bluuebunny/crossref_metadata_2025 huggingface dataset:
Integration of biomechanical compliance, leverage, and power in elephant limbs
Authors: Ren Lei , Miller Charlotte E. , Lair Richard , Hutchinson John R.
Published: March 2010

The structure and motion of elephant limbs are unusual compared with those of other animals. Elephants stand and move with straighter limbs (at least when walking), and have limited speed and gait. We devised novel experiments to examine how the limbs of elephants support and propel their mass and to explore the factors that may constrain locomotor performance in these largest of living land animals. We demonstrate that elephant limbs are remarkably compliant even in walking, which maintains low peak forces. Dogma defines elephant limbs as extremely “columnar” for effective weight support, but we demonstrate that limb effective mechanical advantage (EMA) is roughly one-third of that predicted for their size. EMA in elephants is actually smaller than that in horses, which are only one-tenth their mass; it is comparable to human limb values. EMA drops sharply with speed in elephants, as it does in humans. Muscle forces therefore must increase as the limbs become more flexed, and we show how this flexion translates to greater volumes of muscle recruited for locomotion and hence metabolic cost. Surprisingly, elephants use their forelimbs and hindlimbs in similar braking and propulsive roles, not dividing these functions among limbs as was previously assumed or as in other quadrupeds. Thus, their limb function is analogous to four-wheel-drive vehicles. To achieve the observed limb compliance and low peak forces, elephants synchronize their limb dynamics in the vertical direction, but incur considerable mechanical costs from limbs working against each other horizontally.
Myosin-dependent endoplasmic reticulum motility and F-actin organization in plant cells
Authors: Ueda Haruko , Yokota Etsuo , Kutsuna Natsumaro , Shimada Tomoo , Tamura Kentaro , Shimmen Teruo , Hasezawa Seiichiro , Dolja Valerian V. , Hara-Nishimura Ikuko
Published: March 2010

Plants exhibit an ultimate case of the intracellular motility involving rapid organelle trafficking and continuous streaming of the endoplasmic reticulum (ER). Although it was long assumed that the ER dynamics is actomyosin-driven, the responsible myosins were not identified, and the ER streaming was not characterized quantitatively. Here we developed software to generate a detailed velocity-distribution map for the GFP-labeled ER. This map revealed that the ER in the most peripheral plane was relatively static, whereas the ER in the inner plane was rapidly streaming with the velocities of up to ∼3.5 μm/sec. Similar patterns were observed when the cytosolic GFP was used to evaluate the cytoplasmic streaming. Using gene knockouts, we demonstrate that the ER dynamics is driven primarily by the ER-associated myosin XI-K, a member of a plant-specific myosin class XI. Furthermore, we show that the myosin XI deficiency affects organization of the ER network and orientation of the actin filament bundles. Collectively, our findings suggest a model whereby dynamic three-way interactions between ER, F-actin, and myosins determine the architecture and movement patterns of the ER strands, and cause cytosol hauling traditionally defined as cytoplasmic streaming.
Karrikins enhance light responses during germination and seedling development in
Arabidopsis thaliana
Authors: Nelson David C. , Flematti Gavin R. , Riseborough Julie-Anne , Ghisalberti Emilio L. , Dixon Kingsley W. , Smith Steven M.
Published: March 2010

Karrikins are a class of seed germination stimulants identified in smoke from wildfires. Microarray analysis of imbibed
Arabidopsis thaliana
seeds was performed to identify transcriptional responses to KAR
1
before germination. A small set of genes that are regulated by KAR
1
, even when germination is prevented by the absence of gibberellin biosynthesis or light, were identified. Light-induced genes, putative HY5-binding targets, and ABRE-like promoter motifs were overrepresented among KAR
1
-up-regulated genes. KAR
1
transiently induced the light signal transduction transcription factor genes
HY5
and
HYH
. Germination of afterripened
Arabidopsis
seed was triggered at lower fluences of red light when treated with KAR
1
. Light-dependent cotyledon expansion and inhibition of hypocotyl elongation were enhanced in the presence of germination-active karrikins.
HY5
is important for the
Arabidopsis
hypocotyl elongation, but not seed germination, response to karrikins. These results reveal a role for karrikins in priming light responses in the emerging seedling, and suggest that the influence of karrikins on postfire ecology may not be limited to germination recruitment.
Pantethine rescues a
Drosophila
model for pantothenate kinase–associated neurodegeneration
Authors: Rana Anil , Seinen Erwin , Siudeja Katarzyna , Muntendam Remco , Srinivasan Balaji , van der Want Johannes J. , Hayflick Susan , Reijngoud Dirk-Jan , Kayser Oliver , Sibon Ody C. M.
Published: March 2010

Pantothenate kinase–associated neurodegeneration (PKAN), a progressive neurodegenerative disorder, is associated with impairment of pantothenate kinase function. Pantothenate kinase is the first enzyme required for de novo synthesis of CoA, an essential metabolic cofactor. The pathophysiology of PKAN is not understood, and there is no cure to halt or reverse the symptoms of this devastating disease. Recently, we and others presented a PKAN
Drosophila
model, and we demonstrated that impaired function of pantothenate kinase induces a neurodegenerative phenotype and a reduced lifespan. We have explored this
Drosophila
model further and have demonstrated that impairment of pantothenate kinase is associated with decreased levels of CoA, mitochondrial dysfunction, and increased protein oxidation. Furthermore, we searched for compounds that can rescue pertinent phenotypes of the
Drosophila
PKAN model and identified pantethine. Pantethine feeding restores CoA levels, improves mitochondrial function, rescues brain degeneration, enhances locomotor abilities, and increases lifespan. We show evidence for the presence of a de novo CoA biosynthesis pathway in which pantethine is used as a precursor compound. Importantly, this pathway is effective in the presence of disrupted pantothenate kinase function. Our data suggest that pantethine may serve as a starting point to develop a possible treatment for PKAN.
A nocturnal mammal, the greater mouse-eared bat, calibrates a magnetic compass by the sun
Authors: Holland Richard A. , Borissov Ivailo , Siemers Björn M.
Published: March 2010

Recent evidence suggests that bats can detect the geomagnetic field, but the way in which this is used by them for navigation to a home roost remains unresolved. The geomagnetic field may be used by animals both to indicate direction and to locate position. In birds, directional information appears to be derived from an interaction of the magnetic field with either the sun or the stars, with some evidence suggesting that sunset/sunrise provides the primary directional reference by which a magnetic compass is calibrated daily. We demonstrate that homing greater mouse-eared bats (Myotis myotis) calibrate a magnetic compass with sunset cues by testing their homing response after exposure to an altered magnetic field at and after sunset. Magnetic manipulation at sunset resulted in a counterclockwise shift in orientation compared with controls, consistent with sunset calibration of the magnetic field, whereas magnetic manipulation after sunset resulted in no change in orientation. Unlike in birds, however, the pattern of polarization was not necessary for the calibration. For animals that occupy ecological niches where the sunset is rarely observed, this is a surprising finding. Yet it may indicate the primacy of the sun as an absolute geographical reference not only for birds but also within other vertebrate taxa.
A joint x-ray and neutron study on amicyanin reveals the role of protein dynamics in electron transfer
Authors: Sukumar N. , Mathews F. S. , Langan P. , Davidson V. L.
Published: March 2010

The joint x-ray/neutron diffraction model of the Type I copper protein, amicyanin from
Paracoccus denitrificans
was determined at 1.8 Å resolution. The protein was crystallized using reagents prepared in D
2
O. About 86% of the amide hydrogen atoms are either partially or fully exchanged, which correlates well with the atomic depth of the amide nitrogen atom and the secondary structure type, but with notable exceptions. Each of the four residues that provide copper ligands is partially deuterated. The model reveals the dynamic nature of the protein, especially around the copper-binding site. A detailed analysis of the presence of deuterated water molecules near the exchange sites indicates that amide hydrogen exchange is primarily due to the flexibility of the protein. Analysis of the electron transfer path through the protein shows that residues in that region are highly dynamic, as judged by hydrogen/deuterium exchange. This could increase the rate of electron transfer by transiently shortening through-space jumps in pathways or by increasing the atomic packing density. Analysis of C-H⋯X bonding reveals previously undefined roles of these relatively weak H bonds, which, when present in sufficient number can collectively influence the structure, redox, and electron transfer properties of amicyanin.
Fast molecular tracking maps nanoscale dynamics of plasma membrane lipids
Authors: Sahl Steffen J. , Leutenegger Marcel , Hilbert Michael , Hell Stefan W. , Eggeling Christian
Published: March 2010

We describe an optical method capable of tracking a single fluorescent molecule with a flexible choice of high spatial accuracy (∼10–20 nm standard deviation or ∼20–40 nm full-width-at-half-maximum) and temporal resolution (< 1 ms). The fluorescence signal during individual passages of fluorescent molecules through a spot of excitation light allows the sequential localization and thus spatio-temporal tracking of the molecule if its fluorescence is collected on at least three separate point detectors arranged in close proximity. We show two-dimensional trajectories of individual, small organic dye labeled lipids diffusing in the plasma membrane of living cells and directly observe transient events of trapping on < 20 nm spatial scales. The trapping is cholesterol-assisted and much more pronounced for a sphingo- than for a phosphoglycero-lipid, with average trapping times of ∼15 ms and < 4 ms, respectively. The results support previous STED nanoscopy measurements and suggest that, at least for nontreated cells, the transient interaction of a single lipid is confined to macromolecular dimensions. Our experimental approach demonstrates that fast molecular movements can be tracked with minimal invasion, which can reveal new important details of cellular nano-organization.
Elongated oligomers in
β
2
-microglobulin amyloid assembly revealed by ion mobility spectrometry-mass spectrometry
Authors: Smith David P. , Radford Sheena E. , Ashcroft Alison E.
Published: March 2010

The key to understanding amyloid disease is the characterization of oligomeric species formed during the early stages of fibril assembly. Here we have used electrospray ionisation-ion mobility spectrometry-mass spectrometry to identify and structurally characterize the oligomers formed during amyloid assembly from
β
2
-microglobulin (
β
2
m).
β
2
m oligomers are shown to have collision cross-sections consistent with monomeric units arranged in elongated assemblies prior to fibril formation. Direct observation, separation, and quantification of transient oligomeric species reveals that monomers to tetramers are populated through the lag phase with no evidence for the significant population of larger oligomeric species under the conditions employed. The dynamics of each oligomeric species were monitored directly within the ensemble at concentrations commensurate with amyloid formation by observing the subunit exchange of
14
N- and
15
N- labeled oligomers. Analysis of the data revealed a decrease in oligomer dynamics concomitant with increasing oligomer size and the copopulation of dynamic dimeric and trimeric species with more stable trimeric and tetrameric species. The results presented map the events occurring during the lag phase of fibril formation and give a clear insight into the structural characteristics and dynamic nature of the
β
2
m oligomers, demonstrating the existence of elongated assemblies arising from an intact amyloidogenic protein during fibril formation.
Active galactic nucleus feedback in clusters of galaxies
Authors: Blanton Elizabeth L. , Clarke T. E. , Sarazin Craig L. , Randall Scott W. , McNamara Brian R.
Published: March 2010

Observations made during the last ten years with the Chandra X-ray Observatory have shed much light on the cooling gas in the centers of clusters of galaxies and the role of active galactic nucleus (AGN) heating. Cooling of the hot intracluster medium in cluster centers can feed the supermassive black holes found in the nuclei of the dominant cluster galaxies leading to AGN outbursts which can reheat the gas, suppressing cooling and large amounts of star formation. AGN heating can come in the form of shocks, buoyantly rising bubbles that have been inflated by radio lobes, and the dissipation of sound waves.
Disruption of the right temporoparietal junction with transcranial magnetic stimulation reduces the role of beliefs in moral judgments
Authors: Young Liane , Camprodon Joan Albert , Hauser Marc , Pascual-Leone Alvaro , Saxe Rebecca
Published: March 2010

When we judge an action as morally right or wrong, we rely on our capacity to infer the actor's mental states (e.g., beliefs, intentions). Here, we test the hypothesis that the right temporoparietal junction (RTPJ), an area involved in mental state reasoning, is necessary for making moral judgments. In two experiments, we used transcranial magnetic stimulation (TMS) to disrupt neural activity in the RTPJ transiently before moral judgment (experiment 1, offline stimulation) and during moral judgment (experiment 2, online stimulation). In both experiments, TMS to the RTPJ led participants to rely less on the actor's mental states. A particularly striking effect occurred for attempted harms (e.g., actors who intended but failed to do harm): Relative to TMS to a control site, TMS to the RTPJ caused participants to judge attempted harms as less morally forbidden and more morally permissible. Thus, interfering with activity in the RTPJ disrupts the capacity to use mental states in moral judgment, especially in the case of attempted harms.
Structure of lactococcal phage p2 baseplate and its mechanism of activation
Authors: Sciara Giuliano , Bebeacua Cecilia , Bron Patrick , Tremblay Denise , Ortiz-Lombardia Miguel , Lichière Julie , van Heel Marin , Campanacci Valérie , Moineau Sylvain , Cambillau Christian
Published: March 2010

Siphoviridae
is the most abundant viral family on earth which infects bacteria as well as archaea. All known siphophages infecting gram+
Lactococcus lactis
possess a baseplate at the tip of their tail involved in host recognition and attachment. Here, we report analysis of the p2 phage baseplate structure by X-ray crystallography and electron microscopy and propose a mechanism for the baseplate activation during attachment to the host cell. This ∼1 MDa,
Escherichia coli
-expressed baseplate is composed of three protein species, including six trimers of the receptor-binding protein (RBP). RBPs host-recognition domains point upwards, towards the capsid, in agreement with the electron-microscopy map of the free virion. In the presence of Ca
2+
, a cation mandatory for infection, the RBPs rotated 200° downwards, presenting their binding sites to the host, and a channel opens at the bottom of the baseplate for DNA passage. These conformational changes reveal a novel siphophage activation and host-recognition mechanism leading ultimately to DNA ejection.
Assessing respondent-driven sampling
Authors: Goel Sharad , Salganik Matthew J.
Published: March 2010

Respondent-driven sampling (RDS) is a network-based technique for estimating traits in hard-to-reach populations, for example, the prevalence of HIV among drug injectors. In recent years RDS has been used in more than 120 studies in more than 20 countries and by leading public health organizations, including the Centers for Disease Control and Prevention in the United States. Despite the widespread use and growing popularity of RDS, there has been little empirical validation of the methodology. Here we investigate the performance of RDS by simulating sampling from 85 known, network populations. Across a variety of traits we find that RDS is substantially less accurate than generally acknowledged and that reported RDS confidence intervals are misleadingly narrow. Moreover, because we model a best-case scenario in which the theoretical RDS sampling assumptions hold exactly, it is unlikely that RDS performs any better in practice than in our simulations. Notably, the poor performance of RDS is driven not by the bias but by the high variance of estimates, a possibility that had been largely overlooked in the RDS literature. Given the consistency of our results across networks and our generous sampling conditions, we conclude that RDS as currently practiced may not be suitable for key aspects of public health surveillance where it is now extensively applied.
Use of multiple dispersal pathways facilitates amphibian persistence in stream networks
Authors: Campbell Grant Evan H. , Nichols James D. , Lowe Winsor H. , Fagan William F.
Published: March 2010

Although populations of amphibians are declining worldwide, there is no evidence that salamanders occupying small streams are experiencing enigmatic declines, and populations of these species seem stable. Theory predicts that dispersal through multiple pathways can stabilize populations, preventing extinction in habitat networks. However, empirical data to support this prediction are absent for most species, especially those at risk of decline. Our mark-recapture study of stream salamanders reveals both a strong upstream bias in dispersal and a surprisingly high rate of overland dispersal to adjacent headwater streams. This evidence of route-dependent variation in dispersal rates suggests a spatial mechanism for population stability in headwater-stream salamanders. Our results link the movement behavior of stream salamanders to network topology, and they underscore the importance of identifying and protecting critical dispersal pathways when addressing region-wide population declines.
Activation of the planar cell polarity formin DAAM1 leads to inhibition of endothelial cell proliferation, migration, and angiogenesis
Authors: Ju Rong , Cirone Pasquale , Lin Shengda , Griesbach Hilary , Slusarski Diane C. , Crews Craig M.
Published: March 2010

The Wnt/planar cell polarity (PCP) pathway regulates directed cell movement during development and was recently found to play a critical role in endothelial cell proliferation and angiogenesis [Zhang Y, et al. (2006)
Chem Biol
13:1001–1009; Masckauchan TN, et al. (2006)
Mol Biol Cell
17:5163–5172]. However, the mechanisms by which PCP signaling components regulate angiogenesis remain unknown. We report that expression of a constitutively active C-terminal domain of Dishevelled-associated activator of morphogenesis 1 (DAAM1) selectively inhibited endothelial cell proliferation. Moreover, this activated construct suppressed endothelial cell migration and the ability to form coordinated networks in vivo and in vitro. Although constitutively active DAAM1 (CDAAM1) induced both actin polymerization and microtubule (MT) stabilization, the stabilization of MTs alone was sufficient to inhibit endothelial cell growth selectively. Inhibition of actin polymerization alone by jasplakinolide treatment failed to reproduce the inhibitory effects of CDAAM1. These results indicate that DAAM1 regulates endothelial cell growth through MT stabilization in a cell type-selective manner and suggest that PCP signaling plays a pivotal role in angiogenesis by regulating MT stabilization.
A prospective analysis of the Ab response to
Plasmodium falciparum
before and after a malaria season by protein microarray
Authors: Crompton Peter D. , Kayala Matthew A. , Traore Boubacar , Kayentao Kassoum , Ongoiba Aissata , Weiss Greta E. , Molina Douglas M. , Burk Chad R. , Waisberg Michael , Jasinskas Algis , Tan Xiaolin , Doumbo Safiatou , Doumtabe Didier , Kone Younoussou , Narum David L. , Liang Xiaowu , Doumbo Ogobara K. , Miller Louis H. , Doolan Denise L. , Baldi Pierre , Felgner Philip L. , Pierce Susan K.
Published: March 2010

Abs are central to malaria immunity, which is only acquired after years of exposure to
Plasmodium falciparum
(
Pf
). Despite the enormous worldwide burden of malaria, the targets of protective Abs and the basis of their inefficient acquisition are unknown. Addressing these knowledge gaps could accelerate malaria vaccine development. To this end, we developed a protein microarray containing ∼23% of the
Pf
5,400-protein proteome and used this array to probe plasma from 220 individuals between the ages of 2–10 years and 18–25 years in Mali before and after the 6-month malaria season. Episodes of malaria were detected by passive surveillance over the 8-month study period. Ab reactivity to
Pf
proteins rose dramatically in children during the malaria season; however, most of this response appeared to be short-lived based on cross-sectional analysis before the malaria season, which revealed only modest incremental increases in Ab reactivity with age. Ab reactivities to 49
Pf
proteins measured before the malaria season were significantly higher in 8–10-year-old children who were infected with
Pf
during the malaria season but did not experience malaria (
n
= 12) vs. those who experienced malaria (
n
= 29). This analysis also provided insight into patterns of Ab reactivity against
Pf
proteins based on the life cycle stage at which proteins are expressed, subcellular location, and other proteomic features. This approach, if validated in larger studies and in other epidemiological settings, could prove to be a useful strategy for better understanding fundamental properties of the human immune response to
Pf
and for identifying previously undescribed vaccine targets.
Transcriptional activation in the context of repression mediated by archaeal histones
Authors: Wilkinson Steven P. , Ouhammouch Mohamed , Geiduschek E. Peter
Published: March 2010

Many archaea (including all the methanogens, nearly all euryarchaeotes, and some crenarchaeotes) use histones as components of the chromatin that compacts their genomes. The archaeal histones are homo- and heterodimers that pair on DNA to form tetrasomes (as the eukaryotic histones H3 and H4 do). The resulting DNA packaging is known to interfere with assembly of the archaeal transcription apparatus at promoters; the ability of transcriptional activation to function in repressive archaeal chromatin has not yet been explored in vitro. Using four of the
Methanocaldococcus jannaschii
(
Mja
) histones, we have examined activation of the model
Mja rb2
transcription unit by the
Mja
transcriptional activator Ptr2 in this simplified-chromatin context. Using hydroxyl radical footprinting, we find that the Ptr2-specific
rb2
upstream activating site is a preferred histone-localizing site that nucleates histone: DNA-binding radiating from the
rb2
promoter. Nevertheless, Ptr2 competes effectively with histones for access to the
rb2
promoter and most potently activates transcription in vitro at histone concentrations that extensively coat DNA and essentially silence basal transcription.
Phosphate-activated glutaminase (GLS2), a p53-inducible regulator of glutamine metabolism and reactive oxygen species
Authors: Suzuki Sawako , Tanaka Tomoaki , Poyurovsky Masha V. , Nagano Hidekazu , Mayama Takafumi , Ohkubo Shuichi , Lokshin Maria , Hosokawa Hiroyuki , Nakayama Toshinori , Suzuki Yutaka , Sugano Sumio , Sato Eiichi , Nagao Toshitaka , Yokote Koutaro , Tatsuno Ichiro , Prives Carol
Published: March 2010

We identified a p53 target gene, phosphate-activated mitochondrial glutaminase (GLS2), a key enzyme in conversion of glutamine to glutamate, and thereby a regulator of glutathione (GSH) synthesis and energy production. GLS2 expression is induced in response to DNA damage or oxidative stress in a p53-dependent manner, and p53 associates with the GLS2 promoter. Elevated GLS2 facilitates glutamine metabolism and lowers intracellular reactive oxygen species (ROS) levels, resulting in an overall decrease in DNA oxidation as determined by measurement of 8-OH-dG content in both normal and stressed cells. Further, siRNA down-regulation of either GLS2 or p53 compromises the GSH-dependent antioxidant system and increases intracellular ROS levels. High ROS levels following GLS2 knockdown also coincide with stimulation of p53-induced cell death. We propose that GLS2 control of intracellular ROS levels and the apoptotic response facilitates the ability of p53 to protect cells from accumulation of genomic damage and allows cells to survive after mild and repairable genotoxic stress. Indeed, overexpression of GLS2 reduces the growth of tumor cells and colony formation. Further, compared with normal tissue, GLS2 expression is reduced in liver tumors. Thus, our results provide evidence for a unique metabolic role for p53, linking glutamine metabolism, energy, and ROS homeostasis, which may contribute to p53 tumor suppressor function.
Modulation of mismatch repair and genomic stability by miR-155
Authors: Valeri Nicola , Gasparini Pierluigi , Fabbri Muller , Braconi Chiara , Veronese Angelo , Lovat Francesca , Adair Brett , Vannini Ivan , Fanini Francesca , Bottoni Arianna , Costinean Stefan , Sandhu Sukhinder K. , Nuovo Gerard J , Alder Hansjuerg , Gafa Roberta , Calore Federica , Ferracin Manuela , Lanza Giovanni , Volinia Stefano , Negrini Massimo , McIlhatton Michael A. , Amadori Dino , Fishel Richard , Croce Carlo M.
Published: March 2010

Inactivation of mismatch repair (MMR) is the cause of the common cancer predisposition disorder Lynch syndrome (LS), also known as hereditary nonpolyposis colorectal cancer (HNPCC), as well as 10–40% of sporadic colorectal, endometrial, ovarian, gastric, and urothelial cancers. Elevated mutation rates (mutator phenotype), including simple repeat instability [microsatellite instability (MSI)] are a signature of MMR defects. MicroRNAs (miRs) have been implicated in the control of critical cellular pathways involved in development and cancer. Here we show that overexpression of miR-155 significantly down-regulates the core MMR proteins, hMSH2, hMSH6, and hMLH1, inducing a mutator phenotype and MSI. An inverse correlation between the expression of miR-155 and the expression of MLH1 or MSH2 proteins was found in human colorectal cancer. Finally, a number of MSI tumors with unknown cause of MMR inactivation displayed miR-155 overexpression. These data provide support for miR-155 modulation of MMR as a mechanism of cancer pathogenesis.
Induction of cortical endoplasmic reticulum by dimerization of a coatomer-binding peptide anchored to endoplasmic reticulum membranes
Authors: Lavieu Grégory , Orci Lelio , Shi Lei , Geiling Michael , Ravazzola Mariella , Wieland Felix , Cosson Pierre , Rothman James E.
Published: March 2010

Cortical endoplasmic reticulum (cER) is a permanent feature of yeast cells but occurs transiently in most animal cell types. Ist2p is a transmembrane protein that permanently localizes to the cER in yeast. When Ist2 is expressed in mammalian cells, it induces abundant cER containing Ist2. Ist2 cytoplasmic C-terminal peptide is necessary and sufficient to induce cER. This peptide sequence resembles classic coat protein complex I (COPI) coatomer protein-binding KKXX signals, and indeed the dimerized peptide binds COPI in vitro. Controlled dimerization of this peptide induces cER in cells. RNA interference experiments confirm that coatomer is required for cER induction in vivo, as are microtubules and the microtubule plus-end binding protein EB1. We suggest that Ist2 dimerization triggers coatomer binding and clustering of this protein into domains that traffic at the microtubule growing plus-end to generate the cER beneath the plasma membrane. Sequences similar to the Ist2 lysine-rich tail are found in mammalian STIM proteins that reversibly induce the formation of cER under calcium control.
Alternative splicing of human papillomavirus type-16 E6/E6* early mRNA is coupled to EGF signaling via Erk1/2 activation
Authors: Rosenberger Simone , Arce Johanna De-Castro , Langbein Lutz , Steenbergen Renske D. M. , Rösl Frank
Published: March 2010

Certain types of human papillomaviruses (HPVs) are etiologically linked to cervical cancer. Their transforming capacity is encoded by a polycistronic premRNA, where alternative splicing leads to the translation of functional distinct proteins such as E6, E6*, and E7. Here we show that splicing of HPV16 E6/E7 ORF cassette is regulated by the epidermal growth factor (EGF) pathway. The presence of EGF was coupled to preferential E6 expression, whereas depletion of EGF, or treatment with EGF receptor (EGFR) neutralizing antibodies or the EGFR inhibitor tyrphostin AG1478, resulted in E6 exon exclusion in favor of E6*. As a consequence, increased p53 levels and enhanced translation of E7 with a subsequent reduction of the retinoblastoma protein pRb could be discerned. E6 exon exclusion upon EGF depletion was independent from promoter usage, mRNA stability, or selective mRNA transport. Time-course experiments and incubation with cycloheximide demonstrated that E6 alternative splicing is a direct and reversible effect of EGF signal transduction, not depending on de novo protein synthesis. Within this process, Erk1/2-kinase activation was the critical event for E6 exon inclusion, mediated by the upstream MAP kinase MEK1/2. Moreover, siRNA knockdown experiments revealed an involvement of splicing factors hnRNPA1 and hnRNPA2 in E6 exon exclusion, whereas the splicing factors Brm and Sam68 were found to promote E6 exon inclusion. Because there is a natural gradient of EGF and EGF receptor expression in the stratified epithelium, it is reasonable to assume that EGF modulates E6/E7 splicing during the viral life cycle and transformation.
Residues in the central β-hairpin of the DNA helicase of bacteriophage T7 are important in DNA unwinding
Authors: Satapathy Ajit K. , Kochaniak Anna B. , Mukherjee Sourav , Crampton Donald J. , van Oijen Antoine , Richardson Charles C.
Published: March 2010

The ring-shaped helicase of bacteriophage T7 (gp4), the product of gene 4, has basic β-hairpin loops lining its central core where they are postulated to be the major sites of DNA interaction. We have altered multiple residues within the β-hairpin loop to determine their role during dTTPase-driven DNA unwinding. Residues His-465, Leu-466, and Asn-468 are essential for both DNA unwinding and DNA synthesis mediated by T7 DNA polymerase during leading-strand DNA synthesis. Gp4-K467A, gp4-K471A, and gp4-K473A form fewer hexamers than heptamers compared to wild-type helicase and alone are deficient in DNA unwinding. However, they complement for the growth of T7 bacteriophage lacking gene 4. Single-molecule studies show that these three altered helicases support rates of leading-strand DNA synthesis comparable to that observed with wild-type gp4. Gp4-K467A, devoid of unwinding activity alone, supports leading-strand synthesis in the presence of T7 DNA polymerase. We propose that DNA polymerase limits the backward movement of the helicase during unwinding as well as assisting the forward movement necessary for strand separation.
ErbB3/HER3 intracellular domain is competent to bind ATP and catalyze autophosphorylation
Authors: Shi Fumin , Telesco Shannon E. , Liu Yingting , Radhakrishnan Ravi , Lemmon Mark A.
Published: March 2010

ErbB3/HER3 is one of four members of the human epidermal growth factor receptor (EGFR/HER) or ErbB receptor tyrosine kinase family. ErbB3 binds neuregulins via its extracellular region and signals primarily by heterodimerizing with ErbB2/HER2/Neu. A recently appreciated role for ErbB3 in resistance of tumor cells to EGFR/ErbB2-targeted therapeutics has made it a focus of attention. However, efforts to inactivate ErbB3 therapeutically in parallel with other ErbB receptors are challenging because its intracellular kinase domain is thought to be an inactive pseudokinase that lacks several key conserved (and catalytically important) residues—including the catalytic base aspartate. We report here that, despite these sequence alterations, ErbB3 retains sufficient kinase activity to robustly
trans
-autophosphorylate its intracellular region—although it is substantially less active than EGFR and does not phosphorylate exogenous peptides. The ErbB3 kinase domain binds ATP with a
K
d
of approximately 1.1 μM. We describe a crystal structure of ErbB3 kinase bound to an ATP analogue, which resembles the inactive EGFR and ErbB4 kinase domains (but with a shortened αC-helix). Whereas mutations that destabilize this configuration activate EGFR and ErbB4 (and promote EGFR-dependent lung cancers), a similar mutation conversely inactivates ErbB3. Using quantum mechanics/molecular mechanics simulations, we delineate a reaction pathway for ErbB3-catalyzed phosphoryl transfer that does not require the conserved catalytic base and can be catalyzed by the “inactive-like” configuration observed crystallographically. These findings suggest that ErbB3 kinase activity within receptor dimers may be crucial for signaling and could represent an important therapeutic target.
Identification of neuronal subpopulations that project from hypothalamus to both liver and adipose tissue polysynaptically
Authors: Stanley Sarah , Pinto Shirly , Segal Jeremy , Pérez Cristian A. , Viale Agnes , DeFalco Jeff , Cai XiaoLi , Heisler Lora K. , Friedman Jeffrey M.
Published: March 2010

The autonomic nervous system regulates fuel availability and energy storage in the liver, adipose tissue, and other organs; however, the molecular components of this neural circuit are poorly understood. We sought to identify neural populations that project from the CNS indirectly through multisynaptic pathways to liver and epididymal white fat in mice using pseudorabies virus strains expressing different reporters together with BAC transgenesis and immunohistochemistry. Neurons common to both circuits were identified in subpopulations of the paraventricular nucleus of the hypothalamus (PVH) by double labeling with markers expressed in viruses injected in both sites. The lateral hypothalamus and arcuate nucleus of the hypothalamus and brainstem regions (nucleus of the solitary tract and A5 region) also project to both tissues but are labeled at later times. Connections from these same sites to the PVH were evident after direct injection of virus into the PVH, suggesting that these regions lie upstream of the PVH in a common pathway to liver and adipose tissue (two metabolically active organs). These common populations of brainstem and hypothalamic neurons express neuropeptide Y and proopiomelanocortin in the arcuate nucleus, melanin-concentrating hormone, and orexin in the lateral hypothalamus and in the corticotrophin-releasing hormone and oxytocin in the PVH. The delineation of this circuitry will facilitate a functional analysis of the possible role of these potential command-like neurons to modulate autonomic outflow and coordinate metabolic responses in liver and adipose tissue.
Teaching Experimental Method Using the Feature-Present/Feature-Absent Effect
Authors: Balch William R.
Published: March 2010

To determine whether a classroom experiment improved the learning of experimental method, at the start of the semester 2 introductory psychology classes took a 10-question multiple-choice pretest on experimental method. Two days later, before the instructor covered the relevant material in the course, 1 class took part in a classroom experiment on the feature-present/feature-absent effect followed by a debriefing. The other class heard only a comparable lecture. Then each class took a posttest identical to the pretest. On the posttest, but not on the pretest, the classroom experiment class significantly outperformed the lecture-only class. The results suggest that, for teaching experimental method, the feature-present/feature-absent experiment is an effective supplement to lecturing.
Does the First Week of Class Matter? A Quasi-Experimental Investigation of Student Satisfaction
Authors: Hermann Anthony D. , Foster David A. , Hardin Erin E.
Published: March 2010

Teaching experts suggest that establishing clear expectations and a supportive environment at the beginning of a college course has a lasting impact on student attitudes. However, minimal empirical evidence exists to support these suggestions. Consequently, we randomly assigned instructors to either begin their course with a reciprocal interview activity aimed at these goals or in their typical fashion. At term's end, students experiencing the activity (n = 187) reported greater clarity regarding their course responsibilities, more support from their instructor, and greater course satisfaction on both official evaluations and experimenter-administered measures, compared to students who had not (n = 190). These results contribute to a converging body of evidence regarding the effectiveness of reciprocal interviews and similar activities generally.
Teaching and Assessing Critical Thinking Skills for Argument Analysis in Psychology
Authors: Bensley D. Alan , Crowe Deborah S. , Bernhardt Paul , Buckner Camille , Allman Amanda L.
Published: March 2010

Critical thinking is a valued educational outcome; however, little is known about whether psychology courses, especially ones such as research methods courses that might be expected to promote critical thinking skills, actually improve them. We compared the acquisition of critical thinking skills for analyzing psychological arguments in 3 groups of research methods students, 1 getting critical thinking skills infused directly into their course and 2 other groups getting no explicit critical thinking skills instruction. We found that the group receiving explicit critical thinking skills instruction showed significantly greater gains in their argument analysis skills than the groups receiving no explicit critical thinking instruction. These results support the effectiveness of explicitly teaching critical thinking skills infused directly into regular course instruction.
Group-Based Formative Summative Assessment Relates to Improved Student Performance and Satisfaction
Authors: Drouin Michelle A.
Published: March 2010

In this study, I examined the effectiveness of a group exam review activity on students' long-term retention of concepts and satisfaction. As part of a formative summative assessment activity (FSA; Wininger, 2005), students worked either individually or collaboratively on an exam review activity in the class periods following the 2 unit exams. Students indicated that both activities were useful and enjoyable; however, the group activity had a more positive effect on retention of concepts and student satisfaction. At the 5-week posttest, students who completed the group activity scored 10% higher (on average) than their original exam scores, whereas the students who completed the individual activity scored only 1.2% higher. I discuss these results with regard to a multidimensional FSA framework.
Changes in Critical Thinking Skills following a Course on Science and Pseudoscience: A Quasi-Experimental Study
Authors: McLean Carmen P. , Miller Nathan A.
Published: March 2010

We assessed changes in paranormal beliefs and general critical thinking skills among students (n = 23) enrolled in an experimental course designed to teach distinguishing science from pseudoscience and a comparison group of students (n = 30) in an advanced research methods course. On average, both courses were successful in reducing paranormal beliefs and increasing both abstract and psychology-specific critical thinking skills. However, the only difference that emerged between the courses was that the experimental course was superior with regard to reducing specific paranormal beliefs.
A Demonstration of Approach and Avoidance Conflicts
Authors: Terry W. Scott
Published: March 2010

Choosing between 2 unpleasant alternatives (Would you rather be less intelligent or less attractive?) is more difficult than choosing between two desirable options (Would you rather be more intelligent or more attractive?). Here I describe a classroom demonstration of avoidance–avoidance conflicts. Students make a series of approach–approach and avoidance–avoidance choices. The avoidance choices take longer to make than the approach decisions. The students also rate the avoidance choices as less satisfactory, more difficult to make, and subject to change. Avoidance conflicts are relevant to contemporary ideas of loss aversion, decision making, and negative self-evaluation.
The adaptor molecule CARD9 is essential for tuberculosis control
Authors: Dorhoi Anca , Desel Christiane , Yeremeev Vladimir , Pradl Lydia , Brinkmann Volker , Mollenkopf Hans-Joachim , Hanke Karin , Gross Olaf , Ruland Jürgen , Kaufmann Stefan H.E.
Published: March 2010

The cross talk between host and pathogen starts with recognition of bacterial signatures through pattern recognition receptors (PRRs), which mobilize downstream signaling cascades. We investigated the role of the cytosolic adaptor caspase recruitment domain family, member 9 (CARD9) in tuberculosis. This adaptor was critical for full activation of innate immunity by converging signals downstream of multiple PRRs. Card9−/− mice succumbed early after aerosol infection, with higher mycobacterial burden, pyogranulomatous pneumonia, accelerated granulocyte recruitment, and higher abundance of proinflammatory cytokines and granulocyte colony-stimulating factor (G-CSF) in serum and lung. Neutralization of G-CSF and neutrophil depletion significantly prolonged survival, indicating that an exacerbated systemic inflammatory disease triggered lethality of Card9−/− mice. CARD9 deficiency had no apparent effect on T cell responses, but a marked impact on the hematopoietic compartment. Card9−/− granulocytes failed to produce IL-10 after Mycobaterium tuberculosis infection, suggesting that an absent antiinflammatory feedback loop accounted for granulocyte-dominated pathology, uncontrolled bacterial replication, and, ultimately, death of infected Card9−/− mice. Our data provide evidence that deregulated innate responses trigger excessive lung inflammation and demonstrate a pivotal role of CARD9 signaling in autonomous innate host defense against tuberculosis.
Peripheral CD103+ dendritic cells form a unified subset developmentally related to CD8α+ conventional dendritic cells
Authors: Edelson Brian T. , KC Wumesh , Juang Richard , Kohyama Masako , Benoit Loralyn A. , Klekotka Paul A. , Moon Clara , Albring Jörn C. , Ise Wataru , Michael Drew G. , Bhattacharya Deepta , Stappenbeck Thaddeus S. , Holtzman Michael J. , Sung Sun-Sang J. , Murphy Theresa L. , Hildner Kai , Murphy Kenneth M.
Published: March 2010

Although CD103-expressing dendritic cells (DCs) are widely present in nonlymphoid tissues, the transcription factors controlling their development and their relationship to other DC subsets remain unclear. Mice lacking the transcription factor Batf3 have a defect in the development of CD8α+ conventional DCs (cDCs) within lymphoid tissues. We demonstrate that Batf3−/− mice also lack CD103+CD11b− DCs in the lung, intestine, mesenteric lymph nodes (MLNs), dermis, and skin-draining lymph nodes. Notably, Batf3−/− mice displayed reduced priming of CD8 T cells after pulmonary Sendai virus infection, with increased pulmonary inflammation. In the MLNs and intestine, Batf3 deficiency resulted in the specific lack of CD103+CD11b− DCs, with the population of CD103+CD11b+ DCs remaining intact. Batf3−/− mice showed no evidence of spontaneous gastrointestinal inflammation and had a normal contact hypersensitivity (CHS) response, despite previous suggestions that CD103+ DCs were required for immune homeostasis in the gut and CHS. The relationship between CD8α+ cDCs and nonlymphoid CD103+ DCs implied by their shared dependence on Batf3 was further supported by similar patterns of gene expression and their shared developmental dependence on the transcription factor Irf8. These data provide evidence for a developmental relationship between lymphoid organ–resident CD8α+ cDCs and nonlymphoid CD103+ DCs.
Nuclear expression of a group II intron is consistent with spliceosomal intron ancestry
Authors: Chalamcharla Venkata R. , Curcio M. Joan , Belfort Marlene
Published: March 2010

Group II introns are self-splicing RNAs found in eubacteria, archaea, and eukaryotic organelles. They are mechanistically similar to the metazoan nuclear spliceosomal introns; therefore, group II introns have been invoked as the progenitors of the eukaryotic pre-mRNA introns. However, the ability of group II introns to function outside of the bacteria-derived organelles is debatable, since they are not found in the nuclear genomes of eukaryotes. Here, we show that the Lactococcus lactis Ll.LtrB group II intron splices accurately and efficiently from different pre-mRNAs in a eukaryote, Saccharomyces cerevisiae. However, a pre-mRNA harboring a group II intron is spliced predominantly in the cytoplasm and is subject to nonsense-mediated mRNA decay (NMD), and the mature mRNA from which the group II intron is spliced is poorly translated. In contrast, a pre-mRNA bearing the Tetrahymena group I intron or the yeast spliceosomal ACT1 intron at the same location is not subject to NMD, and the mature mRNA is translated efficiently. Thus, a group II intron can splice from a nuclear transcript, but RNA instability and translation defects would have favored intron loss or evolution into protein-dependent spliceosomal introns, consistent with the bacterial group II intron ancestry hypothesis.
An epigenetic switch governing daughter cell separation in Bacillus subtilis
Authors: Chai Yunrong , Norman Thomas , Kolter Roberto , Losick Richard
Published: March 2010

Growing cells of Bacillus subtilis are a bistable mixture of individual motile cells in which genes for daughter cell separation and motility are ON, and chains of sessile cells in which these genes are OFF. How this ON/OFF switch is controlled has been mysterious. Here we report that a complex of the SinR and SlrR proteins binds to and represses genes involved in cell separation and motility. We also report that SinR and SlrR constitute a double-negative feedback loop in which SinR represses the gene for SlrR (slrR), and, by binding to (titrating) SinR, SlrR prevents SinR from repressing slrR. Thus, SlrR indirectly derepresses its own gene, creating a self-reinforcing loop. Finally, we show that, once activated, the loop remains locked in a high SlrR state in which cell separation and motility genes are OFF for extended periods of time. SinR and SlrR constitute an epigenetic switch for controlling genes involved in cell separation and motility.
Distinctions between optimal and expected support
Authors: Wheeler Ward C.
Published: March 2010

Several commonly used support measures are discussed and described as either optimal or expected support. This distinction is based on whether the indices are based on a function of optimal and non‐optimal hypotheses, or on the statistical expectation of clades.

© The Willi Hennig Society 2010.