bluuebunny/crossref_metadata_2025 huggingface dataset:
The Object of Regulation: Tending the Tensions of Food Safety
Authors: Bingham Nick , Lavau Stephanie
Published: August 2012

“I'm struggling to see what it actually is”, says Alison, peering into a colander of defrosting meat. What ‘it’ is, we propose in this paper, is helpfully thought of as ‘the object of regulation’ in at least three senses which together signal both our inheritance of a Foucauldian problematic and our departure from it. Our suggestion is that much of even the best work on biopolitics, biopower, and biosecurity that has been inspired and informed by these writings has replicated Foucault's own struggle to get to grips with the complexity of matters that he variously refers to as “natural” or “artificial” “givens”. By following science and technology studies scholars in using broadly ethnographic techniques to explore objects as and at the intersection of practices, we redress this balance somewhat by thinking through an empirical study of the securing of food safety—specifically Alison's inspection of a restaurant kitchen. What we find is that the securing of meat as a material object of regulation is primarily done by in-volving multiple versions of the future, something which requires a great deal of usually underrecognised, undervalued, and undertheorised articulation work. With risk-based regulation, cost sharing, and public sector cuts in the UK set to redefine the ways in which Alison and her colleagues engage with food business operators, we conclude by arguing for a greater appreciation of the skilful work of tending the tensions of food safety, as well as recognition of its limitations.
Knowledge in the Air and Cooperation among Firms: Traditions of Secrecy and the Reluctant Emergence of Specialization in the Ceramic Manufacturing District of Lampang, Thailand
Authors: Kamnungwut Weeranan , Guy Frederick
Published: August 2012

We study interfirm relations among ceramic tableware manufacturers in the city of Lampang, Thailand. Data consist of face-to-face interviews with the principals of thirty-four manufacturers, and with representatives of supporting institutions. We find that specialization in production and knowledge sharing are complementary; that knowledge sharing is substantially discretionary, rather than taking the form of passive spillovers; and that a weak knowledge base, built on firm-based training within vertically integrated mass producers, constrains the development of flexible specialization, despite the efforts of numerous local and external actors.
Holding the Future Together: Towards a Theorisation of the Spaces and Times of Transition
Authors: Brown Gavin , Kraftl Peter , Pickerill Jenny , Upton Caroline
Published: August 2012

Social scientists often use the notion of ‘transition’ to denote diverse trajectories of change in different types of bodies: from individuals, to communities, to nation-states. Yet little work has theorised how transition might occur across, between, or beyond these bodies. The aim of this paper is to sketch out a multiple, synthetic, and generative (but by no means universal) theory of transition. Primarily drawing on the British context, we explore and exemplify two contentions. Firstly, that the notion of transition is increasingly being deployed to frame and combine discourses in terms of community development, responses to environmental change, and the individual lifecourse. Specifically framed as ‘transition’, such discourses are gaining increasing purchase in imagining futures that reconfigure, but do not transform, assumed neoliberal futures. Our second contention is that these discourses and policies must try to ‘hold the future together’ in one or more senses. They must wrestle with a tension between imminent threats (climate change, economic nonproductivity) which weigh heavily on the present and its possible futures, and the precarious act of redirecting those futures in ways that might better hold together diverse social groups, communities, and places.
Saving, Spending, and Future-Making: Time, Discipline, and Money in Development
Authors: Green Maia , Kothari Uma , Mercer Claire , Mitlin Diana
Published: August 2012

Money is a distributed technology for the government of futures. Using ethnographically informed accounts of social practices around saving and collective remittances in poor countries this paper examines how the malleability of money enables it to have the potential for formalisation which allows it to be brought into formal relations of future-making and foreclosure, at the same time as its potential for investments and reallocation enables it to be the basis of flexible and adaptive strategies of future-making. We show how individuals engaged in development aspirations strive to achieve futures through the collection, care, and use of money, and how strategies of formalisation, discipline, and framing accord money developmental capacities. The liquidity of money renders it a flexible vehicle for personal and collective aspirations while representing risk of leakage to other persons and ventures. The paper examines the strategies used by low-income savers and hometown associations in their concerns with establishing rules and discipline around the flexibility of money.
AS1DHRS4, a head-to-head natural antisense transcript, silences the
DHRS4
gene cluster in
cis
and
trans
Authors: Li Qi , Su Zhongjing , Xu Xiaoyuan , Liu Gefei , Song Xuhong , Wang Ruijian , Sui Xuxia , Liu Ting , Chang Xiaolan , Huang Dongyang
Published: August 2012

The human genome, like other mammalian genomes, encodes numerous natural antisense transcripts (NATs) that have been classified into head-to-head, tail-to-tail, or fully overlapped categories in reference to their sense transcripts. Evidence for NAT-mediated epigenetic silencing of sense transcription remains scanty. The
DHRS4
gene encodes a metabolic enzyme and forms a gene cluster with its two immediately downstream homologous genes,
DHRS4L2
and
DHRS4L1
, generated by gene duplication. We identified a head-to-head NAT of
DHRS4
, designated AS1DHRS4, which markedly regulates the expression of these three genes in the
DHRS4
gene cluster. By pairing with ongoing sense transcripts, AS1DHRS4 not only mediates deacetylation of histone H3 and demethylation of H3K4 in
cis
for the
DHRS4
gene, but also interacts physically in
trans
with the epigenetic modifiers H3K9- and H3K27-specific histone methyltransferases G9a and EZH2, targeting the promoters of the downstream
DHRS4L2
and
DHRS4L1
genes to induce local repressive H3K9me2 and H3K27me3 histone modifications. Furthermore, AS1DHRS4 induces DNA methylation in the promoter regions of
DHRS4L2
by recruiting DNA methyltransferases. This study demonstrates that AS1DHRS4, as a long noncoding RNA, simultaneously controls the chromatin state of each gene within the
DHRS4
gene cluster in a discriminative manner. This finding provides an example of transcriptional control over the multiple and highly homologous genes in a tight gene cluster, and may help explain the role of antisense RNAs in the regulation of duplicated genes as the result of genomic evolution.
Nuclear factor-κB binding motifs specify Toll-like receptor-induced gene repression through an inducible repressosome
Authors: Yan Qin , Carmody Ruaidhri J. , Qu Zhonghua , Ruan Qingguo , Jager Jennifer , Mullican Shannon E. , Lazar Mitchell A. , Chen Youhai H.
Published: August 2012

Sustained Toll-like receptor (TLR) stimulation continuously activates antimicrobial genes but paradoxically represses inflammatory genes. This phenomenon, termed TLR tolerance, is essential for preventing fatal inflammatory conditions such as sepsis, but its underlying mechanisms are unclear. We report here that NF-κB binding nucleic acids of gene promoters are tolerogenic motifs, which selectively recruit an NcoR–Hdac3–deacetylated-p50 repressosome to inflammatory genes. Genome-wide analyses of TLR4-induced genes revealed that NF-κB motifs were the only regulatory elements significantly enriched in tolerizable genes. Mutating the NF-κB motifs of tolerizable genes converted them into nontolerizable ones, whereas inserting NF-κB binding motifs into nontolerizable genes conferred the tolerance. Although NF-κB p50 was essential for assembling the repressosome, genetic disruption of the NcoR–Hdac3 interaction alone was sufficient to completely abolish TLR4 tolerance and to render mice vulnerable to sepsis. Thus, the specificity of TLR tolerance is dictated by evolutionally conserved nucleic acid motifs that bound by NF-κB and the NcoR repressosome.
Thyroid hormone triggers the developmental loss of axonal regenerative capacity via thyroid hormone receptor α1 and krüppel-like factor 9 in Purkinje cells
Authors: Avci Hasan X. , Lebrun Clement , Wehrlé Rosine , Doulazmi Mohamed , Chatonnet Fabrice , Morel Marie-Pierre , Ema Masatsugu , Vodjdani Guilan , Sotelo Constantino , Flamant Frédéric , Dusart Isabelle
Published: August 2012

Neurons in the CNS of higher vertebrates lose their ability to regenerate their axons at a stage of development that coincides with peak circulating thyroid hormone (T3) levels. Here, we examined whether this peak in T3is involved in the loss of axonal regenerative capacity in Purkinje cells (PCs). This event occurs at the end of the first postnatal week in mice. Using organotypic culture, we found that the loss of axon regenerative capacity was triggered prematurely by early exposure of mouse PCs to T3, whereas it was delayed in the absence of T3. Analysis of mutant mice showed that this effect was mainly mediated by the T3receptor α1. Using gain- and loss-of-function approaches, we also showed that Krüppel-like factor 9 was a key mediator of this effect of T3. These results indicate that the sudden physiological increase in T3during development is involved in the onset of the loss of axon regenerative capacity in PCs. This loss of regenerative capacity might be part of the general program triggered by T3throughout the body, which adapts the animal to its postnatal environment.
Dynamically varying interactions between heregulin and ErbB proteins detected by single-molecule analysis in living cells
Authors: Hiroshima Michio , Saeki Yuko , Okada-Hatakeyama Mariko , Sako Yasushi
Published: August 2012

Heregulin (HRG) belongs to the family of EGFs and activates the receptor proteins ErbB3 and ErbB4 in a variety of cell types to regulate cell fate. The interactions between HRG and ErbB3/B4 are important to the pathological mechanisms underlying schizophrenia and some cancers. Here, we observed the reaction kinetics between fluorescently labeled single HRG molecules and ErbB3/B4 on the surfaces of MCF-7 human breast cancer cells. The equilibrium association and the dissociation from equilibrium were also measured using single-molecule imaging techniques. The unitary association processes mirrored the EGF and ErbB1 interactions in HeLa cells [Teramura Y, et al. (2006)
EMBO J
25:4215–4222], suggesting that the predimerization of the receptors, followed by intermediate formation (between the first and second ligand-binding events to a receptor dimer), accelerated the formation of doubly liganded signaling dimers of the receptor molecules. However, the dissociation analysis suggested that the first HRG dissociation from the doubly liganded dimer was rapid, but the second dissociation from the singly liganded dimer was slow. The dissociation rate constant from the liganded monomer was intermediate. The dynamic changes in the association and dissociation kinetics in relation to the dimerization of ErbB displayed negative cooperativity, which resulted in apparent low- and high-affinity sites of HRG association on the cell surface.
STAT3 negatively regulates thyroid tumorigenesis
Authors: Couto Joana Pinto , Daly Laura , Almeida Ana , Knauf Jeffrey A. , Fagin James A. , Sobrinho-Simões Manuel , Lima Jorge , Máximo Valdemar , Soares Paula , Lyden David , Bromberg Jacqueline F.
Published: August 2012

Although tyrosine-phosphorylated or activated STAT3 (pY-STAT3) is a well-described mediator of tumorigenesis, its role in thyroid cancer has not been investigated. We observed that 63 of 110 (57%) human primary papillary thyroid carcinoma (PTC) cases expressed nuclear pY-STAT3 in tumor cells, preferentially in association with the tumor stroma. An inverse relationship between pY-STAT3 expression with tumor size and the presence of distant metastases was observed. Using human thyroid cancer-derived cell lines [harboring rearranged during transfection (RET)/PTC, v-RAF murine sarcoma viral oncogene homolog B (BRAF), or rat sarcoma virus oncogene (RAS) alterations], we determined that IL-6/gp130/JAK signaling is responsible for STAT3 activation. STAT3 knockdown by shRNA in representative thyroid cancer cell lines that express high levels of pY-STAT3 had no effect on in vitro growth. However, xenografted short hairpin STAT3 cells generated larger tumors than control cells. Similarly, STAT3 deficiency in a murine model ofBRAFV600E-induced PTC led to thyroid tumors that were more proliferative and larger than those tumors expressing STAT3wt. Genome expression analysis revealed that STAT3 knockdown resulted in the down-regulation of multiple transcripts, including the tumor suppressor insulin-like growth factor binding protein 7. Furthermore, STAT3 knockdown led to an increase in glucose consumption, lactate production, and expression of Hypoxia-inducible factor 1 (HIF1α) target genes, suggesting that STAT3 is a negative regulator of aerobic glycolysis. Our studies show that, in the context of thyroid cancer, STAT3 is paradoxically a negative regulator of tumor growth. These findings suggest that targeting STAT3 in these cancers could enhance tumor size and highlight the complexities of the role of STAT3 in tumorigenesis.
Ocean barrier layers’ effect on tropical cyclone intensification
Authors: Balaguru Karthik , Chang Ping , Saravanan R. , Leung L. Ruby , Xu Zhao , Li Mingkui , Hsieh Jen-Shan
Published: August 2012

Improving a tropical cyclone’s forecast and mitigating its destructive potential requires knowledge of various environmental factors that influence the cyclone’s path and intensity. Herein, using a combination of observations and model simulations, we systematically demonstrate that tropical cyclone intensification is significantly affected by salinity-induced barrier layers, which are “quasi-permanent” features in the upper tropical oceans. When tropical cyclones pass over regions with barrier layers, the increased stratification and stability within the layer reduce storm-induced vertical mixing and sea surface temperature cooling. This causes an increase in enthalpy flux from the ocean to the atmosphere and, consequently, an intensification of tropical cyclones. On average, the tropical cyclone intensification rate is nearly 50% higher over regions with barrier layers, compared to regions without. Our finding, which underscores the importance of observing not only the upper-ocean thermal structure but also the salinity structure in deep tropical barrier layer regions, may be a key to more skillful predictions of tropical cyclone intensities through improved ocean state estimates and simulations of barrier layer processes. As the hydrological cycle responds to global warming, any associated changes in the barrier layer distribution must be considered in projecting future tropical cyclone activity.
Energy landscape of knotted protein folding
Authors: Sułkowska Joanna I. , Noel Jeffrey K. , Onuchic Jose N.
Published: August 2012

Recent experiments have conclusively shown that proteins are able to fold from an unknotted, denatured polypeptide to the knotted, native state without the aid of chaperones. These experiments are consistent with a growing body of theoretical work showing that a funneled, minimally frustrated energy landscape is sufficient to fold small proteins with complex topologies. Here, we present a theoretical investigation of the folding of a knotted protein, 2ouf, engineered in the laboratory by a domain fusion that mimics an evolutionary pathway for knotted proteins. Unlike a previously studied knotted protein of similar length, we see reversible folding/knotting and a surprising lack of deep topological traps with a coarse-grained structure-based model. Our main interest is to investigate how evolution might further select the geometry and stiffness of the threading region of the newly fused protein. We compare the folding of the wild-type protein to several mutants. Similarly to the wild-type protein, all mutants show robust and reversible folding, and knotting coincides with the transition state ensemble. As observed experimentally, our simulations show that the knotted protein folds about ten times slower than an unknotted construct with an identical contact map. Simulated folding kinetics reflect the experimentally observed rollover in the folding limbs of chevron plots. Successful folding of the knotted protein is restricted to a narrow range of temperature as compared to the unknotted protein and fits of the kinetic folding data below folding temperature suggest slow, nondiffusive dynamics for the knotted protein.
Sparse code of conflict in a primate society
Authors: Daniels Bryan C. , Krakauer David C. , Flack Jessica C.
Published: August 2012

Animals living in groups collectively produce social structure. In this context individuals make strategic decisions about when to cooperate and compete. This requires that individuals can perceive patterns in collective dynamics, but how this pattern extraction occurs is unclear. Our goal is to identify a model that extracts meaningful social patterns from a behavioral time series while remaining cognitively parsimonious by making the fewest demands on memory. Using fine-grained conflict data from macaques, we show that sparse coding, an important principle of neural compression, is an effective method for compressing collective behavior. The sparse code is shown to be efficient, predictive, and socially meaningful. In our monkey society, the sparse code of conflict is composed of related individuals, the policers, and the alpha female. Our results suggest that sparse coding is a natural technique for pattern extraction when cognitive constraints and small sample sizes limit the complexity of inferential models. Our approach highlights the need for cognitive experiments addressing how individuals perceive collective features of social organization.
Impact of genetic dynamics and single-cell heterogeneity on development of nonstandard personalized medicine strategies for cancer
Authors: Beckman Robert A. , Schemmann Gunter S. , Yeang Chen-Hsiang
Published: August 2012

Cancers are heterogeneous and genetically unstable. Current practice of personalized medicine tailors therapy to heterogeneity between cancers of the same organ type. However, it does not yet systematically address heterogeneity at the single-cell level within a single individual’s cancer or the dynamic nature of cancer due to genetic and epigenetic change as well as transient functional changes. We have developed a mathematical model of personalized cancer therapy incorporating genetic evolutionary dynamics and single-cell heterogeneity, and have examined simulated clinical outcomes. Analyses of an illustrative case and a virtual clinical trial of over 3 million evaluable “patients” demonstrate that augmented (and sometimes counterintuitive) nonstandard personalized medicine strategies may lead to superior patient outcomes compared with the current personalized medicine approach. Current personalized medicine matches therapy to a tumor molecular profile at diagnosis and at tumor relapse or progression, generally focusing on the average, static, and current properties of the sample. Nonstandard strategies also consider minor subclones, dynamics, and predicted future tumor states. Our methods allow systematic study and evaluation of nonstandard personalized medicine strategies. These findings may, in turn, suggest global adjustments and enhancements to translational oncology research paradigms.
Single mutation to a sex pheromone receptor provides adaptive specificity between closely related moth species
Authors: Leary Greg P. , Allen Jean E. , Bunger Peggy L. , Luginbill Jena B. , Linn Charles E. , Macallister Irene E. , Kavanaugh Michael P. , Wanner Kevin W.
Published: August 2012

Sex pheromone communication, acting as a prezygotic barrier to mating, is believed to have contributed to the speciation of moths and butterflies in the order Lepidoptera. Five decades after the discovery of the first moth sex pheromone, little is known about the molecular mechanisms that underlie the evolution of pheromone communication between closely related species. Although Asian and European corn borers (ACB and ECB) can be interbred in the laboratory, they are behaviorally isolated from mating naturally by their responses to subtly different sex pheromone isomers, (E)-12- and (Z)-12-tetradecenyl acetate and (E)-11- and (Z)-11-tetradecenyl acetate (ACB: E12, Z12; ECB; E11, Z11). Male moth olfactory systems respond specifically to the pheromone blend produced by their conspecific females. In vitro, ECB(Z) odorant receptor 3 (OR3), a sex pheromone receptor expressed in male antennae, responds strongly to E11 but also generally to the Z11, E12, and Z12 pheromones. In contrast, we show that ACB OR3, a gene that has been subjected to positive selection (ω = 2.9), responds preferentially to the ACB E12 and Z12 pheromones. InOstriniaspecies the amino acid residue corresponding to position 148 in transmembrane domain 3 of OR3 is alanine (A), except for ACB OR3 that has a threonine (T) in this position. Mutation of this residue from A to T alters the pheromone recognition pattern by selectively reducing the E11 response ∼14-fold. These results suggest that discrete mutations that narrow the specificity of more broadly responsive sex pheromone receptors may provide a mechanism that contributes to speciation.
Temperature during embryonic development has persistent effects on thermal acclimation capacity in zebrafish
Authors: Scott Graham R. , Johnston Ian A.
Published: August 2012

Global warming is intensifying interest in the mechanisms enabling ectothermic animals to adjust physiological performance and cope with temperature change. Here we show that embryonic temperature can have dramatic and persistent effects on thermal acclimation capacity at multiple levels of biological organization. Zebrafish embryos were incubated until hatching at control temperature (
T
E
= 27 °C) or near the extremes for normal development (
T
E
= 22 °C or 32 °C) and were then raised to adulthood under common conditions at 27 °C. Short-term temperature challenge affected aerobic exercise performance (
U
crit
), but each
T
E
group had reduced thermal sensitivity at its respective
T
E
. In contrast, unexpected differences arose after long-term acclimation to 16 °C, when performance in the cold was ∼20% higher in both 32 °C and 22 °C
T
E
groups compared with 27 °C
T
E
controls. Differences in performance after acclimation to cold or warm (34 °C) temperatures were partially explained by variation in fiber type composition in the swimming muscle. Cold acclimation changed the abundance of 3,452 of 19,712 unique and unambiguously identified transcripts detected in the fast muscle using RNA-Seq. Principal components analysis differentiated the general transcriptional responses to cold of the 27 °C and 32 °C
T
E
groups. Differences in expression were observed for individual genes involved in energy metabolism, angiogenesis, cell stress, muscle contraction and remodeling, and apoptosis. Therefore, thermal acclimation capacity is not fixed and can be modified by temperature during early development. Developmental plasticity may thus help some ectothermic organisms cope with the more variable temperatures that are expected under future climate-change scenarios.
High-throughput screen using a single-cell tyrosine phosphatase assay reveals biologically active inhibitors of tyrosine phosphatase CD45
Authors: Stanford Stephanie M. , Panchal Rekha G. , Walker Logan M. , Wu Dennis J. , Falk Matthew D. , Mitra Sayantan , Damle Sagar S. , Ruble David , Kaltcheva Teodora , Zhang Sheng , Zhang Zhong-Yin , Bavari Sina , Barrios Amy M. , Bottini Nunzio
Published: August 2012

Many cellular signaling events are regulated by tyrosine phosphorylation and mediated by the opposing actions of protein tyrosine kinases and phosphatases. Protein tyrosine phosphatases are emerging as drug targets, but poor cell permeability of inhibitors has limited the development of drugs targeting these enzymes [Tautz L, et al. (2006)
Expert Opin Ther Targets
10:157–177]. Here we developed a method to monitor tyrosine phosphatase activity at the single-cell level and applied it to the identification of cell-permeable inhibitors. The method takes advantage of the fluorogenic properties of phosphorylated coumaryl amino propionic acid (pCAP), an analog of phosphotyrosine, which can be incorporated into peptides. Once delivered into cells, pCAP peptides were dephosphorylated by protein tyrosine phosphatases, and the resulting cell fluorescence could be monitored by flow cytometry and high-content imaging. The robustness and sensitivity of the assay was validated using peptides preferentially dephosphorylated by CD45 and T-cell tyrosine phosphatase and available inhibitors of these two enzymes. The assay was applied to high-throughput screening for inhibitors of CD45, an important target for autoimmunity and infectious diseases [Hermiston ML, et al. (2003)
Annu Rev Immunol
21:107–137]. We identified four CD45 inhibitors that showed activity in T cells and macrophages. These results indicate that our assay can be applied to primary screening for inhibitors of CD45 and of other protein tyrosine phosphatases to increase the yield of biologically active inhibitors.
Regulatory T cells that recognize a ubiquitous stress-inducible self-antigen are long-lived suppressors of autoimmune arthritis
Authors: van Herwijnen Martijn J. C. , Wieten Lotte , van der Zee Ruurd , van Kooten Peter J. , Wagenaar-Hilbers Josée P. , Hoek Aad , den Braber Ineke , Anderton Stephen M. , Singh Mahavir , Meiring Hugo D. , van Els Cécile A. C. M. , van Eden Willem , Broere Femke
Published: August 2012

Reestablishing self-tolerance in autoimmunity is thought to depend on self-reactive regulatory T cells (Tregs). Exploiting these antigen-specific regulators is hampered by the obscure nature of disease-relevant autoantigens. We have uncovered potent disease-suppressive Tregs recognizing Heat Shock Protein (Hsp) 70 self-antigens, enabling selective activity in inflamed tissues. Hsp70 is a major contributor to the MHC class II ligandome. Here we show that a conserved Hsp70 epitope (B29) is present in murine MHC class II and that upon transfer, B29-induced CD4+CD25+Foxp3+T cells suppress established proteoglycan-induced arthritis in mice. These self-antigen–specific Tregs were activated in vivo, and when using Lymphocyte Activation Gene-3 as a selection marker, as few as 4,000 cells sufficed. Furthermore, depletion of transferred Tregs abrogated disease suppression. Transferred cells exhibited a stable phenotype and were found in joints and draining lymph nodes up to 2 mo after transfer. Given that (i) B29 administration by itself suppressed disease, (ii) our findings were made with wild-type (T-cell receptor nontransgenic) Tregs, and (iii) the B29 human homolog is presented by HLA class II, we are nearing translation of antigen-specific Treg activation as a promising intervention for chronic inflammatory diseases.
Retinal prosthetic strategy with the capacity to restore normal vision
Authors: Nirenberg Sheila , Pandarinath Chethan
Published: August 2012

Retinal prosthetics offer hope for patients with retinal degenerative diseases. There are 20–25 million people worldwide who are blind or facing blindness due to these diseases, and they have few treatment options. Drug therapies are able to help a small fraction of the population, but for the vast majority, their best hope is through prosthetic devices [reviewed in Chader et al. (2009)
Prog Brain Res
175:317–332]. Current prosthetics, however, are still very limited in the vision that they provide: for example, they allow for perception of spots of light and high-contrast edges, but not natural images. Efforts to improve prosthetic capabilities have focused largely on increasing the resolution of the device’s stimulators (either electrodes or optogenetic transducers). Here, we show that a second factor is also critical: driving the stimulators with the retina’s neural code. Using the mouse as a model system, we generated a prosthetic system that incorporates the code. This dramatically increased the system’s capabilities—well beyond what can be achieved just by increasing resolution. Furthermore, the results show, using 9,800 optogenetically stimulated ganglion cell responses, that the combined effect of using the code and high-resolution stimulation is able to bring prosthetic capabilities into the realm of normal image representation.
Ectopic assembly of heterochromatin in
Drosophila melanogaster
triggered by transposable elements
Authors: Sentmanat Monica F. , Elgin Sarah C. R.
Published: August 2012

A persistent question in biology is how
cis
-acting sequence elements influence
trans
-acting factors and the local chromatin environment to modulate gene expression. We reported previously that the DNA transposon
1360
can enhance silencing of a reporter in a heterochromatic domain of
Drosophila melanogaster
. We have now generated a collection of variegating phiC31 landing-pad insertion lines containing
1360
and a heat-shock protein 70 (
hsp70
)-driven
white
reporter to explore the mechanism of
1360
-sensitive silencing. Many
1360
-sensitive sites were identified, some in apparently euchromatic domains, although all are close to heterochromatic masses. One such site (line 1198; insertion near the base of chromosome arm 2L) has been investigated in detail. ChIP analysis shows
1360
-dependent Heterochromatin Protein 1a (HP1a) accumulation at this otherwise euchromatic site. The phiC31 landing pad system allows different
1360
constructs to be swapped with the full-length element at the same genomic site to identify the sequences that mediate
1360
-sensitive silencing. Short deletions over sites with homology to PIWI-interacting RNAs (piRNAs) are sufficient to compromise
1360
-sensitive silencing. Similar results were obtained on replacing
1360
with
Invader4
(a retrotransposon), suggesting that this phenomenon likely applies to a broader set of transposable elements. Our results suggest a model in which piRNA sequence elements behave as
cis
-acting targets for heterochromatin assembly, likely in the early embryo, where piRNA pathway components are abundant, with the heterochromatic state subsequently propagated by chromatin modifiers present in somatic tissue.
Indole peroxygenase activity of indoleamine 2,3-dioxygenase
Authors: Kuo Hsin H. , Mauk A. Grant
Published: August 2012

The heme enzyme indoleamine 2,3-dioxygenase (IDO) was found to catalyze the oxidation of indole by H
2
O
2
, with generation of 2- and 3-oxoindole as the major products. This reaction occurred in the absence of O
2
and reducing agents and was not inhibited by superoxide dismutase or hydroxyl radical scavengers, although it was strongly inhibited by
l
-Trp. The stoichiometry of the reaction indicated a one-to-one correspondence for the consumption of indole and H
2
O
2
. The
18
O-labeling experiments indicated that the oxygen incorporated into the monooxygenated products was derived almost exclusively from H
2
18
O
2
, suggesting that electron transfer was coupled to the transfer of oxygen from a ferryl intermediate of IDO. These results demonstrate that IDO oxidizes indole by means of a previously unrecognized peroxygenase activity. We conclude that IDO inserts oxygen into indole in a reaction that is mechanistically analogous to the “peroxide shunt” pathway of cytochrome P450.
Climate-driven regime shifts in Arctic marine benthos
Authors: Kortsch Susanne , Primicerio Raul , Beuchel Frank , Renaud Paul E. , Rodrigues João , Lønne Ole Jørgen , Gulliksen Bjørn
Published: August 2012

Climate warming can trigger abrupt ecosystem changes in the Arctic. Despite the considerable interest in characterizing and understanding the ecological impact of rapid climate warming in the Arctic, few long time series exist that allow addressing these research goals. During a 30-y period (1980–2010) of gradually increasing seawater temperature and decreasing sea ice cover in Svalbard, we document rapid and extensive structural changes in the rocky-bottom communities of two Arctic fjords. The most striking component of the benthic reorganization was an abrupt fivefold increase in macroalgal cover in 1995 in Kongsfjord and an eightfold increase in 2000 in Smeerenburgfjord. Simultaneous changes in the abundance of benthic invertebrates suggest that the macroalgae played a key structuring role in these communities. The abrupt, substantial, and persistent nature of the changes observed is indicative of a climate-driven ecological regime shift. The ecological processes thought to drive the observed regime shifts are likely to promote the borealization of these Arctic marine communities in the coming years.
PIP
2
controls voltage-sensor movement and pore opening of Kv channels through the S4–S5 linker
Authors: Rodriguez-Menchaca Aldo A. , Adney Scott K. , Tang Qiong-Yao , Meng Xuan-Yu , Rosenhouse-Dantsker Avia , Cui Meng , Logothetis Diomedes E.
Published: August 2012

Voltage-gated K
+
(Kv) channels couple the movement of a voltage sensor to the channel gate(s) via a helical intracellular region, the S4–S5 linker. A number of studies link voltage sensitivity to interactions of S4 charges with membrane phospholipids in the outer leaflet of the bilayer. Although the phospholipid phosphatidylinositol-4,5-bisphosphate (PIP
2
) in the inner membrane leaflet has emerged as a universal activator of ion channels, no such role has been established for mammalian Kv channels. Here we show that PIP
2
depletion induced two kinetically distinct effects on Kv channels: an increase in voltage sensitivity and a concomitant decrease in current amplitude. These effects are reversible, exhibiting distinct molecular determinants and sensitivities to PIP
2
. Gating current measurements revealed that PIP
2
constrains the movement of the sensor through interactions with the S4–S5 linker. Thus, PIP
2
controls both the movement of the voltage sensor and the stability of the open pore through interactions with the linker that connects them.
Molecular target validation, antimicrobial delivery, and potential treatment of
Toxoplasma gondii
infections
Authors: Lai Bo-Shiun , Witola William H. , El Bissati Kamal , Zhou Ying , Mui Ernest , Fomovska Alina , McLeod Rima
Published: August 2012

Toxoplasma gondii
persistently infects over two billion people worldwide. It can cause substantial morbidity and mortality. Existing treatments have associated toxicities and hypersensitivity and do not eliminate encysted bradyzoites that recrudesce. New, improved medicines are needed. Transductive peptides carry small molecule cargos across multiple membranes to enter intracellular tachyzoites and encysted bradyzoites. They also carry cargos into retina when applied topically to eyes, and cross blood brain barrier when administered intravenously. Phosphorodiamidate morpholino oligomers (PMO) inhibit gene expression in a sequence-specific manner. Herein, effect of transductive peptide conjugated PMO (PPMO) on tachyzoite protein expression and replication in vitro and in vivo was studied. Initially, sequence-specific PPMO successfully reduced transfected
T. gondii
’s fluorescence and luminescence. PPMO directed against
T. gondii
’s dihydrofolate reductase (DHFR), an enzyme necessary for folate synthesis, limited tachyzoite replication. Rescue with exogenous folate demonstrated DHFR PPMO‘s specificity. PPMO directed against enoyl-ACP reductase (ENR), an enzyme of type II fatty acid synthesis that is structurally distinct in
T. gondii
from ENR in mammalian cells was investigated. PPMO directed against plant-like Apetela 2 (AP2) domain transcription factor XI-3 (AP2XI-3), not present in human cells, was characterized. ENR and AP2XI-3 PPMO each restricted intracellular parasite replication validating these molecular targets in tachyzoites. DHFR-specific PPMO administered to infected mice diminished parasite burden. Thus, these antisense oligomers are a versatile approach to validate
T. gondii
molecular targets, reduce essential
T. gondii
proteins in vitro and in vivo, and have potential for development as curative medicines.
Triclosan impairs excitation–contraction coupling and Ca
2+
dynamics in striated muscle
Authors: Cherednichenko Gennady , Zhang Rui , Bannister Roger A. , Timofeyev Valeriy , Li Ning , Fritsch Erika B. , Feng Wei , Barrientos Genaro C. , Schebb Nils H. , Hammock Bruce D. , Beam Kurt G. , Chiamvimonvat Nipavan , Pessah Isaac N.
Published: August 2012

Triclosan (TCS), a high-production-volume chemical used as a bactericide in personal care products, is a priority pollutant of growing concern to human and environmental health. TCS is capable of altering the activity of type 1 ryanodine receptor (RyR1), but its potential to influence physiological excitation–contraction coupling (ECC) and muscle function has not been investigated. Here, we report that TCS impairs ECC of both cardiac and skeletal muscle in vitro and in vivo. TCS acutely depresses hemodynamics and grip strength in mice at doses ≥12.5 mg/kg i.p., and a concentration ≥0.52 μM in water compromises swimming performance in larval fathead minnow. In isolated ventricular cardiomyocytes, skeletal myotubes, and adult flexor digitorum brevis fibers TCS depresses electrically evoked ECC within ∼10–20 min. In myotubes, nanomolar to low micromolar TCS initially potentiates electrically evoked Ca
2+
transients followed by complete failure of ECC, independent of Ca
2+
store depletion or block of RyR1 channels. TCS also completely blocks excitation-coupled Ca
2+
entry. Voltage clamp experiments showed that TCS partially inhibits L-type Ca
2+
currents of cardiac and skeletal muscle, and [
3
H]PN200 binding to skeletal membranes is noncompetitively inhibited by TCS in the same concentration range that enhances [
3
H]ryanodine binding. TCS potently impairs orthograde and retrograde signaling between L-type Ca
2+
and RyR channels in skeletal muscle, and L-type Ca
2+
entry in cardiac muscle, revealing a mechanism by which TCS weakens cardiac and skeletal muscle contractility in a manner that may negatively impact muscle health, especially in susceptible populations.
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution
Authors: Langergraber Kevin E. , Prüfer Kay , Rowney Carolyn , Boesch Christophe , Crockford Catherine , Fawcett Katie , Inoue Eiji , Inoue-Muruyama Miho , Mitani John C. , Muller Martin N. , Robbins Martha M. , Schubert Grit , Stoinski Tara S. , Viola Bence , Watts David , Wittig Roman M. , Wrangham Richard W. , Zuberbühler Klaus , Pääbo Svante , Vigilant Linda
Published: August 2012

Fossils and molecular data are two independent sources of information that should in principle provide consistent inferences of when evolutionary lineages diverged. Here we use an alternative approach to genetic inference of species split times in recent human and ape evolution that is independent of the fossil record. We first use genetic parentage information on a large number of wild chimpanzees and mountain gorillas to directly infer their average generation times. We then compare these generation time estimates with those of humans and apply recent estimates of the human mutation rate per generation to derive estimates of split times of great apes and humans that are independent of fossil calibration. We date the human–chimpanzee split to at least 7–8 million years and the population split between Neanderthals and modern humans to 400,000–800,000 y ago. This suggests that molecular divergence dates may not be in conflict with the attribution of 6- to 7-million-y-old fossils to the human lineage and 400,000-y-old fossils to the Neanderthal lineage.
Resistance to EGF receptor inhibitors in glioblastoma mediated by phosphorylation of the PTEN tumor suppressor at tyrosine 240
Authors: Fenton Tim R. , Nathanson David , Ponte de Albuquerque Claudio , Kuga Daisuke , Iwanami Akio , Dang Julie , Yang Huijun , Tanaka Kazuhiro , Oba-Shinjo Sueli Mieko , Uno Miyuki , del Mar Inda Maria , Wykosky Jill , Bachoo Robert M. , James C. David , DePinho Ronald A. , Vandenberg Scott R. , Zhou Huilin , Marie Suely K. N. , Mischel Paul S. , Cavenee Webster K. , Furnari Frank B.
Published: August 2012

Glioblastoma multiforme (GBM) is the most aggressive of the astrocytic malignancies and the most common intracranial tumor in adults. Although the epidermal growth factor receptor (EGFR) is overexpressed and/or mutated in at least 50% of GBM cases and is required for tumor maintenance in animal models, EGFR inhibitors have thus far failed to deliver significant responses in GBM patients. One inherent resistance mechanism in GBM is the coactivation of multiple receptor tyrosine kinases, which generates redundancy in activation of phosphoinositide-3′-kinase (PI3K) signaling. Here we demonstrate that the phosphatase and tensin homolog deleted on chromosome 10 (PTEN) tumor suppressor is frequently phosphorylated at a conserved tyrosine residue, Y240, in GBM clinical samples. Phosphorylation of Y240 is associated with shortened overall survival and resistance to EGFR inhibitor therapy in GBM patients and plays an active role in mediating resistance to EGFR inhibition in vitro. Y240 phosphorylation can be mediated by both fibroblast growth factor receptors and SRC family kinases (SFKs) but does not affect the ability of PTEN to antagonize PI3K signaling. These findings show that, in addition to genetic loss and mutation of PTEN, its modulation by tyrosine phosphorylation has important implications for the development and treatment of GBM.
The Hippo pathway target, YAP, promotes metastasis through its TEAD-interaction domain
Authors: Lamar John M. , Stern Patrick , Liu Hui , Schindler Jeffrey W. , Jiang Zhi-Gang , Hynes Richard O.
Published: August 2012

The transcriptional coactivator Yes-associated protein (YAP) is a major regulator of organ size and proliferation in vertebrates. As such, YAP can act as an oncogene in several tissue types if its activity is increased aberrantly. Although no activating mutations in the
yap1
gene have been identified in human cancer,
yap1
is located on the 11q22 amplicon, which is amplified in several human tumors. In addition, mutations or epigenetic silencing of members of the Hippo pathway, which represses YAP function, have been identified in human cancers. Here we demonstrate that, in addition to increasing tumor growth, increased YAP activity is potently prometastatic in breast cancer and melanoma cells. Using a Luminex-based approach to multiplex in vivo assays, we determined that the domain of YAP that interacts with the TEAD/TEF family of transcription factors but not the WW domains or PDZ-binding motif, is essential for YAP-mediated tumor growth and metastasis. We further demonstrate that, through its TEAD-interaction domain, YAP enhances multiple processes known to be important for tumor progression and metastasis, including cellular proliferation, transformation, migration, and invasion. Finally, we found that the metastatic potential of breast cancer and melanoma cells is strongly correlated with increased TEAD transcriptional activity. Together, our results suggest that increased YAP/TEAD activity plays a causal role in cancer progression and metastasis.
Movement and Capture Efficiency of Radio-Tagged Salmonids Sampled by Electrofishing
Authors: Young Michael K. , Schmetterling David A.
Published: August 2012

Electrofishing-based estimates of fish abundance are common. Most population models assume that samples are drawn from a closed population, but population closure is sometimes difficult to achieve. Consequently, we individually electrofished 103 radio-tagged trout of two species, westslope cutthroat trout Oncorhynchus clarkii lewisi and brook trout Salvelinus fontinalis, in five streams in western Montana to quantify the influence of habitat and fish size on capture efficiency and movement related to electrofishing with unpulsed DC. First-pass capture efficiency was 46% and declined on subsequent passes. No variables were related to capture efficiency, and only the percentage of cobble or larger substrate was related to the probability that uncaptured fish would move during the first electrofishing pass. About 20% of the uncaptured fish did not move, and 95% traveled less than 18 m. We concluded that for these streams, the bias in abundance estimates from disregarding movement would be relatively minor.

Received January 18, 2011; accepted June 11, 2012
Clathrin helps maintain the centrosome's integrity
Authors: Short Ben
Published: August 2012

Inactivating clathrin in S phase reveals the protein's involvement in centrosome maturation.
Mammalian GW220/TNGW1 is essential for the formation of GW/P bodies containing miRISC
Authors: Castilla-Llorente Virginia , Spraggon Lee , Okamura Miwako , Naseeruddin Saif , Adamow Matthew , Qamar Sarah , Liu Jidong
Published: August 2012

The microRNA (miRNA)-induced silencing complex (miRISC) controls gene expression by a posttranscriptional mechanism involving translational repression and/or promoting messenger RNA (mRNA) deadenylation and degradation. The GW182/TNRC6 (GW) family proteins are core components of the miRISC and are essential for miRNA function. We show that mammalian GW proteins have distinctive functions in the miRNA pathway, with GW220/TNGW1 being essential for the formation of GW/P bodies containing the miRISC. miRISC aggregation and formation of GW/P bodies sequestered and stabilized translationally repressed target mRNA. Depletion of GW220 led to the loss of GW/P bodies and destabilization of miRNA-targeted mRNA. These findings support a model in which the cellular localization of the miRISC regulates the fate of the target mRNA.
A steep phosphoinositide bis-phosphate gradient forms during fungal filamentous growth
Authors: Vernay Aurélia , Schaub Sébastien , Guillas Isabelle , Bassilana Martine , Arkowitz Robert A.
Published: August 2012

Membrane lipids have been implicated in many critical cellular processes, yet little is known about the role of asymmetric lipid distribution in cell morphogenesis. The phosphoinositide bis-phosphate PI(4,5)P2 is essential for polarized growth in a range of organisms. Although an asymmetric distribution of this phospholipid has been observed in some cells, long-range gradients of PI(4,5)P2 have not been observed. Here, we show that in the human pathogenic fungus Candida albicans a steep, long-range gradient of PI(4,5)P2 occurs concomitant with emergence of the hyphal filament. Both sufficient PI(4)P synthesis and the actin cytoskeleton are necessary for this steep PI(4,5)P2 gradient. In contrast, neither microtubules nor asymmetrically localized mRNAs are critical. Our results indicate that a gradient of PI(4,5)P2, crucial for filamentous growth, is generated and maintained by the filament tip–localized PI(4)P-5-kinase Mss4 and clearing of this lipid at the back of the cell. Furthermore, we propose that slow membrane diffusion of PI(4,5)P2 contributes to the maintenance of such a gradient.