bluuebunny/crossref_metadata_2025 huggingface dataset:
Direct detection of guidance receptor activity during border cell migration
Authors: Janssens Katrien , Sung Hsin-Ho , Rørth Pernille
Published: April 2010

Guidance receptor signaling is crucial for steering migrating cells. Despite this, we generally lack direct measurements of such signaling. Border cells in Drosophila migrate as a tightly associated group, but dynamically, with front and rear cells exchanging places. They use the receptor tyrosine kinase (RTK) PDGF/VEGF receptor (PVR) as a guidance receptor, perceiving the attractant Pvf1. Here we determine the spatial distribution of PVR signaling by generating an antibody that specifically detects activated PVR in situ. PVR activity is very low in migrating border cells, due to strong activity of cellular phosphatases. Measurements of signal at the cell cortex show variability but a strong bias for both total active PVR and specific activity of PVR to be elevated at the front versus side of the leading cell, often with several-fold difference in signal levels. This polarized active PVR signal requires the E3 ubiquitin ligase Cbl and the recycling regulator Rab11, indicating a dependency on receptor trafficking. The endogenous ligand gradient contributes to shaping of signaling by increasing the specific activity of PVR toward the source in front cells. Surprisingly, signaling is also elevated at the back versus the side of rear cells. This distally polarized distribution of active PVR is ligand independent. Thus the actual guidance signal transmitted in border cells appears to integrate perceived ligand distribution with cell polarity or cell orientation with respect to the cluster. A general implication is that both group configuration and extrinsic cues can directly modulate guidance receptor signaling during collective cell migration.
Histone H3K27 methyltransferase Ezh2 represses
Wnt
genes to facilitate adipogenesis
Authors: Wang Lifeng , Jin Qihuang , Lee Ji-Eun , Su I-hsin , Ge Kai
Published: April 2010

Wnt/β-catenin signaling inhibits adipogenesis. Genome-wide profiling studies have revealed the enrichment of histone H3K27 methyltransferase Ezh2 on
Wnt
genes. However, the functional significance of such a direct link between the two types of developmental regulators in mammalian cells, and the role of Ezh2 in adipogenesis, remain unclear. Here we show Ezh2 and its H3K27 methyltransferase activity are required for adipogenesis. Ezh2 directly represses
Wnt1
, -
6
, -
10a
, and -
10b
genes in preadipocytes and during adipogenesis. Deletion of Ezh2 eliminates H3K27me3 on
Wnt
promoters and derepresses
Wnt
expression, which leads to activation of Wnt/β-catenin signaling and inhibition of adipogenesis. Ectopic expression of the wild-type (WT) Ezh2, but not the enzymatically inactive F667I mutant, prevents the loss of H3K27me3 and the defects in adipogenesis in
Ezh2
−/−
preadipocytes. The adipogenesis defects in
Ezh2
−/−
cells can be rescued by expression of adipogenic transcription factors PPARγ, C/EBPα, or inhibitors of Wnt/β-catenin signaling. Interestingly,
Ezh2
−/−
cells show marked increase of H3K27 acetylation globally as well as on
Wnt
promoters. These results indicate that H3K27 methyltransferase Ezh2 directly represses
Wnt
genes to facilitate adipogenesis and suggest that acetylation and trimethylation on H3K27 play opposing roles in regulating
Wnt
expression.
The
bba64
gene of
Borrelia burgdorferi
, the Lyme disease agent, is critical for mammalian infection via tick bite transmission
Authors: Gilmore Robert D. , Howison Rebekah R. , Dietrich Gabrielle , Patton Toni G. , Clifton Dawn R. , Carroll James A.
Published: April 2010

The spirochetal agent of Lyme disease,
Borrelia burgdorferi
, is transmitted by bites of
Ixodes
ticks to mammalian reservoir hosts and humans. The mechanism(s) by which the organism is trafficked from vector to host is poorly understood. In this study, we demonstrate that a
B. burgdorferi
mutant strain deficient in the synthesis of the
bba64
gene product was incapable of infecting mice via tick bite even though the mutant was (
i
) infectious in mice when introduced by needle inoculation, (
ii
) acquired by larval ticks feeding on infected mice, and (
iii
) able to persist through tick molting stages. This finding of a
B. burgdorferi
gene required for pathogen transfer and/or survival from the tick to the susceptible host represents an important breakthrough toward understanding transmission mechanisms involved for the Lyme disease agent.
Structural and functional analysis of the YAP-binding domain of human TEAD2
Authors: Tian Wei , Yu Jianzhong , Tomchick Diana R. , Pan Duojia , Luo Xuelian
Published: April 2010

The Hippo pathway controls organ size and suppresses tumorigenesis in metazoans by blocking cell proliferation and promoting apoptosis. The TEAD1-4 proteins (which contain a DNA-binding domain but lack an activation domain) interact with YAP (which lacks a DNA-binding domain but contains an activation domain) to form functional heterodimeric transcription factors that activate proliferative and prosurvival gene expression programs. The Hippo pathway inhibits the YAP-TEAD hybrid transcription factors by phosphorylating and promoting cytoplasmic retention of YAP. Here we report the crystal structure of the YAP-binding domain (YBD) of human TEAD2. TEAD2 YBD adopts an immunoglobulin-like β-sandwich fold with two extra helix-turn-helix inserts. NMR studies reveal that the TEAD-binding domain of YAP is natively unfolded and that TEAD binding causes localized conformational changes in YAP. In vitro binding and in vivo functional assays define an extensive conserved surface of TEAD2 YBD as the YAP-binding site. Therefore, our studies suggest that a short segment of YAP adopts an extended conformation and forms extensive contacts with a rigid surface of TEAD. Targeting a surface-exposed pocket of TEAD might be an effective strategy to disrupt the YAP-TEAD interaction and to reduce the oncogenic potential of YAP.
Cretaceous African life captured in amber
Authors: Schmidt Alexander R. , Perrichot Vincent , Svojtka Matthias , Anderson Ken B. , Belete Kebede H. , Bussert Robert , Dörfelt Heinrich , Jancke Saskia , Mohr Barbara , Mohrmann Eva , Nascimbene Paul C. , Nel André , Nel Patricia , Ragazzi Eugenio , Roghi Guido , Saupe Erin E. , Schmidt Kerstin , Schneider Harald , Selden Paul A. , Vávra Norbert
Published: April 2010

Amber is of great paleontological importance because it preserves a diverse array of organisms and associated remains from different habitats in and close to the amber-producing forests. Therefore, the discovery of amber inclusions is important not only for tracing the evolutionary history of lineages with otherwise poor fossil records, but also for elucidating the composition, diversity, and ecology of terrestrial paleoecosystems. Here, we report a unique find of African amber with inclusions, from the Cretaceous of Ethiopia. Ancient arthropods belonging to the ants, wasps, thrips, zorapterans, and spiders are the earliest African records of these ecologically important groups and constitute significant discoveries providing insight into the temporal and geographical origins of these lineages. Together with diverse microscopic inclusions, these findings reveal the interactions of plants, fungi and arthropods during an epoch of major change in terrestrial ecosystems, which was caused by the initial radiation of the angiosperms. Because of its age, paleogeographic location and the exceptional preservation of the inclusions, this fossil resin broadens our understanding of the ecology of Cretaceous woodlands.
Organic particulate material levels in the atmosphere: Conditions favoring sensitivity to varying relative humidity and temperature
Authors: Pankow James F.
Published: April 2010

This study examines the sensitivity in predicted levels of atmospheric organic particulate matter (
M
o
, μg m
-3
) as those levels may potentially be affected by changes in relative humidity and temperature. In a given system, for each partitioning compound,
f
g
and
f
p
represent the gaseous and particulate fractions (
f
g
 + 
f
p
 = 1). Sensitivity in the
M
o
levels becomes
dampened
as the compounds contributing significantly to
M
o
are increasingly found in the
particle phase
(
f
p
 → 1). Thus, although local maxima in sensitivity can be encountered as
M
o
levels increase, because as
M
o
increases each
f
p
 → 1, then increasing
M
o
levels generally tend to reduce sensitivity in
M
o
levels to changes in relative humidity and temperature. Experiments designed to elucidate the potential magnitudes of the effects of relative humidity and temperature on
M
o
levels must be carried out at
M
o
levels that are relevant for the ambient atmosphere: The
f
p
values for the important partitioning compounds must not be elevated above ambient-relevant values. Systems in which
M
o
levels are low (e.g., 1–2 μg m
-3
) and/or composed of unaged secondary organic aerosol are the ones most likely to show sensitivity to changing relative humidity and temperature. Results from two published chamber studies are examined in the above regard: [Warren B, et al. (2009)
Atmos Environ
43:1789–1795] and [Prisle NL, et al. (2010)
Geophys Res Lett
37:L01802].
Monitoring of NY-ESO-1 specific CD4
+
T cells using molecularly defined MHC class II/His-tag-peptide tetramers
Authors: Ayyoub Maha , Dojcinovic Danijel , Pignon Pascale , Raimbaud Isabelle , Schmidt Julien , Luescher Immanuel , Valmori Danila
Published: April 2010

MHC-peptide tetramers have become essential tools for T-cell analysis, but few MHC class II tetramers incorporating peptides from human tumor and self-antigens have been developed. Among limiting factors are the high polymorphism of class II molecules and the low binding capacity of the peptides. Here, we report the generation of molecularly defined tetramers using His-tagged peptides and isolation of folded MHC/peptide monomers by affinity purification. Using this strategy we generated tetramers of DR52b (DRB3*0202), an allele expressed by approximately half of Caucasians, incorporating an epitope from the tumor antigen NY-ESO-1. Molecularly defined tetramers avidly and stably bound to specific CD4
+
T cells with negligible background on nonspecific cells. Using molecularly defined DR52b/NY-ESO-1 tetramers, we could demonstrate that in DR52b
+
cancer patients immunized with a recombinant NY-ESO-1 vaccine, vaccine-induced tetramer-positive cells represent ex vivo in average 1:5,000 circulating CD4
+
T cells, include central and transitional memory polyfunctional populations, and do not include CD4
+
CD25
+
CD127
−
regulatory T cells. This approach may significantly accelerate the development of reliable MHC class II tetramers to monitor immune responses to tumor and self-antigens.
Generation and control of sound bullets with a nonlinear acoustic lens
Authors: Spadoni Alessandro , Daraio Chiara
Published: April 2010

Acoustic lenses are employed in a variety of applications, from biomedical imaging and surgery to defense systems and damage detection in materials. Focused acoustic signals, for example, enable ultrasonic transducers to image the interior of the human body. Currently however the performance of acoustic devices is limited by their linear operational envelope, which implies relatively inaccurate focusing and low focal power. Here we show a dramatic focusing effect and the generation of compact acoustic pulses (sound bullets) in solid and fluid media, with energies orders of magnitude greater than previously achievable. This focusing is made possible by a tunable, nonlinear acoustic lens, which consists of ordered arrays of granular chains. The amplitude, size, and location of the sound bullets can be controlled by varying the static precompression of the chains. Theory and numerical simulations demonstrate the focusing effect, and photoelasticity experiments corroborate it. Our nonlinear lens permits a qualitatively new way of generating high-energy acoustic pulses, which may improve imaging capabilities through increased accuracy and signal-to-noise ratios and may lead to more effective nonintrusive scalpels, for example, for cancer treatment.
Reasoning about social conflicts improves into old age
Authors: Grossmann Igor , Na Jinkyung , Varnum Michael E. W. , Park Denise C. , Kitayama Shinobu , Nisbett Richard E.
Published: April 2010

It is well documented that aging is associated with cognitive declines in many domains. Yet it is a common lay belief that some aspects of thinking improve into old age. Specifically, older people are believed to show better competencies for reasoning about social dilemmas and conflicts. Moreover, the idea of aging-related gains in wisdom is consistent with views of the aging mind in developmental psychology. However, to date research has provided little evidence corroborating this assumption. We addressed this question in two studies, using a representative community sample. We asked participants to read stories about intergroup conflicts and interpersonal conflicts and predict how these conflicts would unfold. We show that relative to young and middle-aged people, older people make more use of higher-order reasoning schemes that emphasize the need for multiple perspectives, allow for compromise, and recognize the limits of knowledge. Our coding scheme was validated by a group of professional counselors and wisdom researchers. Social reasoning improves with age despite a decline in fluid intelligence. The results suggest that it might be advisable to assign older individuals to key social roles involving legal decisions, counseling, and intergroup negotiations. Furthermore, given the abundance of research on negative effects of aging, this study may help to encourage clinicians to emphasize the inherent strengths associated with aging.
Interactions among predators and the cascading effects of vertebrate insectivores on arthropod communities and plants
Authors: Mooney Kailen A. , Gruner Daniel S. , Barber Nicholas A. , Van Bael Sunshine A. , Philpott Stacy M. , Greenberg Russell
Published: April 2010

Theory on trophic interactions predicts that predators increase plant biomass by feeding on herbivores, an indirect interaction called a trophic cascade. Theory also predicts that predators feeding on predators, or intraguild predation, will weaken trophic cascades. Although past syntheses have confirmed cascading effects of terrestrial arthropod predators, we lack a comprehensive analysis for vertebrate insectivores—which by virtue of their body size and feeding habits are often top predators in these systems—and of how intraguild predation mediates trophic cascade strength. We report here on a meta-analysis of 113 experiments documenting the effects of insectivorous birds, bats, or lizards on predaceous arthropods, herbivorous arthropods, and plants. Although vertebrate insectivores fed as intraguild predators, strongly reducing predaceous arthropods (38%), they nevertheless suppressed herbivores (39%), indirectly reduced plant damage (40%), and increased plant biomass (14%). Furthermore, effects of vertebrate insectivores on predatory and herbivorous arthropods were positively correlated. Effects were strongest on arthropods and plants in communities with abundant predaceous arthropods and strong intraguild predation, but weak in communities depauperate in arthropod predators and intraguild predation. The naturally occurring ratio of arthropod predators relative to herbivores varied tremendously among the studied communities, and the skew to predators increased with site primary productivity and in trees relative to shrubs. Although intraguild predation among arthropod predators has been shown to weaken herbivore suppression, we find this paradigm does not extend to vertebrate insectivores in these communities. Instead, vertebrate intraguild preda-tion is associated with strengthened trophic cascades, and insectivores function as dominant predators in terrestrial plant-arthropod communities.
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins
Authors: Turnbaugh Peter J. , Quince Christopher , Faith Jeremiah J. , McHardy Alice C. , Yatsunenko Tanya , Niazi Faheem , Affourtit Jason , Egholm Michael , Henrissat Bernard , Knight Rob , Gordon Jeffrey I.
Published: April 2010

We deeply sampled the organismal, genetic, and transcriptional diversity in fecal samples collected from a monozygotic (MZ) twin pair and compared the results to 1,095 communities from the gut and other body habitats of related and unrelated individuals. Using a new scheme for noise reduction in pyrosequencing data, we estimated the total diversity of species-level bacterial phylotypes in the 1.2-1.5 million bacterial 16S rRNA reads obtained from each deeply sampled cotwin to be ~800 (35.9%, 49.1% detected in both). A combined 1.1 million read 16S rRNA dataset representing 281 shallowly sequenced fecal samples from 54 twin pairs and their mothers contained an estimated 4,018 species-level phylotypes, with each sample having a unique species assemblage (53.4 ± 0.6% and 50.3 ± 0.5% overlap with the deeply sampled cotwins). Of the 134 phylotypes with a relative abundance of >0.1% in the combined dataset, only 37 appeared in >50% of the samples, with one phylotype in the Lachnospiraceae family present in 99%. Nongut communities had significantly reduced overlap with the deeply sequenced twins’ fecal microbiota (18.3 ± 0.3%, 15.3 ± 0.3%). The MZ cotwins’ fecal DNA was deeply sequenced (3.8-6.3 Gbp/sample) and assembled reads were assigned to 25 genus-level phylogenetic bins. Only 17% of the genes in these bins were shared between the cotwins. Bins exhibited differences in their degree of sequence variation, gene content including the repertoire of carbohydrate active enzymes present within and between twins (e.g., predicted cellulases, dockerins), and transcriptional activities. These results provide an expanded perspective about features that make each of us unique life forms and directions for future characterization of our gut ecosystems.
Clinical response and
miR-29b
predictive significance in older AML patients treated with a 10-day schedule of decitabine
Authors: Blum William , Garzon Ramiro , Klisovic Rebecca B. , Schwind Sebastian , Walker Alison , Geyer Susan , Liu Shujun , Havelange Violaine , Becker Heiko , Schaaf Larry , Mickle Jon , Devine Hollie , Kefauver Cheryl , Devine Steven M. , Chan Kenneth K. , Heerema Nyla A. , Bloomfield Clara D. , Grever Michael R. , Byrd John C. , Villalona-Calero Miguel , Croce Carlo M. , Marcucci Guido
Published: April 2010

A phase II clinical trial with single-agent decitabine was conducted in older patients (≥60 years) with previously untreated acute myeloid leukemia (AML) who were not candidates for or who refused intensive chemotherapy. Subjects received low-dose decitabine at 20 mg/m
2
i.v. over 1 h on days 1 to 10. Fifty-three subjects enrolled with a median age of 74 years (range, 60–85). Nineteen (36%) had antecedent hematologic disorder or therapy-related AML; 16 had complex karyotypes (≥3 abnormalities). The complete remission rate was 47% (
n
= 25), achieved after a median of three cycles of therapy. Nine additional subjects had no morphologic evidence of disease with incomplete count recovery, for an overall response rate of 64% (
n
= 34). Complete remission was achieved in 52% of subjects presenting with normal karyotype and in 50% of those with complex karyotypes. Median overall and disease-free survival durations were 55 and 46 weeks, respectively. Death within 30 days of initiation of treatment occurred in one subject (2%), death within 8 weeks in 15% of subjects. Given the DNA hypomethylating effect of decitabine, we examined the relationship of clinical response and pretreatment level of
miR-29b
, previously shown to target DNA methyltransferases. Higher levels of
miR-29b
were associated with clinical response (
P
= 0.02). In conclusion, this schedule of decitabine was highly active and well tolerated in this poor-risk cohort of older AML patients. Levels of
miR-29b
should be validated as a predictive factor for stratification of older AML patients to decitabine treatment.
Comprehensive assessment of variation at the transforming growth factor β type 1 receptor locus and colorectal cancer predisposition
Authors: Carvajal-Carmona Luis G. , Churchman Mike , Bonilla Carolina , Walther Axel , Lefèvre Jeremie H. , Kerr David , Dunlop Malcolm , Houlston Richard , Bodmer Walter F. , Tomlinson Ian
Published: April 2010

The role of transforming growth factor β receptor type 1 (
TGFBR1
) polymorphisms, particularly a coding CGC insertion (rs11466445,
TGFBR1*6A/9A
) in exon 1, has been extensively investigated in regard to colorectal cancer (CRC) risk. These investigations have generated conflicting results. More recently, allele-specific expression (ASE) of
TGFBR1
mRNA has been suggested as predisposing to CRC, with a relative risk of nearly 10-fold and a population attributable risk of ∼10%. Owing to the potential importance of
TGFBR1
variants in CRC, we performed a comprehensive examination of tagging SNPs at and around the gene in 3,101 CRC cases and 3,334 controls of northern European ancestry. To test whether rare or subpolymorphic
TGFBR1
variants were associated with CRC risk, we sequenced the gene's exons in a subset of patients. We also evaluated
TGFBR1
ASE in a panel of CRC cases and controls. Overall, we found no association between
TGFBR1
polymorphisms and CRC risk. The rare variant screen did not identify any changes of potentially pathogenic effects. No evidence of greater ASE in cases than controls was detected, and no haplotype around
TGFBR1
could account for the ASE reported in other studies. We conclude that neither genetic variation nor ASE at
TGFBR1
is likely to be a major CRC risk factor.
Nrf2 responses and the therapeutic selectivity of electrophilic compounds in chronic lymphocytic leukemia
Authors: Wu Raymond P. , Hayashi Tomoko , Cottam Howard B. , Jin Guangyi , Yao Shiyin , Wu Christina C. N. , Rosenbach Michael D. , Corr Maripat , Schwab Richard B. , Carson Dennis A.
Published: April 2010

Recent studies show that redox-active small molecules are selectively cytotoxic to chronic lymphocytic leukemia (CLL). Although elevated levels of reactive oxygen species in CLL cells have been implicated, the molecular mechanism underlying this selectivity is unclear. In other cell types, the nuclear factor erythroid 2–related factor 2 (Nrf2) signaling pathway regulates the oxidative stress response. We found elevated Nrf2 signaling in untreated CLL cells compared with normal lymphocytes. Therefore, we tested 27 known electrophilic and antioxidant compounds with drug-like properties and determined their CLL-selective cytotoxicity and effect on Nrf2 signaling. The selected compounds were from five distinct structural classes; α-β unsaturated carbonyls, isothiocyanates, sulfhydryl reactive metals, flavones, and polyphenols. Our results show that compounds containing α-β unsaturated carbonyls, sulfhydryl reactive metals, and isothiocyanates are strong activators of Nrf2 in a reporter assay system and in primary human CLL based on increased expression of the Nrf2 target heme oxygenase–1. α-β Unsaturated carbonyl–containing compounds were selectively cytotoxic to CLL, and loss of the α-β unsaturation abrogated Nrf2 activity and CLL toxicity. The α-β unsaturated carbonyl containing compounds ethacrynic acid and parthenolide activated Nrf2 in normal peripheral blood mononuclear cells, but had a less potent effect in CLL cells. Furthermore, ethacrynic acid bound directly to the Nrf2-negative regulator Kelch-like ECH-associated protein 1 (Keap1) in CLL cells. These experiments document the presence of Nrf2 signaling in human CLL and suggest that altered Nrf2 responses may contribute to the observed selective cytotoxicity of electrophilic compounds in this disease.
Tomato Cf resistance proteins mediate recognition of cognate homologous effectors from fungi pathogenic on dicots and monocots
Authors: Stergiopoulos Ioannis , van den Burg Harrold A. , Ökmen Bilal , Beenen Henriek G. , van Liere Sabine , Kema Gert H. J. , de Wit Pierre J. G. M.
Published: April 2010

Most fungal effectors characterized so far are species-specific and facilitate virulence on a particular host plant. During infection of its host tomato,
Cladosporium fulvum
secretes effectors that function as virulence factors in the absence of cognate Cf resistance proteins and induce effector-triggered immunity in their presence. Here we show that homologs of the
C. fulvum
Avr4 and Ecp2 effectors are present in other pathogenic fungi of the Dothideomycete class, including
Mycosphaerella fijiensis
, the causal agent of black Sigatoka disease of banana. We demonstrate that the Avr4 homolog of
M. fijiensis
is a functional ortholog of
C. fulvum
Avr4 that protects fungal cell walls against hydrolysis by plant chitinases through binding to chitin and, despite the low overall sequence homology, triggers a Cf-4-mediated hypersensitive response (HR) in tomato. Furthermore, three homologs of
C. fulvum
Ecp2 are found in
M. fijiensis
, one of which induces different levels of necrosis or HR in tomato lines that lack or contain a putative cognate Cf-Ecp2 protein, respectively. In contrast to Avr4, which acts as a defensive virulence factor,
M. fijiensis
Ecp2 likely promotes virulence by interacting with a putative host target causing host cell necrosis, whereas Cf-Ecp2 could possibly guard the virulence target of Ecp2 and trigger a Cf-Ecp2-mediated HR. Overall our data suggest that Avr4 and Ecp2 represent core effectors that are collectively recognized by single cognate Cf-proteins. Transfer of these
Cf
genes to plant species that are attacked by fungi containing these cognate core effectors provides unique ways for breeding disease-resistant crops.
Function-based gene identification using enzymatically generated normalized shRNA library and massive parallel sequencing
Authors: Shtutman Michael , Maliyekkel Anil , Shao Yu , Carmack C. Steven , Baig Mirza , Warholic Natalie , Cole Kelly , Broude Eugenia V. , Harkins Timothy T. , Ding Ye , Roninson Igor B.
Published: April 2010

As a general strategy for function-based gene identification, an shRNA library containing ≈150 shRNAs per gene was enzymatically generated from normalized (reduced-redundance) human cDNA. The library was constructed in an inducible lentiviral vector, enabling propagation of growth-inhibiting shRNAs and controlled activity measurements. RNAi activities were measured for 101 shRNA clones representing 100 human genes and for 201 shRNAs derived from a firefly luciferase gene. Structure-activity analysis of these two datasets yielded a set of structural criteria for shRNA efficacy, increasing the frequencies of active shRNAs up to 5-fold relative to random sampling. The same library was used to select shRNAs that inhibit breast carcinoma cell growth by targeting potential oncogenes. Genes targeted by the selected shRNAs were enriched for 10 pathways, 9 of which have been previously associated with various cancers, cell cycle progression, or apoptosis. One hundred nineteen genes, enriched through this selection and represented by two to six shRNAs each, were identified as potential cancer drug targets. Short interfering RNAs against 19 of 22 tested genes in this group inhibited cell growth, validating the efficiency of this strategy for high-throughput target gene identification.
Multiple reciprocal adaptations and rapid genetic change upon experimental coevolution of an animal host and its microbial parasite
Authors: Schulte Rebecca D. , Makus Carsten , Hasert Barbara , Michiels Nico K. , Schulenburg Hinrich
Published: April 2010

The coevolution between hosts and parasites is predicted to have complex evolutionary consequences for both antagonists, often within short time periods. To date, conclusive experimental support for the predictions is available mainly for microbial host systems, but for only a few multicellular host taxa. We here introduce a model system of experimental coevolution that consists of the multicellular nematode host
Caenorhabditis elegans
and the microbial parasite
Bacillus thuringiensis
. We demonstrate that 48 host generations of experimental coevolution under controlled laboratory conditions led to multiple changes in both parasite and host. These changes included increases in the traits of direct relevance to the interaction such as parasite virulence (i.e., host killing rate) and host resistance (i.e., the ability to survive pathogens). Importantly, our results provide evidence of reciprocal effects for several other central predictions of the coevolutionary dynamics, including (
i
) possible adaptation costs (i.e., reductions in traits related to the reproductive rate, measured in the absence of the antagonist), (
ii
) rapid genetic changes, and (
iii
) an overall increase in genetic diversity across time. Possible underlying mechanisms for the genetic effects were found to include increased rates of genetic exchange in the parasite and elevated mutation rates in the host. Taken together, our data provide comprehensive experimental evidence of the consequences of host–parasite coevolution, and thus emphasize the pace and complexity of reciprocal adaptations associated with these antagonistic interactions.
Dissociating neural subsystems for grammar by contrasting word order and inflection
Authors: Newman Aaron J. , Supalla Ted , Hauser Peter , Newport Elissa L. , Bavelier Daphne
Published: April 2010

An important question in understanding language processing is whether there are distinct neural mechanisms for processing specific types of grammatical structure, such as syntax versus morphology, and, if so, what the basis of the specialization might be. However, this question is difficult to study: A given language typically conveys its grammatical information in one way (e.g., English marks “who did what to whom” using word order, and German uses inflectional morphology). American Sign Language permits either device, enabling a direct within-language comparison. During functional (f)MRI, native signers viewed sentences that used only word order and sentences that included inflectional morphology. The two sentence types activated an overlapping network of brain regions, but with differential patterns. Word order sentences activated left-lateralized areas involved in working memory and lexical access, including the dorsolateral prefrontal cortex, the inferior frontal gyrus, the inferior parietal lobe, and the middle temporal gyrus. In contrast, inflectional morphology sentences activated areas involved in building and analyzing combinatorial structure, including bilateral inferior frontal and anterior temporal regions as well as the basal ganglia and medial temporal/limbic areas. These findings suggest that for a given linguistic function, neural recruitment may depend upon on the cognitive resources required to process specific types of linguistic cues.
Human cytomegalovirus elicits fetal γδ T cell responses in utero
Authors: Vermijlen David , Brouwer Margreet , Donner Catherine , Liesnard Corinne , Tackoen Marie , Van Rysselberge Michel , Twité Nicolas , Goldman Michel , Marchant Arnaud , Willems Fabienne
Published: April 2010

The fetus and infant are highly susceptible to viral infections. Several viruses, including human cytomegalovirus (CMV), cause more severe disease in early life compared with later life. It is generally accepted that this is a result of the immaturity of the immune system. γδ T cells are unconventional T cells that can react rapidly upon activation and show major histocompatibility complex–unrestricted activity. We show that upon CMV infection in utero, fetal γδ T cells expand and become differentiated. The expansion was restricted to Vγ9-negative γδ T cells, irrespective of their Vδ chain expression. Differentiated γδ T cells expressed high levels of IFN-γ, transcription factors T-bet and eomes, natural killer receptors, and cytotoxic mediators. CMV infection induced a striking enrichment of a public Vγ8Vδ1-TCR, containing the germline-encoded complementary-determining-region-3 (CDR3) δ1–CALGELGDDKLIF/CDR3γ8–CATWDTTGWFKIF. Public Vγ8Vδ1-TCR–expressing cell clones produced IFN-γ upon coincubation with CMV-infected target cells in a TCR/CD3-dependent manner and showed antiviral activity. Differentiated γδ T cells and public Vγ8Vδ1-TCR were detected as early as after 21 wk of gestation. Our results indicate that functional fetal γδ T cell responses can be generated during development in utero and suggest that this T cell subset could participate in antiviral defense in early life.
Anti-phospholipid human monoclonal antibodies inhibit CCR5-tropic HIV-1 and induce β-chemokines
Authors: Moody M. Anthony , Liao Hua-Xin , Alam S. Munir , Scearce Richard M. , Plonk M. Kelly , Kozink Daniel M. , Drinker Mark S. , Zhang Ruijun , Xia Shi-Mao , Sutherland Laura L. , Tomaras Georgia D. , Giles Ian P. , Kappes John C. , Ochsenbauer-Jambor Christina , Edmonds Tara G. , Soares Melina , Barbero Gustavo , Forthal Donald N. , Landucci Gary , Chang Connie , King Steven W. , Kavlie Anita , Denny Thomas N. , Hwang Kwan-Ki , Chen Pojen P. , Thorpe Philip E. , Montefiori David C. , Haynes Barton F.
Published: April 2010

Traditional antibody-mediated neutralization of HIV-1 infection is thought to result from the binding of antibodies to virions, thus preventing virus entry. However, antibodies that broadly neutralize HIV-1 are rare and are not induced by current vaccines. We report that four human anti-phospholipid monoclonal antibodies (mAbs) (PGN632, P1, IS4, and CL1) inhibit HIV-1 CCR5-tropic (R5) primary isolate infection of peripheral blood mononuclear cells (PBMCs) with 80% inhibitory concentrations of <0.02 to ∼10 µg/ml. Anti-phospholipid mAbs inhibited PBMC HIV-1 infection in vitro by mechanisms involving binding to monocytes and triggering the release of MIP-1α and MIP-1β. The release of these β-chemokines explains both the specificity for R5 HIV-1 and the activity of these mAbs in PBMC cultures containing both primary lymphocytes and monocytes.
Targeting iron homeostasis induces cellular differentiation and synergizes with differentiating agents in acute myeloid leukemia
Authors: Callens Celine , Coulon Séverine , Naudin Jerome , Radford-Weiss Isabelle , Boissel Nicolas , Raffoux Emmanuel , Wang Pamella Huey Mei , Agarwal Saurabh , Tamouza Houda , Paubelle Etienne , Asnafi Vahid , Ribeil Jean-Antoine , Dessen Philippe , Canioni Danielle , Chandesris Olivia , Rubio Marie Therese , Beaumont Carole , Benhamou Marc , Dombret Hervé , Macintyre Elizabeth , Monteiro Renato C. , Moura Ivan C. , Hermine Olivier
Published: April 2010

Differentiating agents have been proposed to overcome the impaired cellular differentiation in acute myeloid leukemia (AML). However, only the combinations of all-trans retinoic acid or arsenic trioxide with chemotherapy have been successful, and only in treating acute promyelocytic leukemia (also called AML3). We show that iron homeostasis is an effective target in the treatment of AML. Iron chelating therapy induces the differentiation of leukemia blasts and normal bone marrow precursors into monocytes/macrophages in a manner involving modulation of reactive oxygen species expression and the activation of mitogen-activated protein kinases (MAPKs). 30% of the genes most strongly induced by iron deprivation are also targeted by vitamin D3 (VD), a well known differentiating agent. Iron chelating agents induce expression and phosphorylation of the VD receptor (VDR), and iron deprivation and VD act synergistically. VD magnifies activation of MAPK JNK and the induction of VDR target genes. When used to treat one AML patient refractory to chemotherapy, the combination of iron-chelating agents and VD resulted in reversal of pancytopenia and in blast differentiation. We propose that iron availability modulates myeloid cell commitment and that targeting this cellular differentiation pathway together with conventional differentiating agents provides new therapeutic modalities for AML.
OX40 is required for regulatory T cell–mediated control of colitis
Authors: Griseri Thibault , Asquith Mark , Thompson Claire , Powrie Fiona
Published: April 2010

The immune response in the gastrointestinal tract is a tightly controlled balance between effector and regulatory cell responses. Here, we have investigated the role of OX40 in influencing the balance between conventional T cells and Foxp3+ regulatory T (T reg) cells. Under steady-state conditions, OX40 was required by T reg cells for their accumulation in the colon, but not peripheral lymphoid organs. Strikingly, under inflammatory conditions OX40 played an essential role in T reg cell–mediated suppression of colitis. OX40−/− T reg cells showed reduced accumulation in the colon and peripheral lymphoid organs, resulting in their inability to keep pace with the effector response. In the absence of OX40 signaling, T reg cells underwent enhanced activation-induced cell death, indicating that OX40 delivers an important survival signal to T reg cells after activation. As OX40 also promoted the colitogenic Th1 response, its expression on T reg cells may be required for effective competition with OX40-dependent effector responses.

These results newly identify a key role for OX40 in the homeostasis of intestinal Foxp3 +T reg cells and in suppression of colitis. These fi ndings should be taken into account when considering OX40 blockade for treatment of IBD.
The Blimp1–Bcl6 axis is critical to regulate osteoclast differentiation and bone homeostasis
Authors: Miyauchi Yoshiteru , Ninomiya Ken , Miyamoto Hiroya , Sakamoto Akemi , Iwasaki Ryotaro , Hoshi Hiroko , Miyamoto Kana , Hao Wu , Yoshida Shigeyuki , Morioka Hideo , Chiba Kazuhiro , Kato Shigeaki , Tokuhisa Takeshi , Saitou Mitinori , Toyama Yoshiaki , Suda Toshio , Miyamoto Takeshi
Published: April 2010

Controlling osteoclastogenesis is critical to maintain physiological bone homeostasis and prevent skeletal disorders. Although signaling activating nuclear factor of activated T cells 1 (NFATc1), a transcription factor essential for osteoclastogenesis, has been intensively investigated, factors antagonistic to NFATc1 in osteoclasts have not been characterized. Here, we describe a novel pathway that maintains bone homeostasis via two transcriptional repressors, B cell lymphoma 6 (Bcl6) and B lymphocyte–induced maturation protein-1 (Blimp1). We show that Bcl6 directly targets ‘osteoclastic’ molecules such as NFATc1, cathepsin K, and dendritic cell-specific transmembrane protein (DC-STAMP), all of which are targets of NFATc1. Bcl6-overexpression inhibited osteoclastogenesis in vitro, whereas Bcl6-deficient mice showed accelerated osteoclast differentiation and severe osteoporosis. We report that Bcl6 is a direct target of Blimp1 and that mice lacking Blimp1 in osteoclasts exhibit osteopetrosis caused by impaired osteoclastogenesis resulting from Bcl6 up-regulation. Indeed, mice doubly mutant in Blimp1 and Bcl6 in osteoclasts exhibited decreased bone mass with increased osteoclastogenesis relative to osteoclast-specific Blimp1-deficient mice. These results reveal a Blimp1–Bcl6–osteoclastic molecule axis, which critically regulates bone homeostasis by controlling osteoclastogenesis and may provide a molecular basis for novel therapeutic strategies.
53BP1 regulates DNA resection and the choice between classical and alternative end joining during class switch recombination
Authors: Bothmer Anne , Robbiani Davide F. , Feldhahn Niklas , Gazumyan Anna , Nussenzweig Andre , Nussenzweig Michel C.
Published: April 2010

Class switch recombination (CSR) diversifies antibodies by joining highly repetitive DNA elements, which are separated by 60–200 kbp. CSR is initiated by activation-induced cytidine deaminase, an enzyme that produces multiple DNA double-strand breaks (DSBs) in switch regions. Switch regions are joined by a mechanism that requires an intact DNA damage response and classical or alternative nonhomologous end joining (A-NHEJ). Among the DNA damage response factors, 53BP1 has the most profound effect on CSR. We explore the role of 53BP1 in intrachromosomal DNA repair using I-SceI to introduce paired DSBs in the IgH locus. We find that the absence of 53BP1 results in an ataxia telangiectasia mutated–dependent increase in DNA end resection and that resected DNA is preferentially repaired by microhomology-mediated A-NHEJ. We propose that 53BP1 favors long-range CSR in part by protecting DNA ends against resection, which prevents A-NHEJ–dependent short-range rejoining of intra–switch region DSBs.
Agarivorans gilvus sp. nov. isolated from seaweed
Authors: Du Zong-Jun , Lv Guo-Qiang , Rooney Alejandro P. , Miao Ting-Ting , Xu Qing-Qiang , Chen Guan-Jun
Published: April 2010

A novel agarase-producing, non-endospore-forming marine bacterium, WH0801T, was isolated from a fresh seaweed sample collected from the coast of Weihai, China. Preliminary characterization based on 16S rRNA gene sequence analysis showed that WH0801Tshared 96.1 % similarity withAgarivorans albusMKT 106T, the type species of the genusAgarivorans. A polyphasic taxonomic study was conducted and confirmed the phylogenetic affiliation of strain WH0801Tto the genusAgarivorans. Isolate WH0801Tproduces light-yellow-pigmented colonies; cells are Gram-stain-negative, straight or curved rods, which are motile with a single polar flagellum. Strain WH0801Tgrew in 0.5–5 % NaCl, with optimum growth at 3 % NaCl, and its optimal pH and cultivation temperature were 8.4–8.6 and 28–32 °C, respectively. Data from biochemical tests, whole-cell fatty acid profiling, 16S rRNA gene sequence studies and DNA–DNA hybridization clearly indicated that isolate WH0801Trepresented a novel species within the genusAgarivorans, for which the nameAgarivorans gilvussp. nov. is proposed. The type strain ofAgarivorans gilvussp. nov. is WH0801T(=NRRL B-59247T=CGMCC 1.10131T).
Leucobacter salsicius sp. nov., from a salt-fermented food
Authors: Yun Ji-Hyun , Roh Seong Woon , Kim Min-Soo , Jung Mi-Ja , Park Eun-Jin , Shin Kee-Sun , Nam Young-Do , Bae Jin-Woo
Published: April 2010

Strain M1-8T was isolated from jeotgal, a Korean salt-fermented food. Cells were aerobic, non-motile, Gram-reaction-positive and rod-shaped. Colonies were cream-coloured and circular with entire margins. Strain M1-8T exhibited optimal growth at 25–30 °C and pH 7.0–8.0 and in 0–4 % (w/v) NaCl. The strain tolerated up to 10.0 mM Cr(VI). Phylogenetic analyses of 16S rRNA gene sequences indicated that strain M1-8T represents a novel species in the genus Leucobacter. The 16S rRNA gene sequence of M1-8T exhibited 98.1 % similarity to that of Leucobacter chromiireducens subsp. chromiireducens L-1T. The new isolate was clustered with Leucobacter species on a 16S rRNA gene sequence-based phylogenetic tree. The chromosomal DNA G+C content of strain M1-8T was 62.8 mol%. Its cell-wall peptidoglycan contained 2,4-diaminobutyric acid, glutamic acid, alanine, glycine and γ-aminobutyric acid. The major menaquinone was MK-11 and the predominant fatty acids were anteiso-C15 : 0 (63.6 %), anteiso-C17 : 0 (16.7 %) and iso-C16 : 0 (14.2 %). The polar lipid profile of strain M1-8T contained diphosphatidylglycerol and one unknown glycolipid. Significant genotypic and phenotypic differences were found between strain M1-8T and other Leucobacter species. These differentiating characteristics indicate that strain M1-8T represents a novel species of the genus Leucobacter, for which the name Leucobacter salsicius sp. nov. is proposed. The type strain is M1-8T (=KACC 21127T =JCM 16362T).
Chryseobacterium chaponense sp. nov., isolated from farmed Atlantic salmon (Salmo salar)
Authors: Kämpfer Peter , Fallschissel Kerstin , Avendaño-Herrera Ruben
Published: April 2010

Two bacterial strains, designated Sa 1147-06T and Sa 1143-06, were isolated from Atlantic salmon (Salmo salar) farmed in Lake Chapo, Chile, and were studied using a polyphasic approach. Both isolates were very similar; cells were rod-shaped, formed yellow-pigmented colonies and were Gram-reaction-negative. Based on 16S rRNA gene sequence analysis, strains Sa 1147-06T and Sa 1143-06 shared 100 % sequence similarity and showed 98.9 and 97.5 % sequence similarity to Chryseobacterium jeonii AT1047T and Chryseobacterium antarcticum AT1013T, respectively. Sequence similarities to all other members of the genus Chryseobacterium were below 97.3 %. The major fatty acids of strain Sa 1147-06T were iso-C13 : 0, iso-C15 : 0, anteiso-C15 : 0 and iso-C17 : 1
ω9c, with iso-C15 : 0 3-OH, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH constituting the major hydroxylated fatty acids. DNA–DNA hybridizations with C. jeonii JMSNU 14049T and C. antarcticum JMNSU 14040T gave relatedness values of 20.7 % (reciprocal 15.1 %) and 15.7 % (reciprocal 25.7 %), respectively. Together, the DNA–DNA hybridization results and differentiating biochemical properties showed that strains Sa 1147-06T and Sa 1143-06 represent a novel species, for which the name Chryseobacterium chaponense sp. nov. is proposed. The type strain is Sa 1147-06T (=DSM 23145T =CCM 7737T).
Saccharospirillum aestuarii sp. nov., isolated from tidal flat sediment, and an emended description of the genus Saccharospirillum
Authors: Choi Ahyoung , Oh Hyun-Myung , Cho Jang-Cheon
Published: April 2010

A Gram-reaction-negative, chemoheterotrophic, non-motile, facultatively anaerobic, curved rod-shaped bacterial strain, IMCC4453T, was isolated from tidal flat sediment and subjected to a taxonomic study using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain IMCC4453T belonged to the genus Saccharospirillum, forming a robust clade with members of the genus, and was most closely related to the type strains of Saccharospirillum salsuginis (97.6 % similarity) and Saccharospirillum impatiens (95.9 %). The DNA–DNA relatedness value between strain IMCC4453T and S. salsuginis YIM-Y25T was 23–30 %. Differences in several physiological and biochemical characteristics between strain IMCC4453T and the two recognized species of the genus Saccharospirillum, together with phylogenetic and genomic distinctiveness, differentiated the novel strain from members of the genus Saccharospirillum. On the basis of the data from the present study, it is concluded that strain IMCC4453T represents a novel species of the genus Saccharospirillum, for which the name Saccharospirillum aestuarii sp. nov. is proposed. The type strain is IMCC4453T (=KCTC 22684T=KCCM 42930T=NBRC 105825T). An emended description of the genus Saccharospirillum is provided.
Genomic, proteomic, and transcriptomic analysis of virulent and avirulentRickettsia prowazekiireveals its adaptive mutation capabilities
Authors: Bechah Yassina , El Karkouri Khalid , Mediannikov Oleg , Leroy Quentin , Pelletier Nicolas , Robert Catherine , Médigue Claudine , Mege Jean-Louis , Raoult Didier
Published: April 2010

Rickettsia prowazekii, the agent of epidemic typhus, is an obligate intracellular bacterium that is transmitted to human beings by the body louse. Several strains that differ considerably in virulence are recognized, but the genetic basis for these variations has remained unknown since the initial description of the avirulent vaccine strain nearly 70 yr ago. We use a recently developed murine model of epidemic typhus and transcriptomic, proteomic, and genetic techniques to identify the factors associated with virulence. We identified four phenotypes ofR. prowazekiithat differed in virulence, associated with the up-regulation of antiapoptotic genes or the interferon I pathway in the host cells. Transcriptional and proteomic analyses ofR. prowazekiisurface protein expression and protein methylation varied with virulence. By sequencing a virulent strain and using comparative genomics, we found hotspots of mutations in homopolymeric tracts of poly(A) and poly(T) in eight genes in an avirulent strain that split and inactivated these genes. These includedrecO, putative methyltransferase, and exported protein. Passage of the avirulent Madrid E strain in cells or in experimental animals was associated with a cascade of gene reactivations, beginning withrecO, that restored the virulent phenotype. An area of genomic plasticity appears to determine virulence inR. prowazekiiand represents an example of adaptive mutation for this pathogen.