), a pseudoreceptor that binds to TGF-β but does not signal, was the only TGF-β-related gene whose expression was changed (it was down-regulated) by LPS treatment of HSCs. Thus, LPS in the liver, by decreasing the abundance of Bambi on the surface of HSCs, increases their responsiveness to Kupffer cell-derived TGF-β, leading to enhanced fibrosis.

E. Seki, S. De Minicis, C. H. Österreicher, J. Kluwe, Y. Osawa, D. A. Brenner, R. F. Schwabe, TLR4 enhances TGF-β signaling and hepatic fibrosis.
Nat
.
Med
.
13
, 1324-1332 (2007).
[PubMed]

S. L. Friedman, A deer in the headlights: BAMBI meets liver fibrosis.
Nat
.
Med
.
13
, 1281-1282 (2007).
[PubMed]
Doing Double Duty
Authors: Hurtley Stella M.
Published: December 2007

During intracellular vesicular trafficking, delivery of Rab guanosine triphosphatases (GTPases) to sites of activation involves their release from a guanine nucleotide dissociation inhibitor (GDI) by a so-called GDI displacement factor (GDF). The identification of GDFs has been difficult. Now Machner and Isberg provide evidence for the existence of such an activity, surprisingly in a bifunctional protein--a guanine nucleotide exchange protein associated with the formation of a replication vacuole by the intracellular pathogen
Legionella pneumophila
.

M. P. Machner, R. R. Isberg, A bifunctional bacterial protein links GDI displacement to Rab1 activation.
Science
318
, 974-977 (2007).
[Abstract]
[Full Text]
LOV to Get Together When It’s Light Out
Authors: Adler Elizabeth M.
Published: December 2007

Like plants and fungi, many bacteria contain proteins with a photosensory LOV (light, oxygen, or voltage) domain. In bacteria, LOV domains are frequently found in sensor histidine kinases; however, the function of presumably photosensory proteins in many bacteria that are neither photosynthetic, phototactic, nor pigmented is unclear. Purcell
et al.
investigated the properties and functions of a two-component signaling system found in
Caulobacter crescentus
, comprising the LOV-histidine kinase LovK and its response regulator LovR. Analysis of purified LovK indicated that it exhibited a reversible photocycle and that both its autophosphorylation activity and its ability to hydrolyze ATP were enhanced by light. Strains of
C. crescentus
that lacked LovR were defective in adhesion to glass, whereas the combined overexpression of LovK and LovR promoted enhanced cell-to-cell adhesion. Mutational analysis indicated that this phenotype of enhanced intercellular adhesion depended on conserved phosphorylation sites in both LovK and LovR. Combined overexpression of LovK and LovR promoted cell adhesion even in the dark. However, adhesion was markedly enhanced by exposure to blue light, an effect that depended on the ability of LovK to undergo photoactivation--a process that requires formation of a transient covalent bond between a cysteine in the LOV domain and a flavin cofactor--as did the light-dependent enhancement of LovK autophosphorylation. Thus, the authors conclude that light-dependent modulation of LovK activity regulates intercellular attachment in
C. crescentus
.

E. B. Purcell, D. Siegal-Gaskins, D. C. Rawling, A. Fiebig, S. Crosson, A photosensory two-component system regulates bacterial cell attachment.
Proc. Natl. Acad. Sci. U.S.A.
104
, 18241-18246 (2007).
[Abstract]
[Full Text]
Modular Control of Kinase Function
Authors: Ray L. Bryan
Published: December 2007

Protein kinase D2 (DKD2) can be activated in response to the peptide hormone gastrin. Blume
et al
. clarify how phosphorylation at multiple sites regulates PKD2’s actions in the cell. In gastric cancer cells that overexpress the gastrin receptors, PKD2 with a fluorescent tag was seen to move to the nucleus when cells were treated with gastrin. Protein kinase C η (PKCη) phosphorylated PKD2 on two sites that must be phosphorylated to activate kinase activity of PKD2, but overexpression of PKCη did not cause nuclear accumulation of PKD2. The authors therefore searched for another phosphorylation site and used mass spectrometry to identify Ser
244
as a site phosphorylated in response to gastrin. Expression of mutant forms of PKD indicated that phosphorylation at the Ser
244
site was critical for nuclear localization and that optimal nuclear localization also required catalytic activity of PKD2. Fluorescence loss in photobleaching studies showed that phosphorylation at Ser
244
primarily prevented nuclear export of the kinase. Inhibitor studies identified casein kinase 1 (CK1) delta and epsilon isoforms as potential mediators of Ser
244
phosphorylation, and the role of CK1 enzymes was confirmed in studies in which the enzymes were depleted with siRNA and others showing gastrin activation of the CKs. Other PKD enzymes regulate transcription by phosphorylating class IIa histone deacetylases, and the authors demonstrated interaction of PKD2 with HDAC7 that was enhanced in gastrin-treated cells. siRNA-mediated depletion of PKD2 showed that the kinase was required for nuclear export of HDAC7, which led to increased transcription of HDAC7 target genes. The authors thus conclude that regulation of gene expression through PKD2 is controlled by one kinase (PKCη) that controls catalytic activity of PKD2 and another (CK1δ) that controls its subcellular localization.

J. von Blume, U. Knippschild, F. Dequiedt, G. Giamas, A. Beck, A. Auer, J. Van Lint, G. Adler, T. Seufferlein, Phosphorylation at Ser244 by CK1 determines nuclear localization and substrate targeting of PKD2.
EMBO J.
26
, 4619-4633 (2007).
[PubMed]