bluuebunny/crossref_metadata_2025 huggingface dataset:
Contesting Genetic Knowledge-Practices in Livestock Breeding: Biopower, Biosocial Collectivities, and Heterogeneous Resistances
Authors: Holloway Lewis , Morris Carol
Published: November 2011

Cattle and sheep breeders in the UK and elsewhere increasingly draw on genetic techniques in order to make breeding decisions. Many breeders support such techniques, while others argue against them for a variety of reasons, including their preference for the ‘traditions’ of visual-based and pedigree-based selections. Meanwhile, even for those institutions and breeders who promote genetic techniques, the outcomes are not always as predicted. We build on our recent use of Foucault's discussions of biopower to examine the effects of the introduction of genetic techniques in UK livestock breeding in order to begin to explore the diffuse and capillary nature of resistance within relations of biopower. We focus specifically on how resistance and contestation can be understood through the joint lenses of biopower and an understanding of livestock breeding as knowledge-practices enacted within heterogeneous biosocial collectivities. In some instances these collectivities coalesce around shared endeavour, such as increasing the valency of genetic evaluation within livestock breeding. Yet such mixed collectivities also open up opportunities for counter-conduct: heterogeneous resistances to and contestations of genetic evaluation as something represented as progressive and inevitable. We focus on exploring such modes of resistance using detailed empirical research with livestock breeders and breeding institutions. We demonstrate how in different and specific ways geneticisation becomes problematised, and is contested and made more complex, through the knowledge-practices of breeders, the bodies of animals, and the complex relationships between different institutions in livestock breeding and rearing.
CD83-stimulated monocytes suppress T-cell immune responses through production of prostaglandin E2
Authors: Chen Liwen , Zhu Yibei , Zhang Guangbo , Gao Chao , Zhong Weixue , Zhang Xueguang
Published: November 2011

CD83 is commonly known as a specific marker for mature dendritic cells. It has been shown to be important for CD4+T-cell development in the thymus. However, its function in the peripheral immune system remains enigmatic. Here, we show that CD83 inhibits proliferation and production of IL-2 and IFN-γ by T cells, and the inhibitory effect of CD83 is mediated by monocytes. Prostaglandin E2 (PGE2), but not IL-10 or TGF-β, was up-regulated specifically by CD83 in monocytes. Consistent with high levels of PGE2, expression of COX-2 also was increased upon CD83 treatment. NF-κB activation also is required for induction of PGE2by CD83. Finally, application of the COX-2–selective inhibitor NS-398 fully prevented CD83-triggered inhibition of T-cell responses. Our study establishes an immune-regulatory mechanism by CD83 via stimulation of PGE2production in monocytes.
The musculoskeletal system of humans is not tuned to maximize the economy of locomotion
Authors: Carrier David R. , Anders Christoph , Schilling Nadja
Published: November 2011

Humans are known to have energetically optimal walking and running speeds at which the cost to travel a given distance is minimized. We hypothesized that “optimal” walking and running speeds would also exist at the level of individual locomotor muscles. Additionally, because humans are 60–70% more economical when they walk than when they run, we predicted that the different muscles would exhibit a greater degree of tuning to the energetically optimal speed during walking than during running. To test these hypotheses, we used electromyography to measure the activity of 13 muscles of the back and legs over a range of walking and running speeds in human subjects and calculated the cumulative activity required from each muscle to traverse a kilometer. We found that activity of each of these muscles was minimized at specific walking and running speeds but the different muscles were not tuned to a particular speed in either gait. Although humans are clearly highly specialized for terrestrial locomotion compared with other great apes, the results of this study indicate that our locomotor muscles are not tuned to specific walking or running speeds and, therefore, do not maximize the economy of locomotion. This pattern may have evolved in response to selection to broaden the range of sustainable running speeds, to improve performance in motor behaviors not related to endurance locomotion, or in response to selection for both.
α-Synuclein fate is determined by USP9X-regulated monoubiquitination
Authors: Rott Ruth , Szargel Raymonde , Haskin Joseph , Bandopadhyay Rina , Lees Andrew J. , Shani Vered , Engelender Simone
Published: November 2011

α-Synuclein is central to the pathogenesis of Parkinson disease (PD). Mutations as well as accumulation of α-synuclein promote the death of dopaminergic neurons and the formation of Lewy bodies. α-Synuclein is monoubiquitinated by SIAH, but the regulation and roles of monoubiquitination in α-synuclein biology are poorly understood. We now report that the deubiquitinase USP9X interacts in vivo with and deubiquitinates α-synuclein. USP9X levels are significantly lower in cytosolic fractions of PD substantia nigra and Diffuse Lewy Body disease (DLBD) cortices compared to controls. This was associated to lower deubiquitinase activity toward monoubiquitinated α-synuclein in DLBD cortical extracts. A fraction of USP9X seems to be aggregated in PD and DLBD, as USP9X immunoreactivity is detected in Lewy bodies. Knockdown of USP9X expression promotes accumulation of monoubiquitinated α-synuclein species and enhances the formation of toxic α-synuclein inclusions upon proteolytic inhibition. On the other hand, by manipulating USP9X expression levels in the absence of proteolytic impairment, we demonstrate that monoubiquitination controls the partition of α-synuclein between different protein degradation systems. Deubiquitinated α-synuclein is mostly degraded by autophagy, while monoubiquitinated α-synuclein is preferentially degraded by the proteasome. Moreover, monoubiquitination promotes the degradation of α-synuclein, whereas deubiquitination leads to its accumulation, suggesting that the degradation of deubiquitinated α-synuclein by the autophagy pathway is less efficient than the proteasomal one. Lower levels of cytosolic USP9X and deubiquitinase activity in α-synucleinopathies may contribute to the accumulation and aggregation of monoubiquitinated α-synuclein in Lewy bodies. Our data indicate that monoubiquitination is a key determinant of α-synuclein fate.
Genotypes of predomestic horses match phenotypes painted in Paleolithic works of cave art
Authors: Pruvost Melanie , Bellone Rebecca , Benecke Norbert , Sandoval-Castellanos Edson , Cieslak Michael , Kuznetsova Tatyana , Morales-Muñiz Arturo , O'Connor Terry , Reissmann Monika , Hofreiter Michael , Ludwig Arne
Published: November 2011

Archaeologists often argue whether Paleolithic works of art, cave paintings in particular, constitute reflections of the natural environment of humans at the time. They also debate the extent to which these paintings actually contain creative artistic expression, reflect the phenotypic variation of the surrounding environment, or focus on rare phenotypes. The famous paintings “The Dappled Horses of Pech-Merle,” depicting spotted horses on the walls of a cave in Pech-Merle, France, date back ∼25,000 y, but the coat pattern portrayed in these paintings is remarkably similar to a pattern known as “leopard” in modern horses. We have genotyped nine coat-color loci in 31 predomestic horses from Siberia, Eastern and Western Europe, and the Iberian Peninsula. Eighteen horses had bay coat color, seven were black, and six shared an allele associated with the leopard complex spotting (
LP
), representing the only spotted phenotype that has been discovered in wild, predomestic horses thus far.
LP
was detected in four Pleistocene and two Copper Age samples from Western and Eastern Europe, respectively. In contrast, this phenotype was absent from predomestic Siberian horses. Thus, all horse color phenotypes that seem to be distinguishable in cave paintings have now been found to exist in prehistoric horse populations, suggesting that cave paintings of this species represent remarkably realistic depictions of the animals shown. This finding lends support to hypotheses arguing that cave paintings might have contained less of a symbolic or transcendental connotation than often assumed.
A yeast functional screen predicts new candidate ALS disease genes
Authors: Couthouis Julien , Hart Michael P. , Shorter James , DeJesus-Hernandez Mariely , Erion Renske , Oristano Rachel , Liu Annie X. , Ramos Daniel , Jethava Niti , Hosangadi Divya , Epstein James , Chiang Ashley , Diaz Zamia , Nakaya Tadashi , Ibrahim Fadia , Kim Hyung-Jun , Solski Jennifer A. , Williams Kelly L. , Mojsilovic-Petrovic Jelena , Ingre Caroline , Boylan Kevin , Graff-Radford Neill R. , Dickson Dennis W. , Clay-Falcone Dana , Elman Lauren , McCluskey Leo , Greene Robert , Kalb Robert G. , Lee Virginia M.-Y. , Trojanowski John Q. , Ludolph Albert , Robberecht Wim , Andersen Peter M. , Nicholson Garth A. , Blair Ian P. , King Oliver D. , Bonini Nancy M. , Van Deerlin Vivianna , Rademakers Rosa , Mourelatos Zissimos , Gitler Aaron D.
Published: November 2011

Amyotrophic lateral sclerosis (ALS) is a devastating and universally fatal neurodegenerative disease. Mutations in two related RNA-binding proteins, TDP-43 and FUS, that harbor prion-like domains, cause some forms of ALS. There are at least 213 human proteins harboring RNA recognition motifs, including FUS and TDP-43, raising the possibility that additional RNA-binding proteins might contribute to ALS pathogenesis. We performed a systematic survey of these proteins to find additional candidates similar to TDP-43 and FUS, followed by bioinformatics to predict prion-like domains in a subset of them. We sequenced one of these genes,
TAF15
, in patients with ALS and identified missense variants, which were absent in a large number of healthy controls. These disease-associated variants of TAF15 caused formation of cytoplasmic foci when expressed in primary cultures of spinal cord neurons. Very similar to TDP-43 and FUS, TAF15 aggregated in vitro and conferred neurodegeneration in
Drosophila
, with the ALS-linked variants having a more severe effect than wild type. Immunohistochemistry of postmortem spinal cord tissue revealed mislocalization of TAF15 in motor neurons of patients with ALS. We propose that aggregation-prone RNA-binding proteins might contribute very broadly to ALS pathogenesis and the genes identified in our yeast functional screen, coupled with prion-like domain prediction analysis, now provide a powerful resource to facilitate ALS disease gene discovery.
Increased functional connectivity indicates the severity of cognitive impairment in multiple sclerosis
Authors: Hawellek David J. , Hipp Joerg F. , Lewis Christopher M. , Corbetta Maurizio , Engel Andreas K.
Published: November 2011

Correlations in spontaneous brain activity provide powerful access to large-scale organizational principles of the CNS. However, making inferences about cognitive processes requires a detailed understanding of the link between these couplings and the structural integrity of the CNS. We studied the impact of multiple sclerosis, which leads to the severe disintegration of the central white matter, on functional connectivity patterns in spontaneous cortical activity. Using a data driven approach based on the strength of a salient pattern of cognitive pathology, we identified distinct networks that exhibit increases in functional connectivity despite the presence of strong and diffuse reductions of the central white-matter integrity. The default mode network emerged as a core target of these connectivity modulations, showing enhanced functional coupling in bilateral inferior parietal cortex, posterior cingulate, and medial prefrontal cortex. These findings imply a complex and diverging relation of anatomical and functional connectivity in early multiple sclerosis and, thus, add an important observation for understanding how cognitive abilities and CNS integrity may be reflected in the intrinsic covariance of functional signals.
Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate
Authors: Wu Xudong , Bradley Michael J. , Cai Yiying , Kümmel Daniel , De La Cruz Enrique M. , Barr Francis A. , Reinisch Karin M.
Published: November 2011

Rab GTPases are key regulators of membrane traffic pathways within eukaryotic cells. They are specifically activated by guanine nucleotide exchange factors (GEFs), which convert them from their “inactive” GDP-bound form to the “active” GTP-bound form. In higher eukaryotes, proteins containing DENN-domains comprise a major GEF family. Here we describe at 2.1-Å resolution the first structure of a DENN-domain protein, DENND1B-S, complexed with its substrate Rab35, providing novel insights as to how DENN-domain GEFs interact with and activate Rabs. DENND1B-S is bi-lobed, and interactions with Rab35 are through conserved surfaces in both lobes. Rab35 binds via switch regions I and II, around the nucleotide-binding pocket. Positional shifts in Rab residues required for nucleotide binding may lower its affinity for bound GDP, and a conformational change in switch I, which makes the nucleotide-binding pocket more solvent accessible, likely also facilitates exchange.
Flux through hepatic pyruvate carboxylase and phosphoenolpyruvate carboxykinase detected by hyperpolarized
13
C magnetic resonance
Authors: Merritt Matthew E. , Harrison Crystal , Sherry A. Dean , Malloy Craig R. , Burgess Shawn C.
Published: November 2011

In the heart, detection of hyperpolarized [
13
C]bicarbonate and
13
CO
2
by magnetic resonance (MR) after administration of hyperpolarized [1-
13
C]pyruvate is caused exclusively by oxidative decarboxylation of pyruvate via the pyruvate dehydrogenase complex (PDH). However, liver mitochondria possess alternative anabolic pathways accessible by [1-
13
C]pyruvate, which may allow a wider diagnostic range for hyperpolarized MR compared with other tissue. Metabolism of hyperpolarized [1-
13
C]pyruvate in the tricarboxylic acid (TCA) cycle was monitored in the isolated perfused liver from fed and fasted mice. Hyperpolarized [1-
13
C]pyruvate was rapidly converted to [1-
13
C]lactate, [1-
13
C]alanine, [1-
13
C]malate, [4-
13
C]malate, [1-
13
C]aspartate, [4-
13
C]aspartate, and [
13
C]bicarbonate. Livers from fasted animals had increased lactate:alanine, consistent with elevated NADH:NAD
+
. The appearance of asymmetrically enriched malate and aspartate indicated high rates of anaplerotic pyruvate carboxylase activity and incomplete equilibration with fumarate. Hyperpolarized [
13
C]bicarbonate was also detected, consistent with multiple mechanisms, including cataplerotic decarboxylation of [4-
13
C]oxaloacetate via phosphoenolpyruvate carboxykinase (PEPCK), forward TCA cycle flux of [4-
13
C]oxaloacetate to generate
13
CO
2
at isocitrate dehydrogenase, or decarboxylation of [1-
13
C]pyruvate by PDH. Isotopomer analysis of liver glutamate confirmed that anaplerosis was sevenfold greater than flux through PDH. In addition, signal from [4-
13
C]malate and [4-
13
C]aspartate was markedly blunted and signal from [
13
C]bicarbonate was completely abolished in livers from PEPCK KO mice, indicating that the major pathway for entry of hyperpolarized [1-
13
C]pyruvate into the hepatic TCA cycle is via pyruvate carboxylase, and that cataplerotic flux through PEPCK is the primary source of [
13
C]bicarbonate. We conclude that MR detection of hyperpolarized TCA intermediates and bicarbonate is diagnostic of pyruvate carboxylase and PEPCK flux in the liver.
Fcγ receptor IIB (FcγRIIB) maintains humoral tolerance in the human immune system in vivo
Authors: Baerenwaldt Anne , Lux Anja , Danzer Heike , Spriewald Bernd M. , Ullrich Evelyn , Heidkamp Gordon , Dudziak Diana , Nimmerjahn Falk
Published: November 2011

Maintenance of immunological tolerance is crucial to prevent development of autoimmune disease. The production of autoantibodies is a hallmark of many autoimmune diseases and studies in mouse model systems suggest that inhibitory signaling molecules may be important checkpoints of humoral tolerance. By generating humanized mice with normal and functionally impaired Fcγ receptor IIB (FcγRIIB) variants, we show that the inhibitory Fcγ-receptor is a checkpoint of humoral tolerance in the human immune system in vivo. Impaired human FcγRIIB function resulted in the generation of higher levels of serum immunoglobulins, the production of different autoantibody specificities, and a higher proportion of human plasmablasts and plasma cells in vivo. Our results suggest that the inhibitory FcγRIIB may be an important checkpoint of humoral tolerance in the human immune system.
Energetic consequences of thermal and nonthermal food processing
Authors: Carmody Rachel N. , Weintraub Gil S. , Wrangham Richard W.
Published: November 2011

Processing food extensively by thermal and nonthermal techniques is a unique and universal human practice. Food processing increases palatability and edibility and has been argued to increase energy gain. Although energy gain is a well-known effect from cooking starch-rich foods, the idea that cooking meat increases energy gain has never been tested. Moreover, the relative energetic advantages of cooking and nonthermal processing have not been assessed, whether for meat or starch-rich foods. Here, we describe a system for characterizing the energetic effects of cooking and nonthermal food processing. Using mice as a model, we show that cooking substantially increases the energy gained from meat, leading to elevations in body mass that are not attributable to differences in food intake or activity levels. The positive energetic effects of cooking were found to be superior to the effects of pounding in both meat and starch-rich tubers, a conclusion further supported by food preferences in fasted animals. Our results indicate significant contributions from cooking to both modern and ancestral human energy budgets. They also illuminate a weakness in current food labeling practices, which systematically overestimate the caloric potential of poorly processed foods.
Surface-engineered substrates for improved human pluripotent stem cell culture under fully defined conditions
Authors: Saha Krishanu , Mei Ying , Reisterer Colin M. , Pyzocha Neena Kenton , Yang Jing , Muffat Julien , Davies Martyn C. , Alexander Morgan R. , Langer Robert , Anderson Daniel G. , Jaenisch Rudolf
Published: November 2011

The current gold standard for the culture of human pluripotent stem cells requires the use of a feeder layer of cells. Here, we develop a spatially defined culture system based on UV/ozone radiation modification of typical cell culture plastics to define a favorable surface environment for human pluripotent stem cell culture. Chemical and geometrical optimization of the surfaces enables control of early cell aggregation from fully dissociated cells, as predicted from a numerical model of cell migration, and results in significant increases in cell growth of undifferentiated cells. These chemically defined xeno-free substrates generate more than three times the number of cells than feeder-containing substrates per surface area. Further, reprogramming and typical gene-targeting protocols can be readily performed on these engineered surfaces. These substrates provide an attractive cell culture platform for the production of clinically relevant factor-free reprogrammed cells from patient tissue samples and facilitate the definition of standardized scale-up friendly methods for disease modeling and cell therapeutic applications.
Malaria antifolate resistance with contrasting
Plasmodium falciparum
dihydrofolate reductase (DHFR) polymorphisms in humans and
Anopheles
mosquitoes
Authors: Mharakurwa Sungano , Kumwenda Taida , Mkulama Mtawa A. P. , Musapa Mulenga , Chishimba Sandra , Shiff Clive J. , Sullivan David J. , Thuma Philip E. , Liu Kun , Agre Peter
Published: November 2011

Surveillance for drug-resistant parasites in human blood is a major effort in malaria control. Here we report contrasting antifolate resistance polymorphisms in
Plasmodium falciparum
when parasites in human blood were compared with parasites in
Anopheles
vector mosquitoes from sleeping huts in rural Zambia. DNA encoding
P. falciparum
dihydrofolate reductase (EC 1.5.1.3) was amplified by PCR with allele-specific restriction enzyme digestions. Markedly prevalent pyrimethamine-resistant mutants were evident in human
P. falciparum
infections—S108N (>90%), with N51I, C59R, and 108N+51I+59R triple mutants (30–80%). This resistance level may be from selection pressure due to decades of sulfadoxine/pyrimethamine use in the region. In contrast, cycloguanil-resistant mutants were detected in very low frequency in parasites from human blood samples—S108T (13%), with A16V and 108T+16V double mutants (∼4%). Surprisingly, pyrimethamine-resistant mutants were of very low prevalence (2–12%) in the midguts of
Anopheles arabiensis
vector mosquitoes, but cycloguanil-resistant mutants were highly prevalent—S108T (90%), with A16V and the 108T+16V double mutant (49–57%). Structural analysis of the dihydrofolate reductase by in silico modeling revealed a key difference in the enzyme within the NADPH binding pocket, predicting the S108N enzyme to have reduced stability but the S108T enzyme to have increased stability. We conclude that
P. falciparum
can bear highly host-specific drug-resistant polymorphisms, most likely reflecting different selective pressures found in humans and mosquitoes. Thus, it may be useful to sample both human and mosquito vector infections to accurately ascertain the epidemiological status of drug-resistant alleles.
Low paternity skew and the influence of maternal kin in an egalitarian, patrilocal primate
Authors: Strier Karen B. , Chaves Paulo B. , Mendes Sérgio L. , Fagundes Valéria , Di Fiore Anthony
Published: November 2011

Levels of reproductive skew vary in wild primates living in multimale groups depending on the degree to which high-ranking males monopolize access to females. Still, the factors affecting paternity in egalitarian societies remain unexplored. We combine unique behavioral, life history, and genetic data to evaluate the distribution of paternity in the northern muriqui (Brachyteles hypoxanthus), a species known for its affiliative, nonhierarchical relationships. We genotyped 67 individuals (22 infants born over a 3-y period, their 21 mothers, and all 24 possible sires) at 17 microsatellite marker loci and assigned paternity to all infants. None of the 13 fathers were close maternal relatives of females with which they sired infants, and the most successful male sired a much lower percentage of infants (18%) than reported for the most successful males in other species. Our findings of inbreeding avoidance and low male reproductive skew are consistent with the muriqui's observed social and sexual behavior, but the long delay (≥2.08 y) between the onset of male sexual behavior and the age at which males first sire young is unexpected. The allocation of paternity implicates individual male life histories and access to maternal kin as key factors influencing variation in paternal—and grandmaternal—fitness. The apparent importance of lifelong maternal investment in coresident sons resonates with other recent examinations of maternal influences on offspring reproduction. This importance also extends the implications of the “grandmother hypothesis” in human evolution to include the possible influence of mothers and other maternal kin on male reproductive success in patrilocal societies.
HSV-1 gene expression from reactivated ganglia is disordered and concurrent with suppression of latency-associated transcript and miRNAs
Authors: Du Te , Zhou Guoying , Roizman Bernard
Published: November 2011

In cell cultures, HSV-1 replication is initiated by recruitment by virion protein 16 of transcriptional factors and histone-modifying enzymes to immediate early (α) gene promoters. HSV establishes latent infections characterized by suppression of viral gene expression except for latency-associated transcripts (LATs) and miRNAs. The latent virus reactivates in stressed neurons. A fundamental question is how reactivation initiates in the absence of virion protein 16. We report the following findings in the ganglion explant model. (
i
) Anti-nerve growth factor antibody accelerated the reactivation of latent virus. Viral mRNAs were detected as early as 9 h after explantation. (
ii
) After explantation the amounts of viral mRNAs increased whereas amounts of miRNAs and LATs decreased. The decrease in miRNAs and LATs required ongoing protein synthesis, raising the possibility that LAT and miRNAs were degraded by a viral gene product. (
iii
) The expression of viral genes in explanted ganglia was disordered rather than sequentially ordered as in infected cells in culture. These findings suggest that in reactivating ganglia gene expression is totally derepressed and challenge the current models in that establishment of or exit from latency could not be dependent on the suppression or activation of single or small clusters of viral genes. Finally, miRNAs and LATs reached peak levels 9–11 d after corneal inoculation, thus approximating the pattern of virus replication in these ganglia. These findings suggest that the patterns of accumulation of LATs and miRNAs reflect many different stages in the infection of neurons.
Researching the benefits of learning: the persuasive power of longitudinal studies
Authors: Field John
Published: November 2011

Recent years have witnessed considerable growth of research on the benefits of adult learning. Much of this is UK-based, and draws on evidence from large scale longitudinal data sets. Overwhelmingly, these studies have found clear evidence of economic, social and individual benefits
as a result of participating in adult learning. While these claims are important and influential ones, there has to date been little discussion of the nature of the data and analytical techniques being used. Nor has there been sufficient attention to the possibility that learning may have
negative outcomes. The paper identifies and explores some limitations of longitudinal research in the study of adult learning, but concludes that despite the problems, this body of work still represents an important departure in the field, with considerable international significance.
Strangers in a strange land – on becoming scholars of teaching
Authors: Adendorff Hanelie
Published: November 2011

This paper reports on a qualitative study that explored the challenges experienced by nine emerging scholars of teaching at a research-intensive university in South Africa. It details three problem areas encountered during the process of becoming scholars of teaching: (1) negative perceptions
about the work and related reward concerns, (2) concerns about mastering this form of enquiry, and (3) identity issues. Whilst the first two have been described in SoTL literature, the third – identity issues – has not received attention in the literature in this area. These concerns
are discussed using the constructs of Discourse, academic cultures and communities of practice.
The British higher education funding debate: the perils of 'talking economics'
Authors: Dodds Anneliese
Published: November 2011

This article examines current debates surrounding British higher education funding from a political economy perspective, drawing on 'positive' and 'institutionalist' political economy. Adopting the lens of political economy enables a critical assessment of the use of terms drawn from
economics by many higher education decision-makers. Current discussions embody particular assumptions about the nature of producers and consumers in higher education, the relationship between supply and demand, and the role of information in the higher education 'market'. They also frequently
fail to acknowledge the active rather than passive role of higher education institutions in shaping policy discussions surrounding higher education funding.
An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation
Authors: Morin-Leisk Jeanne , Saini Simran G. , Meng Xin , Makhov Alexander M. , Zhang Peijun , Lee Tina H.
Published: November 2011

Endoplasmic reticulum (ER) network branching requires homotypic tethering and fusion of tubules mediated by the atlastin (ATL) guanosine triphosphatase (GTPase). Recent structural studies on the ATL soluble domain reveal two dimeric conformers proposed to correspond to a tethered prefusion state and a postfusion state. How the prefusion conformer transitions to the postfusion conformer is unknown. In this paper, we identify an intramolecular salt bridge mediated by two residues outside the GTPase domain near the point of rotation that converts the prefusion dimer to the postfusion state. Charge reversal of either residue blocked ER network branching, whereas a compensatory charge reversal to reestablish electrostatic attraction restored function. In vitro assays using the soluble domain revealed that the salt bridge was dispensable for GTP binding and hydrolysis but was required for forming the postfusion dimer. Unexpectedly, the postfusion conformation of the soluble domain was achieved when bound to the nonhydrolyzable GTP analogue guanosine 5′-[β,γ-imido]triphosphate, suggesting that nucleotide hydrolysis might not be required for the prefusion to postfusion conformational change.
Cdk1 phosphorylation of the kinetochore protein Nsk1 prevents error-prone chromosome segregation
Authors: Chen Jun-Song , Lu Lucy X. , Ohi Melanie D. , Creamer Kevin M. , English Chauca , Partridge Janet F. , Ohi Ryoma , Gould Kathleen L.
Published: November 2011

Cdk1 controls many aspects of mitotic chromosome behavior and spindle microtubule (MT) dynamics to ensure accurate chromosome segregation. In this paper, we characterize a new kinetochore substrate of fission yeast Cdk1, Nsk1, which promotes proper kinetochore–MT (k-MT) interactions and chromosome movements in a phosphoregulated manner. Cdk1 phosphorylation of Nsk1 antagonizes Nsk1 kinetochore and spindle localization during early mitosis. A nonphosphorylatable Nsk1 mutant binds prematurely to kinetochores and spindle, cementing improper k-MT attachments and leading to high rates of lagging chromosomes that missegregate. Accordingly, cells lacking nsk1 exhibit synthetic growth defects with mutations that disturb MT dynamics and/or kinetochore structure, and lack of proper phosphoregulation leads to even more severe defects. Intriguingly, Nsk1 is stabilized by binding directly to the dynein light chain Dlc1 independently of the dynein motor, and Nsk1–Dlc1 forms chainlike structures in vitro. Our findings establish new roles for Cdk1 and the Nsk1–Dlc1 complex in regulating the k-MT interface and chromosome segregation.
Cryoelectron tomography of radial spokes in cilia and flagella
Authors: Pigino Gaia , Bui Khanh Huy , Maheshwari Aditi , Lupetti Pietro , Diener Dennis , Ishikawa Takashi
Published: November 2011

Radial spokes (RSs) are ubiquitous components in the 9 + 2 axoneme thought to be mechanochemical transducers involved in local control of dynein-driven microtubule sliding. They are composed of >23 polypeptides, whose interactions and placement must be deciphered to understand RS function. In this paper, we show the detailed three-dimensional (3D) structure of RS in situ in Chlamydomonas reinhardtii flagella and Tetrahymena thermophila cilia that we obtained using cryoelectron tomography (cryo-ET). We clarify similarities and differences between the three spoke species, RS1, RS2, and RS3, in T. thermophila and in C. reinhardtii and show that part of RS3 is conserved in C. reinhardtii, which only has two species of complete RSs. By analyzing C. reinhardtii mutants, we identified the specific location of subsets of RS proteins (RSPs). Our 3D reconstructions show a twofold symmetry, suggesting that fully assembled RSs are produced by dimerization. Based on our cryo-ET data, we propose models of subdomain organization within the RS as well as interactions between RSPs and with other axonemal components.
Synthetic double-stranded RNA induces innate immune responses similar to a live viral vaccine in humans
Authors: Caskey Marina , Lefebvre François , Filali-Mouhim Abdelali , Cameron Mark J. , Goulet Jean-Philippe , Haddad Elias K. , Breton Gaëlle , Trumpfheller Christine , Pollak Sarah , Shimeliovich Irina , Duque-Alarcon Angela , Pan Li , Nelkenbaum Annette , Salazar Andres M. , Schlesinger Sarah J. , Steinman Ralph M. , Sékaly Rafick P.
Published: November 2011

Adjuvants are critical for the success of vaccines. Agonists of microbial pattern recognition receptors (PRRs) are promising new adjuvant candidates. A mechanism through which adjuvants enhance immune responses is to stimulate innate immunity. We studied the innate immune response in humans to synthetic double-stranded RNA (polyinosinic:polycytidylic acid [poly IC] stabilized with poly-l-lysine [poly ICLC]), an agonist for toll-like receptor (TLR) 3, and the cytosolic RNA helicase MDA-5. Transcriptional analysis of blood samples from eight volunteers, after subcutaneous administration of poly ICLC, showed up-regulation of genes involved in multiple innate immune pathways in all subjects, including interferon (IFN) and inflammasome signaling. Blocking type I IFN receptor ex vivo significantly dampened the response to poly IC. Comparative transcriptional analysis showed that several innate immune pathways were similarly induced in volunteers immunized with the highly efficacious yellow fever vaccine. Therefore, a chemically defined PRR agonist like poly ICLC can be a reliable and authentic microbial mimic for inducing innate immune responses in humans.
Nucleoid-Enriched Proteomes in Developing Plastids and Chloroplasts from Maize Leaves: A New Conceptual Framework for Nucleoid Functions
Authors: Majeran Wojciech , Friso Giulia , Asakura Yukari , Qu Xian , Huang Mingshu , Ponnala Lalit , Watkins Kenneth P. , Barkan Alice , van Wijk Klaas J.
Published: November 2011

Plastids contain multiple copies of the plastid chromosome, folded together with proteins and RNA into nucleoids. The degree to which components of the plastid gene expression and protein biogenesis machineries are nucleoid associated, and the factors involved in plastid DNA organization, repair, and replication, are poorly understood. To provide a conceptual framework for nucleoid function, we characterized the proteomes of highly enriched nucleoid fractions of proplastids and mature chloroplasts isolated from the maize (Zea mays) leaf base and tip, respectively, using mass spectrometry. Quantitative comparisons with proteomes of unfractionated proplastids and chloroplasts facilitated the determination of nucleoid-enriched proteins. This nucleoid-enriched proteome included proteins involved in DNA replication, organization, and repair as well as transcription, mRNA processing, splicing, and editing. Many proteins of unknown function, including pentatricopeptide repeat (PPR), tetratricopeptide repeat (TPR), DnaJ, and mitochondrial transcription factor (mTERF) domain proteins, were identified. Strikingly, 70S ribosome and ribosome assembly factors were strongly overrepresented in nucleoid fractions, but protein chaperones were not. Our analysis strongly suggests that mRNA processing, splicing, and editing, as well as ribosome assembly, take place in association with the nucleoid, suggesting that these processes occur cotranscriptionally. The plastid developmental state did not dramatically change the nucleoid-enriched proteome but did quantitatively shift the predominating function from RNA metabolism in undeveloped plastids to translation and homeostasis in chloroplasts. This study extends the known maize plastid proteome by hundreds of proteins, including more than 40 PPR and mTERF domain proteins, and provides a resource for targeted studies on plastid gene expression. Details of protein identification and annotation are provided in the Plant Proteome Database.
Randomised clinical trial: the efficacy of prucalopride in patients with chronic intestinal pseudo‐obstruction – a double‐blind, placebo‐controlled, cross‐over, multiple n = 1 study
Authors: Emmanuel A. V. , Kamm M. A. , Roy A. J. , Kerstens R. , Vandeplassche L.
Published: November 2011

Aliment Pharmacol Ther 2012; 35: 48–55

Background  Chronic intestinal pseudo‐obstruction is a disabling condition for which there are no established drug therapies. The condition is caused by a diverse range of intestinal myopathies and neuropathies.

Aim  To assess the therapeutic efficacy of prucalopride, a selective high‐affinity 5‐HT4 receptor agonist, we employed a multiple n = 1 study design. Each patient acted as his/her own control, each day counting as one treatment episode, allowing comparison of 168 days on each of active drug and placebo.

Methods  Double‐blind, randomised, placebo‐controlled, cross‐over trial of four 12‐week treatment periods, with 2–4 mg prucalopride or placebo daily. In each of the first and second 6 months there was a prucalopride and a placebo treatment. Patients with proven chronic intestinal pseudo‐obstruction, including dilated gut, were included. Evaluation was by patient diary and global evaluation.

Results  Seven patients participated (mean 42 years, five female, median symptom duration 11 years). Three discontinued, two due to study length, and one on prucalopride due to unrelated malnutrition and bronchopneumonia. Four patients (three visceral myopathy and one visceral neuropathy) completed the study; prucalopride significantly improved pain in three of four patients, nausea in two, vomiting in one, bloating in four and analgesic intake. Bowel function was not changed substantially.

Conclusions  n = 1 studies in rare conditions allow drug efficacy assessment. Prucalopride relieves symptoms in selected patients with chronic pseudo‐obstruction.
Caffeine is protective in patients with non‐alcoholic fatty liver disease
Authors: Birerdinc A. , Stepanova M. , Pawloski L. , Younossi Z. M.
Published: November 2011

Aliment Pharmacol Ther 2012; 35: 76–82

Background  Non‐alcoholic fatty liver disease (NAFLD), the hepatic manifestation of metabolic syndrome, is the most common cause of primary liver disease. Although recent studies have found that coffee drinking is protective against end stage chronic liver disease, there are scarce caffeine intake data in NAFLD specifically.

Aim  To investigate the effects of dietary behaviour in NAFLD patients, using four continuous cycles of the National Health and Nutrition Examination Surveys (NHANES 2001–2008).

Methods  Using data from four continuous cycles of NHANES, dietary intake questionnaires that list 62 nutrition components. Logistic regression was used to identify independent predictors of NAFLD among nutrition components after adjustment for potential clinical confounders. All analyses were run using sas 9.1 and sudaan 10.0 (SAS Institute Inc., Cary, NC, USA).

Results  Of the 62 nutrient components used for the univariate analysis, 38% were significant (P‐value <0.05) in NAFLD with caffeine consumption being higher in the control group (P‐value <0.001). The multivariate analysis using demographics, clinical parameters and nutritional components found five factors independently associated with NAFLD [African American Race P‐value <0.001); Male gender P‐value <0.001); Obesity (BMI ≥ 30) P‐value <0.001); Caffeine intake (mg) P‐value <0.001) and total plain water consumption (g) P‐value ≤0.02)].

Conclusions  Our analysis shows that caffeine intake is independently associated with a lower risk for NAFLD suggesting a potential protective effect. These data necessitate further research to elucidate the mechanism by which caffeine can protect against NAFLD.
Adjacent central venous catheters can result in immediate aspiration of infused drugs during renal replacement therapy*
Authors: Kam K. Y. R. , Mari J. M. , Wigmore T. J.
Published: November 2011

Dual‐lumen haemodiafiltration catheters enable continuous renal replacement therapy in the critically ill and are often co‐located with central venous catheters used to infuse drugs. The extent to which infusions are immediately aspirated by an adjacent haemodiafiltration catheter remains unknown. A bench model was constructed to evaluate this effect. A central venous catheter and a haemodiafiltration catheter were inserted into a simulated central vein and flow generated using centrifugal pumps within the simulated vein and haemodiafiltration circuit. Ink was used as a visual tracer and creatinine solution as a quantifiable tracer. Tracers were completely aspirated by the haemodiafiltration catheter unless the infusion was at least 1 cm downstream to the arterial port. No tracer was aspirated from catheters infusing at least 2 cm downstream. Orientation of side ports did not affect tracer elimination. Co‐location of central venous and haemodiafiltration catheters may lead to complete aspiration of infusions into the haemodiafilter with resultant drug under‐dosing.
Microarray analysis of differential gene expression in sensitive and resistant pig toEscherichia coliF18
Authors: Bao W. B. , Ye L. , Pan Z. Y. , Zhu J. , Du Z. D. , Zhu G. Q. , Huang X. G. , Wu S. L.
Published: November 2011

In this study, Agilent two‐colour microarray‐based gene expression profiling was used to detect differential gene expression in duodenal tissues collected from eight full‐sib pairs of Sutai pigs differing in adhesion phenotype (sensitivity and resistance toEscherichia coliF18). Using a two‐fold change minimum threshold, we found 18 genes that were differentially expressed (10 up‐regulated and eight down‐regulated) between the sensitive and resistant animal groups. Our gene ontology analysis revealed that these differentially expressed genes are involved in a variety of biological processes, including immune responses, extracellular modification (e.g. glycosylation), cell adhesion and signal transduction, all of which are related to the anabolic metabolism of glycolipids, as well as to inflammation‐ and immune‐related pathways. Based on the genes identified in the screen and the pathway analysis results, real‐time PCR was used to test the involvement ofST3GAL1andAgenes (of glycolipid‐related pathways),SLA‐1andSLA‐3genes (of inflammation‐ and immune‐related pathways), as well as the differential genesFUT1,TAP1andSLA‐DQA. Subsequently, real‐time PCR was performed to validate seven differentially expressed genes screened out by the microarray approach, and sufficient consistency was observed between the two methods. The results support the conclusion that these genes are related to theE. coliF18 receptor and susceptibility to E. coli F18.
The development of the Tuebingen Cushing’s disease quality of life inventory (Tuebingen CD‐25). Part II: normative data from 1784 healthy people
Authors: Milian Monika , Teufel Philipp , Honegger Juergen , Gallwitz Baptist , Schnauder Guenter , Psaras Tsambika
Published: November 2011

Objective  In part I of the study, a health‐related quality of life (HRQoL) inventory for Cushing’s disease (CD), the Tuebingen Cushing‐25 quality of life inventory (Tuebingen CD‐25) was developed. In this second part, we aimed to assess normative data from healthy controls (HC) with which the individual patients’ scores can be compared.

Design  Cross‐sectional study.

Participants  Sixty‐three patients with CD (52 women, 11 men) and 1784 HC (1210 women, 574 men) filled out the Tuebingen CD‐25.

Measurements  HC received the inventory as a nondisease‐specific quality of life questionnaire omitting the introductory sentence ‘Because of my Cushing’s disease’ which was included in the CD group to be able to compare HRQoL in persons with and without CD. Slight and severe impairments were categorized according to the following principles: percent ranges >84·0% were classified as slight and percent ranges >95·0% as severe impairment.

Results  In 28·6% of our patients with CD, we found slight and in 41·3% severe impairment in the Total Score of the Tuebingen CD‐25 compared with HC. Less than one‐third of our patient sample presented with unimpaired HRQoL. In the patient population, impairment was found in all scales of the Tuebingen CD‐25 to a similar extent (P = 0·444), pointing to the fact that all HRQoL domains are similarly impaired. We observed that female patients perceived a worse HRQoL than men in the domains depressive symptoms and social environment (P < 0·05).

Conclusion  The Tuebingen CD‐25 is a feasible instrument to assess HRQoL in CD in a clinical and investigative setting and provides normative data for all age groups and genders.
Impact of vitamin D‐related serum PTH reference values on the diagnosis of mild primary hyperparathyroidism, using bivariate calcium/PTH reference regions
Authors: Fillée Catherine , Keller Thomas , Mourad Michel , Brinkmann Thomas , Ketelslegers Jean‐Marie
Published: November 2011

Background, objective  An international consensus conference underlined the importance of defining upper parathyroid hormone (PTH) reference values based on 25‐OH‐vitamin D [25(OH)D] to diagnose mild primary hyperparathyroidism. We determined the importance of this factor in a Belgian population.

Design, patients, methods  Intact PTH and 25(OH)D were measured in 261 healthy controls (18–65 years, winter/summer). They were classified as 25(OH)D replete (50–153 nmol/l; n = 129) or deplete (8–50 nmol/l; n = 132). PTH was determined in 49 patients with surgically proven primary hyperparathyroidism. PTH thresholds for 95% specificities and corresponding sensitivities were computed from both 25(OH)D replete and deplete receiver operating characteristic (ROC) curves. The 95% bivariate reference ellipses, relating PTH to calcium for 25(OH)D replete and deplete controls, were compared to the PTH/calcium pairs of patients with primary hyperparathyroidism.

Results  Parathyroid hormone correlated with 25(OH)D (r = −0·3232; P < 0·0001). PTH normative values were 20% lower in 25(OH)D replete than deplete controls (P < 0·0001). PTH thresholds, providing 95% specificities for primary hyperparathyroidism diagnosis, were 7·6 pmol/l and 5·8 pmol/l, using ROC curves derived from 25(OH)D deplete or replete controls, respectively. Corresponding sensitivities were of 56%vs 88%, respectively (P < 0·05). The 95% PTH/calcium bivariate reference ellipses for?deplete and replete 25(OH)D controls differed, but the PTH/calcium pairs of patients with primary hyperparathyroidism did not overlap these ellipses.

Conclusion  For a given specificity, primary hyperparathyroidism diagnostic parathyroid hormone thresholds were lower and sensitivities higher using ROC curves, derived from 25(OH)D replete vs deplete controls. The 25(OH)D status does not affect the efficiency of primary hyperparathyroidism diagnosis, using bivariate PTH/calcium reference density ellipses.
Intra‐population variability of life‐history traits and growth during range expansion of the invasive round goby,Neogobius melanostomus
Authors: GUTOWSKY L. F. G. , FOX M. G.
Published: November 2011

Abstract Fish can undergo changes in their life‐history traits that correspond with local demographic conditions. Under range expansion, a population of non‐native fish might then be expected to exhibit a suite of life‐history traits that differ between the edge and the centre of the population’s geographic range. To test this hypothesis, life‐history traits of an expanding population of round goby,Neogobius melanostomus(Pallas), in early and newly established sites in the Trent River (Ontario, Canada) were compared in 2007 and 2008. Round goby in the area of first introduction exhibited a significant decrease in age at maturity, increased length at age 1 and they increased in GSI from 2007 to 2008. While individuals at the edges of the range exhibited traits that promote population growth under low intraspecific density, yearly variability in life‐history traits suggests that additional processes such as declining density and fluctuating food availability are influencing the reproductive strategy and growth of round goby during an invasion.