bluuebunny/crossref_metadata_2025 huggingface dataset:
Eradication of melanomas by targeted elimination of a minor subset of tumor cells
Authors: Schmidt Patrick , Kopecky Caroline , Hombach Andreas , Zigrino Paola , Mauch Cornelia , Abken Hinrich
Published: February 2011

Proceeding on the assumption that all cancer cells have equal malignant capacities, current regimens in cancer therapy attempt to eradicate all malignant cells of a tumor lesion. Using in vivo targeting of tumor cell subsets, we demonstrate that selective elimination of a definite, minor tumor cell subpopulation is particularly effective in eradicating established melanoma lesions irrespective of the bulk of cancer cells. Tumor cell subsets were specifically eliminated in a tumor lesion by adoptive transfer of engineered cytotoxic T cells redirected in an antigen-restricted manner via a chimeric antigen receptor. Targeted elimination of less than 2% of the tumor cells that coexpress high molecular weight melanoma-associated antigen (HMW-MAA) (melanoma-associated chondroitin sulfate proteoglycan, MCSP) and CD20 lastingly eradicated melanoma lesions, whereas targeting of any random 10% tumor cell subset was not effective. Our data challenge the biological therapy and current drug development paradigms in the treatment of cancer.
Histone H4 Lys 20 monomethylation by histone methylase SET8 mediates Wnt target gene activation
Authors: Li Zhenfei , Nie Fen , Wang Sheng , Li Lin
Published: February 2011

Histone methylation has an important role in transcriptional regulation. However, unlike H3K4 and H3K9 methylation, the role of H4K20 monomethylation (H4K20me-1) in transcriptional regulation remains unclear. Here, we show that Wnt3a specifically stimulates H4K20 monomethylation at the T cell factor (TCF)-binding element through the histone methylase SET8. Additionally, SET8 is crucial for activation of the Wnt reporter gene and target genes in both mammalian cells and zebrafish. Furthermore, SET8 interacts with lymphoid enhancing factor-1 (LEF1)/TCF4 directly, and this interaction is regulated by Wnt3a. Therefore, we conclude that SET8 is a Wnt signaling mediator and is recruited by LEF1/TCF4 to regulate the transcription of Wnt-activated genes, possibly through H4K20 monomethylation at the target gene promoters. Our findings also indicate that H4K20me-1 is a marker for gene transcription activation, at least in canonical Wnt signaling.
Grb-2–associated binder 1 (Gab1) regulates postnatal ischemic and VEGF-induced angiogenesis through the protein kinase A–endothelial NOS pathway
Authors: Lu Yao , Xiong Yan , Huo Yingqing , Han Jingyan , Yang Xiao , Zhang Rongli , Zhu De-Sheng , Klein-Heßling Stefan , Li Jun , Zhang Xiaoyu , Han Xiaofan , Li Yanli , Shen Bin , He Yulong , Shibuya Masabumi , Feng Gen-Sheng , Luo Jincai
Published: February 2011

The intracellular signaling mechanisms underlying postnatal angiogenesis are incompletely understood. Herein we show that Grb-2–associated binder 1 (Gab1) plays a critical role in ischemic and VEGF-induced angiogenesis. Endothelium-specific Gab1 KO (EGKO) mice displayed impaired angiogenesis in the ischemic hindlimb despite normal induction of VEGF expression. Matrigel plugs with VEGF implanted in EGKO mice induced fewer capillaries than those in control mice. The vessels and endothelial cells (ECs) derived from EGKO mice were defective in vascular sprouting and tube formation induced by VEGF. Biochemical analyses revealed a substantial reduction of endothelial NOS (eNOS) activation in Gab1-deficient vessels and ECs following VEGF stimulation. Interestingly, the phosphorylation of Akt, an enzyme known to promote VEGF-induced eNOS activation, was increased in Gab1-deficient vessels and ECs whereas protein kinase A (PKA) activity was significantly decreased. Introduction of an active form of PKA rescued VEGF-induced eNOS activation and tube formation in EGKO ECs. Reexpression of WT or mutant Gab1 molecules in EGKO ECs revealed requirement of Gab1/Shp2 association for the activation of PKA and eNOS. Taken together, these results identify Gab1 as a critical upstream signaling component in VEGF-induced eNOS activation and tube formation, which is dependent on PKA. Of note, this pathway is conserved in primary human ECs for VEGF-induced eNOS activation and tube formation, suggesting considerable potential in treatment of human ischemic diseases.
The genome of the fire ant
Solenopsis invicta
Authors: Wurm Yannick , Wang John , Riba-Grognuz Oksana , Corona Miguel , Nygaard Sanne , Hunt Brendan G. , Ingram Krista K. , Falquet Laurent , Nipitwattanaphon Mingkwan , Gotzek Dietrich , Dijkstra Michiel B. , Oettler Jan , Comtesse Fabien , Shih Cheng-Jen , Wu Wen-Jer , Yang Chin-Cheng , Thomas Jerome , Beaudoing Emmanuel , Pradervand Sylvain , Flegel Volker , Cook Erin D. , Fabbretti Roberto , Stockinger Heinz , Long Li , Farmerie William G. , Oakey Jane , Boomsma Jacobus J. , Pamilo Pekka , Yi Soojin V. , Heinze Jürgen , Goodisman Michael A. D. , Farinelli Laurent , Harshman Keith , Hulo Nicolas , Cerutti Lorenzo , Xenarios Ioannis , Shoemaker DeWayne , Keller Laurent
Published: February 2011

Ants have evolved very complex societies and are key ecosystem members. Some ants, such as the fire ant
Solenopsis invicta
, are also major pests. Here, we present a draft genome of
S. invicta
, assembled from Roche 454 and Illumina sequencing reads obtained from a focal haploid male and his brothers. We used comparative genomic methods to obtain insight into the unique features of the
S. invicta
genome. For example, we found that this genome harbors four adjacent copies of vitellogenin. A phylogenetic analysis revealed that an ancestral vitellogenin gene first underwent a duplication that was followed by possibly independent duplications of each of the daughter vitellogenins. The vitellogenin genes have undergone subfunctionalization with queen- and worker-specific expression, possibly reflecting differential selection acting on the queen and worker castes. Additionally, we identified more than 400 putative olfactory receptors of which at least 297 are intact. This represents the largest repertoire reported so far in insects.
S. invicta
also harbors an expansion of a specific family of lipid-processing genes, two putative orthologs to the
transformer/feminizer
sex differentiation gene, a functional DNA methylation system, and a single putative telomerase ortholog. EST data indicate that this
S. invicta
telomerase ortholog has at least four spliceforms that differ in their use of two sets of mutually exclusive exons. Some of these and other unique aspects of the fire ant genome are likely linked to the complex social behavior of this species.
Thiol peroxidases mediate specific genome-wide regulation of gene expression in response to hydrogen peroxide
Authors: Fomenko Dmitri E. , Koc Ahmet , Agisheva Natalia , Jacobsen Michael , Kaya Alaattin , Malinouski Mikalai , Rutherford Julian C. , Siu Kam-Leung , Jin Dong-Yan , Winge Dennis R. , Gladyshev Vadim N.
Published: February 2011

Hydrogen peroxide is thought to regulate cellular processes by direct oxidation of numerous cellular proteins, whereas antioxidants, most notably thiol peroxidases, are thought to reduce peroxides and inhibit H
2
O
2
response. However, thiol peroxidases have also been implicated in activation of transcription factors and signaling. It remains unclear if these enzymes stimulate or inhibit redox regulation and whether this regulation is widespread or limited to a few cellular components. Herein, we found that
Saccharomyces cerevisiae
cells lacking all eight thiol peroxidases were viable and withstood redox stresses. They transcriptionally responded to various redox treatments, but were unable to activate and repress gene expression in response to H
2
O
2
. Further studies involving redox transcription factors suggested that thiol peroxidases are major regulators of global gene expression in response to H
2
O
2
. The data suggest that thiol peroxidases sense and transfer oxidative signals to the signaling proteins and regulate transcription, whereas a direct interaction between H
2
O
2
and other cellular proteins plays a secondary role.
Agronomic phosphorus imbalances across the world's croplands
Authors: MacDonald Graham K. , Bennett Elena M. , Potter Philip A. , Ramankutty Navin
Published: February 2011

Increased phosphorus (P) fertilizer use and livestock production has fundamentally altered the global P cycle. We calculated spatially explicit P balances for cropland soils at 0.5° resolution based on the principal agronomic P inputs and outputs associated with production of 123 crops globally for the year 2000. Although agronomic inputs of P fertilizer (14.2 Tg of P·y−1) and manure (9.6 Tg of P·y−1) collectively exceeded P removal by harvested crops (12.3 Tg of P·y−1) at the global scale, P deficits covered almost 30% of the global cropland area. There was massive variation in the magnitudes of these P imbalances across most regions, particularly Europe and South America. High P fertilizer application relative to crop P use resulted in a greater proportion of the intense P surpluses (>13 kg of P·ha−1·y−1) globally than manure P application. High P fertilizer application was also typically associated with areas of relatively low P-use efficiency. Although manure was an important driver of P surpluses in some locations with high livestock densities, P deficits were common in areas producing forage crops used as livestock feed. Resolving agronomic P imbalances may be possible with more efficient use of P fertilizers and more effective recycling of manure P. Such reforms are needed to increase global agricultural productivity while maintaining or improving freshwater quality.
Gradual disintegration of the floral symmetry gene network is implicated in the evolution of a wind-pollination syndrome
Authors: Preston Jill C. , Martinez Ciera C. , Hileman Lena C.
Published: February 2011

Angiosperms exhibit staggering diversity in floral form, and evolution of floral morphology is often correlated with changes in pollination syndrome. The showy, bilaterally symmetrical flowers of the model species
Antirrhinum majus
(Plantaginaceae) are highly specialized for bee pollination. In
A. majus
,
CYCLOIDEA
(
CYC
),
DICHOTOMA
(
DICH
),
RADIALIS
(
RAD
), and
DIVARICATA
(
DIV
) specify the development of floral bilateral symmetry. However, it is unclear to what extent evolution of these genes has resulted in flower morphological divergence among closely related members of Plantaginaceae differing in pollination syndrome. We compared floral symmetry genes from insect-pollinated
Digitalis purpurea
, which has bilaterally symmetrical flowers, with those from closely related
Aragoa abietina
and wind-pollinated
Plantago major
, both of which have radially symmetrical flowers. We demonstrate that
Plantago
, but not
Aragoa
, species have lost a dorsally expressed
CYC
-like gene and downstream targets
RAD
and
DIV
. Furthermore, the single
P. major CYC
-like gene is expressed across all regions of the flower, similar to expression of its ortholog in closely related
Veronica serpyllifolia
. We propose that changes in the expression of duplicated
CYC
-like genes led to the evolution of radial flower symmetry in
Aragoa
/
Plantago
, and that further disintegration of the symmetry gene pathway resulted in the wind-pollination syndrome of
Plantago
. This model underscores the potential importance of gene loss in the evolution of ecologically important traits.
Physical and economic consequences of climate change in Europe
Authors: Ciscar Juan-Carlos , Iglesias Ana , Feyen Luc , Szabó László , Van Regemorter Denise , Amelung Bas , Nicholls Robert , Watkiss Paul , Christensen Ole B. , Dankers Rutger , Garrote Luis , Goodess Clare M. , Hunt Alistair , Moreno Alvaro , Richards Julie , Soria Antonio
Published: February 2011

Quantitative estimates of the economic damages of climate change usually are based on aggregate relationships linking average temperature change to loss in gross domestic product (GDP). However, there is a clear need for further detail in the regional and sectoral dimensions of impact assessments to design and prioritize adaptation strategies. New developments in regional climate modeling and physical-impact modeling in Europe allow a better exploration of those dimensions. This article quantifies the potential consequences of climate change in Europe in four market impact categories (agriculture, river floods, coastal areas, and tourism) and one nonmarket impact (human health). The methodology integrates a set of coherent, high-resolution climate change projections and physical models into an economic modeling framework. We find that if the climate of the 2080s were to occur today, the annual loss in household welfare in the European Union (EU) resulting from the four market impacts would range between 0.2–1%. If the welfare loss is assumed to be constant over time, climate change may halve the EU's annual welfare growth. Scenarios with warmer temperatures and a higher rise in sea level result in more severe economic damage. However, the results show that there are large variations across European regions. Southern Europe, the British Isles, and Central Europe North appear most sensitive to climate change. Northern Europe, on the other hand, is the only region with net economic benefits, driven mainly by the positive effects on agriculture. Coastal systems, agriculture, and river flooding are the most important of the four market impacts assessed.
Impaired theory of mind for moral judgment in high-functioning autism
Authors: Moran Joseph M. , Young Liane L. , Saxe Rebecca , Lee Su Mei , O'Young Daniel , Mavros Penelope L. , Gabrieli John D.
Published: February 2011

High-functioning autism (ASD) is characterized by real-life difficulties in social interaction; however, these individuals often succeed on laboratory tests that require an understanding of another person's beliefs and intentions. This paradox suggests a theory of mind (ToM) deficit in adults with ASD that has yet to be demonstrated in an experimental task eliciting ToM judgments. We tested whether ASD adults would show atypical moral judgments when they need to consider both the intentions (based on ToM) and outcomes of a person's actions. In experiment 1, ASD and neurotypical (NT) participants performed a ToM task designed to test false belief understanding. In experiment 2, the same ASD participants and a new group of NT participants judged the moral permissibility of actions, in a 2 (intention: neutral/negative) × 2 (outcome: neutral/negative) design. Though there was no difference between groups on the false belief task, there was a selective difference in the moral judgment task for judgments of accidental harms, but not neutral acts, attempted harms, or intentional harms. Unlike the NT group, which judged accidental harms less morally wrong than attempted harms, the ASD group did not reliably judge accidental and attempted harms as morally different. In judging accidental harms, ASD participants appeared to show an underreliance on information about a person's innocent intention and, as a direct result, an overreliance on the action's negative outcome. These findings reveal impairments in integrating mental state information (e.g., beliefs, intentions) for moral judgment.
Unique inhibitory synapse with particularly rich endocannabinoid signaling machinery on pyramidal neurons in basal amygdaloid nucleus
Authors: Yoshida Takayuki , Uchigashima Motokazu , Yamasaki Miwako , Katona Istvan , Yamazaki Maya , Sakimura Kenji , Kano Masanobu , Yoshioka Mitsuhiro , Watanabe Masahiko
Published: February 2011

2-Arachidonoylglycerol (2-AG) is the endocannabinoid that mediates retrograde suppression of synaptic transmission in the brain. 2-AG is synthesized in activated postsynaptic neurons by
sn
-1-specific diacylglycerol lipase (DGL), binds to presynaptic cannabinoid CB
1
receptors, suppresses neurotransmitter release, and is degraded mainly by monoacylglycerol lipase (MGL). In the basolateral amygdala complex, it has been demonstrated that CB
1
is particularly enriched in axon terminals of cholecystokinin (CCK)-positive GABAergic interneurons, induces short- and long-term depression at inhibitory synapses, and is involved in extinction of fear memory. Here, we clarified a unique molecular convergence of DGLα, CB
1
, and MGL at specific inhibitory synapses in the basal nucleus (BA), but not lateral nucleus, of the basolateral amygdala. The synapses, termed invaginating synapses, consisted of conventional symmetrical contact and unique perisynaptic invagination of nerve terminals into perikarya. At invaginating synapses, DGLα was preferentially recruited to concave somatic membrane of postsynaptic pyramidal neurons, whereas invaginating presynaptic terminals highly expressed CB
1
, MGL, and CCK. No such molecular convergence was seen for flat perisomatic synapses made by parvalbumin-positive interneurons. On the other hand, DGLα and CB
1
were expressed weakly at axospinous excitatory synapses. Consistent with these morphological data, thresholds for DGLα-mediated depolarization-induced retrograde suppression were much lower for inhibitory synapses than for excitatory synapses in BA pyramidal neurons. Moreover, depolarization-induced suppression was readily saturated for inhibition, but never for excitation. These findings suggest that perisomatic inhibition by invaginating synapses is a key target of 2-AG-mediated control of the excitability of BA pyramidal neurons.
Aphid genome expression reveals host–symbiont cooperation in the production of amino acids
Authors: Hansen Allison K. , Moran Nancy A.
Published: February 2011

The evolution of intimate symbiosis requires the coordination of gene expression and content between the distinct partner genomes; this coordination allows the fusion of capabilities of each organism into a single integrated metabolism. In aphids, the 10 essential amino acids are scarce in the phloem sap diet and are supplied by the obligate bacterial endosymbiont (
Buchnera
), which lives inside specialized cells called bacteriocytes. Although
Buchnera
’s genome encodes most genes for essential amino acid biosynthesis, several genes in essential amino acid pathways are missing, as are most genes for production of nonessential amino acids. Additionally, it is unresolved whether the supply of nitrogen for amino acid biosynthesis is supplemented by recycling of waste ammonia. We compared pea aphid gene expression between bacteriocytes and other body tissues using RNA sequencing and pathway analysis and exploiting the genome sequences available for both partners. We found that 26 genes underlying amino acid biosynthesis were up-regulated in bacteriocytes. Seven of these up-regulated genes fill the gaps of
Buchnera
’s essential amino acid pathways. In addition, genes underlying five nonessential amino acid pathways lost from
Buchnera
are up-regulated in bacteriocytes. Finally, our results reveal that two genes, glutamine synthetase and glutamate synthase, which potentially work together in the incorporation of ammonium nitrogen into glutamate (GOGAT) cycle to assimilate ammonia into glutamate, are up-regulated in bacteriocytes. Thus, host gene expression and symbiont capabilities are closely integrated within bacteriocytes, which function as specialized organs of amino acid production. Furthermore, the GOGAT cycle may be a key source of nitrogen fueling the integrated amino acid metabolism of the aphid–
Buchnera
partnership.
Identification of an antithrombotic allosteric modulator that acts through helix 8 of PAR1
Authors: Dowal Louisa , Sim Derek S. , Dilks James R. , Blair Price , Beaudry Sarah , Denker Bradley M. , Koukos Georgios , Kuliopulos Athan , Flaumenhaft Robert
Published: February 2011

G protein-coupled receptors (GPCRs) can assume multiple conformations and possess multiple binding sites. Whereas endogenous agonists acting at the orthosteric binding site stabilize the active receptor conformation, small molecules that act at nonorthosteric sites can stabilize alternative conformations. The large majority of these allosteric modulators associate with extracellular loops of GPCRs. The role of intracellular domains in mediating allosteric modulation is largely unknown. In screening a small-molecule library for inhibitors of platelet activation, we identified a family of compounds that modified PAR1-mediated granule secretion. The most potent inhibitory compound, termed JF5, also demonstrated noncompetitive inhibition of the α
2A
-adrenergic receptor. Aggregation studies using a battery of platelet GPCR agonists demonstrated that sensitivity to JF5 was limited to GPCRs that possessed a constrained eighth helix, as defined by a C-terminal palmitoylation site and interactions with TM7 and the i1 loop. Inhibition by JF5 was overcome in a PAR1 mutant in which the eighth helix was deleted, confirming a role for helix 8 in JF5 activity. Evaluation of downstream signaling showed that JF5 was selective with regard to G protein coupling, blocking signaling mediated by G
αq
but not G
α12
. The compound inhibited thrombus formation in vivo following vascular injury with an IC
50
of ∼1 mg/kg. These results indicate a role for helix 8 in conferring sensitivity to small molecules, and show that this sensitivity can be exploited to control platelet activation during thrombus formation.
Entropic crystal–crystal transitions of Brownian squares
Authors: Zhao Kun , Bruinsma Robijn , Mason Thomas G.
Published: February 2011

When a monolayer of hard microscale square platelets, produced lithographically, is osmotically concentrated in a flat plane to raise the particle area fraction
ϕ

A

, an order–order transition occurs between a hexagonal rotator crystal and a rhombic crystal. Strikingly, phases having fourfold symmetry are not observed at any
ϕ

A

. The rhombic lattice angle
α
increases continuously with
ϕ

A

, as the system maximizes its total rotational and translational entropy. A cage model, based on packing rotationally swept squares, or “squaroids,” reasonably predicts the measured
α
(
ϕ

A

), indicating that rotational entropy and the square particle shape combine to produce the rhombic unit cell.
Hox gene
Ultrabithorax
regulates distinct sets of target genes at successive stages of
Drosophila
haltere morphogenesis
Authors: Pavlopoulos Anastasios , Akam Michael
Published: February 2011

Hox genes encode highly conserved transcription factors that regionalize the animal body axis by controlling complex developmental processes. Although they are known to operate in multiple cell types and at different stages, we are still missing the batteries of genes targeted by any one Hox gene over the course of a single developmental process to achieve a particular cell and organ morphology. The transformation of wings into halteres by the Hox gene
Ultrabithorax
(
Ubx
) in
Drosophila melanogaster
presents an excellent model system to study the Hox control of transcriptional networks during successive stages of appendage morphogenesis and cell differentiation. We have used an inducible misexpression system to switch on
Ubx
in the wing epithelium at successive stages during metamorphosis—in the larva, prepupa, and pupa. We have then used extensive microarray expression profiling and quantitative RT-PCR to identify the primary transcriptional responses to Ubx. We find that Ubx targets range from regulatory genes like transcription factors and signaling components to terminal differentiation genes affecting a broad repertoire of cell behaviors and metabolic reactions. Ubx up- and down-regulates hundreds of downstream genes at each stage, mostly in a subtle manner. Strikingly, our analysis reveals that Ubx target genes are largely distinct at different stages of appendage morphogenesis, suggesting extensive interactions between Hox genes and hormone-controlled regulatory networks to orchestrate complex genetic programs during metamorphosis.
Use of OmpU porins for attachment and invasion of
Crassostrea gigas
immune cells by the oyster pathogen
Vibrio splendidus
Authors: Duperthuy Marylise , Schmitt Paulina , Garzón Edwin , Caro Audrey , Rosa Rafael D. , Le Roux Frédérique , Lautrédou-Audouy Nicole , Got Patrice , Romestand Bernard , de Lorgeril Julien , Kieffer-Jaquinod Sylvie , Bachère Evelyne , Destoumieux-Garzón Delphine
Published: February 2011

OmpU porins are increasingly recognized as key determinants of pathogenic host
Vibrio
interactions. Although mechanisms remain incompletely understood, various species, including the human pathogen
Vibrio cholera
, require OmpU for host colonization and virulence. We have shown previously that OmpU is essential for virulence in the oyster pathogen
Vibrio splendidus
LGP32. Here, we showed that
V. splendidus
LGP32 invades the oyster immune cells, the hemocytes, through subversion of host-cell actin cytoskeleton. In this process, OmpU serves as an adhesin/invasin required for β-integrin recognition and host cell invasion. Furthermore, the major protein of oyster plasma, the extracellular superoxide dismutase
Cg
-EcSOD, is used as an opsonin mediating the OmpU-promoted phagocytosis through its RGD sequence. Finally, the endocytosed bacteria were found to survive intracellularly, evading the host defense by preventing acidic vacuole formation and limiting reactive oxygen species production. We conclude that (
i
)
V. splendidus
is a facultative intracellular pathogen that manipulates host defense mechanisms to enter and survive in host immune cells, and (
ii
) that OmpU is a major determinant of host cell invasion in
Vibrio
species, used by
V. splendidus
LGP32 to attach and invade oyster hemocytes through opsonisation by the oyster plasma
Cg
-EcSOD.
XMAP215 polymerase activity is built by combining multiple tubulin-binding TOG domains and a basic lattice-binding region
Authors: Widlund Per O. , Stear Jeffrey H. , Pozniakovsky Andrei , Zanic Marija , Reber Simone , Brouhard Gary J. , Hyman Anthony A. , Howard Jonathon
Published: February 2011

XMAP215/Dis1 family proteins positively regulate microtubule growth. Repeats at their N termini, called TOG domains, are important for this function. While TOG domains directly bind tubulin dimers, it is unclear how this interaction translates to polymerase activity. Understanding the functional roles of TOG domains is further complicated by the fact that the number of these domains present in the proteins of different species varies. Here, we take advantage of a recent crystal structure of the third TOG domain from
Caenorhabditis elegans
, Zyg9, and mutate key residues in each TOG domain of XMAP215 that are predicted to be important for interaction with the tubulin heterodimer. We determined the contributions of the individual TOG domains to microtubule growth. We show that the TOG domains are absolutely required to bind free tubulin and that the domains differentially contribute to XMAP215’s overall affinity for free tubulin. The mutants’ overall affinity for free tubulin correlates well with polymerase activity. Furthermore, we demonstrate that an additional basic region is important for targeting to the microtubule lattice and is critical for XMAP215 to function at physiological concentrations. Using this information, we have engineered a “bonsai” protein, with two TOG domains and a basic region, that has almost full polymerase activity.
Differential electrophysiological response during rest, self-referential, and non–self-referential tasks in human posteromedial cortex
Authors: Dastjerdi Mohammad , Foster Brett L. , Nasrullah Sharmin , Rauschecker Andreas M. , Dougherty Robert F. , Townsend Jennifer D. , Chang Catie , Greicius Michael D. , Menon Vinod , Kennedy Daniel P. , Parvizi Josef
Published: February 2011

The electrophysiological basis for higher brain activity during rest and internally directed cognition within the human default mode network (DMN) remains largely unknown. Here we use intracranial recordings in the human posteromedial cortex (PMC), a core node within the DMN, during conditions of cued rest, autobiographical judgments, and arithmetic processing. We found a heterogeneous profile of PMC responses in functional, spatial, and temporal domains. Although the majority of PMC sites showed increased broad gamma band activity (30–180 Hz) during rest, some PMC sites, proximal to the retrosplenial cortex, responded selectively to autobiographical stimuli. However, no site responded to both conditions, even though they were located within the boundaries of the DMN identified with resting-state functional imaging and similarly deactivated during arithmetic processing. These findings, which provide electrophysiological evidence for heterogeneity within the core of the DMN, will have important implications for neuroimaging studies of the DMN.
Lactobacillus reuteri
-produced cyclic dipeptides quench
agr
-mediated expression of toxic shock syndrome toxin-1 in staphylococci
Authors: Li Jingru , Wang Wenliang , Xu Stacey X. , Magarvey Nathan A. , McCormick John K.
Published: February 2011

The production of the staphylococcal exotoxin toxic shock syndrome toxin-1 (TSST-1) by
Staphylococcus aureus
has been associated with essentially all cases of menstruation-associated toxic shock syndrome (TSS). In this work, we show that the human vaginal isolate
Lactobacillus reuteri
RC-14 produces small signaling molecules that are able to interfere with the staphylococcal quorum-sensing system
agr
, a key regulator of virulence genes, and repress the expression of TSST-1 in
S. aureus
MN8, a prototype of menstrual TSS
S. aureus
strains. Quantitative real-time PCR data showed that transcription from the P
tst
promoter, as well as the P2 and P3 promoters of the
agr
system from all four
agr
subgroups of
S. aureus
, was strongly inhibited in response to growth with
L. reuteri
RC-14 cultural supernatant. Alterations in the transcriptional levels of two other virulence-associated regulators
sarA
and
saeRS
were also observed, indicating a potential overall influence of
L. reuteri
RC-14 signals on the production of virulence factors in
S. aureus
.
S. aureus
promoter-
lux
reporter strains were used to screen biochemically fractionated
L. reuteri
RC-14 supernatant, and the cyclic dipeptides cyclo(
l
-Phe-
l
-Pro) and cyclo(
l
-Tyr-
l
-Pro) were identified as the signaling molecules. The results from this work contribute to a better understanding of interspecies cell-to-cell communication between
Lactobacillus
and
Staphylococcus
, and provide a unique mechanism by which endogenous or probiotic strains may attenuate virulence factor production by bacterial pathogens.
Real-time mapping of a hydrogen peroxide concentration profile across a polymicrobial bacterial biofilm using scanning electrochemical microscopy
Authors: Liu Xiuhui , Ramsey Matthew M. , Chen Xiaole , Koley Dipankar , Whiteley Marvin , Bard Allen J.
Published: February 2011

Quantitative detection of hydrogen peroxide in solution above aStreptococcus gordonii(Sg) bacterial biofilm was studied in real time by scanning electrochemical microscopy (SECM). The concentration of hydrogen peroxide was determined to be 0.7 mM to 1.6 mM in the presence of 10 mM glucose over a period of 2 to 8 h. The hydrogen peroxide production measured was higher near the biofilm surface in comparison toSggrown planktonically. Differential hydrogen peroxide production was observed both by fluorometric as well as by SECM measurements. The interaction between two different species in a bacterial biofilm ofSgandAggregatibacter actinomycetemcomitans(Aa) in terms of hydrogen peroxide production was also studied by SECM. One-directional y-scan SECM measurements showed the unique spatial mapping of hydrogen peroxide concentration across a mixed species biofilm and revealed that hydrogen peroxide concentration varies greatly dependent upon local species composition.
Losartan inhibits collagen I synthesis and improves the distribution and efficacy of nanotherapeutics in tumors
Authors: Diop-Frimpong Benjamin , Chauhan Vikash P. , Krane Stephen , Boucher Yves , Jain Rakesh K.
Published: February 2011

The dense collagen network in tumors significantly reduces the penetration and efficacy of nanotherapeutics. We tested whether losartan—a clinically approved angiotensin II receptor antagonist with noted antifibrotic activity—can enhance the penetration and efficacy of nanomedicine. We found that losartan inhibited collagen I production by carcinoma-associated fibroblasts isolated from breast cancer biopsies. Additionally, it led to a dose-dependent reduction in stromal collagen in desmoplastic models of human breast, pancreatic, and skin tumors in mice. Furthermore, losartan improved the distribution and therapeutic efficacy of intratumorally injected oncolytic herpes simplex viruses. Finally, it also enhanced the efficacy of i.v. injected pegylated liposomal doxorubicin (Doxil). Thus, losartan has the potential to enhance the efficacy of nanotherapeutics in patients with desmoplastic tumors.
Crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit
Authors: Belousoff Matthew J. , Shapira Tal , Bashan Anat , Zimmerman Ella , Rozenberg Haim , Arakawa Kenji , Kinashi Haruyasu , Yonath Ada
Published: February 2011

The structures of the large ribosomal subunit of
Deinococcus radiodurans
(D50S) in complex with the antibiotic lankamycin (3.2 Å) and a double antibiotic complex of lankamycin and lankacidin C (3.45 Å) have been determined, in continuation of previous crystallographic studies on lankacidin-D50S complex. These two drugs have been previously reported to inhibit ribosomal function with mild synergistic effect. Lankamycin, a member of the macrolide family, binds in a similar manner to erythromycin. However, when in complex with lankacidin, lankamycin is located so that it can form interactions with lankacidin in the adjacent ribosomal binding site. When compared to the well-documented synergistic antibiotics, Streptogramins A and B, the pair of lankacidin and lankamycin bind in similar sites, the peptidyl transferase center and nascent peptide exit tunnel, respectively. Herein, we discuss the structural basis for antibiotic synergism and highlight the key factors involved in ribosomal inhibition.
Signatures of murine B-cell development implicate Yy1 as a regulator of the germinal center-specific program
Authors: Green Michael R. , Monti Stefano , Dalla-Favera Riccardo , Pasqualucci Laura , Walsh Nicole C. , Schmidt-Supprian Marc , Kutok Jeffery L. , Rodig Scott J. , Neuberg Donna S. , Rajewsky Klaus , Golub Todd R. , Alt Frederick W. , Shipp Margaret A. , Manis John P.
Published: February 2011

We utilized gene expression profiling of a comprehensive panel of purified developmentally defined normal murine B cells to identify unique transcriptional signatures for each subset. To elucidate transcription factor activities that function in a stage-specific fashion, we used gene sets that share transcription factor targets and found that germinal center B cells had a robust enrichment of up-regulated and down-regulated signatures compared with the other B-cell subsets. Notably, we found Yy1 and its targets to be central regulators of the germinal center B (GCB)-specific transcriptional program with binding of Yy1 to select signature genes in GCB cells, and translation of the Yy1 signatures to human GCB cells. We then tested whether our newly generated, stage-specific transcriptional signatures could be used to link murine lymphoma models to stages of normal B-cell development. Although each of the molecularly defined murine lymphoma models conserved certain stage-specific features of normal B-cell development, there was a significant alteration of the normal differentiation signature following malignant transformation. These findings offer important tools and insights for elucidating differences between normal and malignant B cells.
Escherichia coli
sister chromosome separation includes an abrupt global transition with concomitant release of late-splitting intersister snaps
Authors: Joshi Mohan C. , Bourniquel Aude , Fisher Jay , Ho Brian T. , Magnan David , Kleckner Nancy , Bates David
Published: February 2011

The basis for segregation of sister chromosomes in bacteria is not established. We show here that two discrete ~150-kb regions, both located early in the right replichore, exhibit prolonged juxtaposition of sister loci, for 20 and 30 min, respectively, after replication. Flanking regions, meanwhile, separate. Thus, the two identified regions comprise specialized late-splitting intersister connections or snaps. Sister snap loci separate simultaneously in both snap regions, concomitant with a major global nucleoid reorganization that results in emergence of a bilobed nucleoid morphology. Split snap loci move rapidly apart to a separation distance comparable with one-half the length of the nucleoid. Concomitantly, at already split positions, sister loci undergo further separation to a comparable distance. The overall consequence of these and other effects is that thus far replicated sister chromosomes become spatially separated (individualized) into the two nucleoid lobes, while the terminus region (and likely, all unreplicated portions of the chromosome) moves to midcell. These and other findings imply that segregation of
Escherichia coli
sister chromosomes is not a smooth continuous process but involves at least one and likely, two major global transition(s). The presented patterns further suggest that accumulation of internal intranucleoid forces and constraining of these forces by snaps play central roles in global chromosome dynamics. They are consistent with and supportive of our previous proposals that individualization of sisters in
E. coli
is driven primarily by internally generated pushing forces and is directly analogous to sister individualization at the prophase to prometaphase transition of the eukaryotic cell cycle.
Mesodermal developmental gene Tbx15 impairs adipocyte differentiation and mitochondrial respiration
Authors: Gesta Stephane , Bezy Olivier , Mori Marcelo A. , Macotela Yazmin , Lee Kevin Y. , Kahn C. Ronald
Published: February 2011

Increased intraabdominal (visceral) fat is associated with a high risk of diabetes and metabolic syndrome. We have previously shown that the mesodermal developmental transcription factor Tbx15 is highly differentially expressed between visceral and subcutaneous (s.c.) fat in both humans and rodents, and in humans visceral fat Tbx15 expression is decreased in obesity. Here we show that, in mice, Tbx15 is 260-fold more highly expressed in s.c. preadipocytes than in epididymal preadipocytes. Overexpression of Tbx15 in 3T3-L1 preadipocytes impairs adipocyte differentiation and decreases triglyceride content. This defect in differentiation can be corrected by stimulating cells with the PPARγ agonist rosiglitazone (Rosi). However, triglyceride accumulation remains decreased by ∼50%, due to a decrease in basal lipogenic rate and increase in basal lipolytic rate. 3T3-L1 preadipocytes overexpressing Tbx15 also have a 15% reduction in mitochondrial mass and a 28% reduction in basal mitochondrial respiration (P= 0.004) and ATP turnover (P= 0.02), and a 45% (P= 0.003) reduction in mitochondrial respiratory capacity. Thus, differential expression of Tbx15 between fat depots plays an important role in the interdepot differences in adipocyte differentiation, triglyceride accumulation, and mitochondrial function that may contribute to the risk of diabetes and metabolic disease.
A novel role for BRCA1 in regulating breast cancer cell spreading and motility
Authors: Coene Elisabeth D. , Gadelha Catarina , White Nicholas , Malhas Ashraf , Thomas Benjamin , Shaw Michael , Vaux David J.
Published: February 2011

BRCA1 C-terminal (BRCT) domains in BRCA1 are essential for tumor suppressor function, though the underlying mechanisms remain unclear. We identified ezrin, radixin, and moesin as BRCA1 BRCT domain–interacting proteins. Ezrin–radixin–moesin (ERM) and F-actin colocalized with BRCA1 at the plasma membrane (PM) of cancer cells, especially at leading edges and focal adhesion sites. In stably expressing cancer cells, high levels of enhanced green fluorescent protein (EGFP)-BRCA11634–1863 acted as a dominant-negative factor, displacing endogenous BRCA1 from the PM. This led to delayed cell spreading, increased spontaneous motility, and irregular monolayer wound healing. MCF-7 cells (intact BRCA1) showed lower motility than HCC1937 cells (truncated BRCA1), but expression of EGFP-BRCA11634–1863 in MCF-7 increased motility. Conversely, full-length BRCA1 expression in HCC1937 decreased motility but only if the protein retained ubiquitin ligase activity. We conclude that full-length BRCA1 is important for complete tumor suppressor activity via interaction of its BRCT domains with ERM at the PM, controlling spreading and motility of cancer cells via ubiquitin ligase activity.
Replication protein A safeguards genome integrity by controlling NER incision events
Authors: Overmeer René M. , Moser Jill , Volker Marcel , Kool Hanneke , Tomkinson Alan E. , van Zeeland Albert A. , Mullenders Leon H.F. , Fousteri Maria
Published: February 2011

Single-stranded DNA gaps that might arise by futile repair processes can lead to mutagenic events and challenge genome integrity. Nucleotide excision repair (NER) is an evolutionarily conserved repair mechanism, essential for removal of helix-distorting DNA lesions. In the currently prevailing model, NER operates through coordinated assembly of repair factors into pre- and post-incision complexes; however, its regulation in vivo is poorly understood. Notably, the transition from dual incision to repair synthesis should be rigidly synchronized as it might lead to accumulation of unprocessed repair intermediates. We monitored NER regulatory events in vivo using sequential UV irradiations. Under conditions that allow incision yet prevent completion of repair synthesis or ligation, preincision factors can reassociate with new damage sites. In contrast, replication protein A remains at the incomplete NER sites and regulates a feedback loop from completion of DNA repair synthesis to subsequent damage recognition, independently of ATR signaling. Our data reveal an important function for replication protein A in averting further generation of DNA strand breaks that could lead to mutagenic and recombinogenic events.
The serine/threonine kinase Par1b regulates epithelial lumen polarity via IRSp53-mediated cell–ECM signaling
Authors: Cohen David , Fernandez Dawn , Lázaro-Diéguez Francisco , Müsch Anne
Published: February 2011

The serine/threonine kinase Par1b promotes cell–cell adhesion and determines the polarity of the luminal domain in epithelial cells. In this study, we demonstrate that Par1b also regulates cell–extracellular matrix (ECM) signaling in kidney-derived Madin–Darby canine kidney (MDCK) cells and identified the rho–guanosine triphosphatase adaptor and scaffolding protein IRSp53 as a Par1b substrate involved in this pathway. Par1b overexpression inhibits basal lamina formation, cell spreading, focal adhesion, stress fiber formation, and compaction, whereas Par1b depletion has the opposite effect. IRSp53 depletion mimics Par1b overexpression on cell–ECM signaling and lumen polarity but had no effect on adherens junction formation. Par1b directly phosphorylates IRSp53 on S366 in cell lysates and stimulates phosphorylation on S453/3/5 via an indirect mechanism. A Par1b phosphorylation–deficient IRSp53 mutant but not the wild-type protein efficiently rescues both the cell spreading and the lumen polarity defects in Par1b MDCK cells. Our data suggest a model in which Par1b phosphorylation prevents recruitment of IRSp53 effector proteins to its Src homology domain 3 by promoting 14-3-3 binding in the vicinity of that domain.
The full-of-bacteria gene is required for phagosome maturation during immune defense in Drosophila
Authors: Akbar Mohammed Ali , Tracy Charles , Kahr Walter H.A. , Krämer Helmut
Published: February 2011

Arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome is a fatal recessive disorder caused by mutations in the VPS33B or VPS16B genes. Both encode homologues of the Vps33p and Vps16p subunits of the HOPS complex necessary for fusions of vacuoles in yeast. Here, we describe a mutation in the full-of-bacteria (fob) gene, which encodes Drosophila Vps16B. Flies null for fob are homozygous viable and fertile. They exhibit, however, a defect in their immune defense that renders them hypersensitive to infections with nonpathogenic bacteria. fob hemocytes (fly macrophages) engulf bacteria but fail to digest them. Phagosomes undergo early steps of maturation and transition to a Rab7-positive stage, but do not mature to fully acidified phagolysosomes. This reflects a specific requirement of fob in the fusion of phagosomes with late endosomes/lysosomes. In contrast, cargo of autophagosomes as well as endosomes exhibit normal lysosomal delivery in fob cells. These findings suggest that defects in phagosome maturation may contribute to symptoms of ARC patients including recurring infections.
The N-terminal coiled-coil of Ndel1 is a regulated scaffold that recruits LIS1 to dynein
Authors: Żyłkiewicz Eliza , Kijańska Monika , Choi Won-Chan , Derewenda Urszula , Derewenda Zygmunt S. , Stukenberg P. Todd
Published: February 2011

Ndel1 has been implicated in a variety of dynein-related processes, but its specific function is unclear. Here we describe an experimental approach to evaluate a role of Ndel1 in dynein-dependent microtubule self-organization using Ran-mediated asters in meiotic Xenopus egg extracts. We demonstrate that extracts depleted of Ndel1 are unable to form asters and that this defect can be rescued by the addition of recombinant N-terminal coiled-coil domain of Ndel1. Ndel1-dependent microtubule self-organization requires an interaction between Ndel1 and dynein, which is mediated by the dimerization fragment of the coiled-coil. Full rescue by the coiled-coil domain requires LIS1 binding, and increasing LIS1 concentration partly rescues aster formation, suggesting that Ndel1 is a recruitment factor for LIS1. The interactions between Ndel1 and its binding partners are positively regulated by phosphorylation of the unstructured C terminus. Together, our results provide important insights into how Ndel1 acts as a regulated scaffold to temporally and spatially regulate dynein.
FBXW7 influences murine intestinal homeostasis and cancer, targeting Notch, Jun, and DEK for degradation
Authors: Babaei-Jadidi Roya , Li Ningning , Saadeddin Anas , Spencer-Dene Bradley , Jandke Anett , Muhammad Belal , Ibrahim ElSayed E. , Muraleedharan Ranjithmenon , Abuzinadah Mohammed , Davis Hayley , Lewis Annabelle , Watson Susan , Behrens Axel , Tomlinson Ian , Nateri Abdolrahman Shams
Published: February 2011

The Fbxw7 (F-box/WD repeat–containing protein 7; also called CDC4, Sel10, Ago, and Fbw7) component of the SCF (Skp1/Cullin/F-box protein) E3 ubiquitin ligase complex acts as a tumor suppressor in several tissues and targets multiple transcriptional activators and protooncogenes for ubiquitin-mediated degradation. To understand Fbxw7 function in the murine intestine, in this study, we specifically deleted Fbxw7 in the murine gut using Villin-Cre (Fbxw7ΔG). In wild-type mice, loss of Fbxw7 in the gut altered homeostasis of the intestinal epithelium, resulted in elevated Notch and c-Jun expression, and induced development of adenomas at 9–10 mo of age. In the context of APC (adenomatous polyposis coli) deficiency (ApcMin/+ mice), loss of Fbxw7 accelerated intestinal tumorigenesis and death and promoted accumulation of β-catenin in adenomas at late but not early time points. At early time points, Fbxw7 mutant tumors showed accumulation of the DEK protooncogene. DEK expression promoted cell division and altered splicing of tropomyosin (TPM) RNA, which may also influence cell proliferation. DEK accumulation and altered TPM RNA splicing were also detected in FBXW7 mutant human colorectal tumor tissues. Given their reduced lifespan and increased incidence of intestinal tumors, ApcMin/+Fbxw7ΔG mice may be used for testing carcinogenicity and drug screening.