bluuebunny/crossref_metadata_2025 huggingface dataset:
Determining optimal incubation temperature for a head-start program: the effect of incubation temperature on hatchling Burnett River snapping turtles (Elseya albagula)
Authors: Eiby Yvonne A. , Booth David T.
Published: July 2011

This study monitored natural nest temperatures and examined the effect of incubation temperature on hatchling phenotype of the freshwater turtle Elseya albagula to determine the optimal temperature for a potential head-start program. Eggs were incubated at constant temperatures (26°C, 28°C and 30°C) to determine the influence of temperature on incubation period, hatchling morphology, swimming performance and post-hatching growth rate. Hatchlings incubated at 26°C had longer plastrons than hatchlings from 30°C and swam faster, three days after hatching, than did hatchlings incubated at either 28°C or 30°C. Incubation temperature also provided a source of variation in hatchling scute patterns. Clutch of origin influenced hatchling mass and size, growth at 184 days after hatching, and the swimming performance of 3-day and 75-day post-hatch hatchlings. Constant temperatures of 26°C and 28°C produced the highest hatching success and highest-quality hatchlings and are therefore recommended for incubation of eggs in a head-start program. In the field, unshaded nests experienced greater daily fluctuations in temperature and higher temperatures overall compared with shaded nests, such that unshaded nest temperatures approached the upper thermal limit to development.
Haemorheology of the eastern grey kangaroo and the Tasmanian devil
Authors: Simmonds Michael J. , Baskurt Oguz K. , Meiselman Herbert J. , Pyne Michael , Kakanis Michael , Brenu Ekua , Keane James , Christy Rhys , Marshall-Gradisnik Sonya M.
Published: July 2011

The blood of two Australian marsupials, the eastern grey kangaroo (Macropus giganteus) and the Tasmanian devil (Sarcophilus harrisii), has been reported to have greater oxygen-carrying capacity (i.e. haemoglobin content) when compared with that of placental mammals. We investigated whether alterations of blood rheological properties are associated with the increased oxygen-carrying capacity of these marsupials. Eastern grey kangaroos (n = 6) and Tasmanian devils (n = 4) were anaesthetised for blood sampling; human blood (n = 6) was also sampled for comparison. Laboratory measurements included blood and plasma viscosity, red blood cell (RBC) deformability, RBC aggregation and the intrinsic tendency of RBC to aggregate, RBC surface charge and haematological parameters. Scanning electron micrographs of RBC from each species provided morphological information. High-shear blood viscosity at native haematocrit was highest for the Tasmanian devil. When haematocrit was adjusted to 0.4 L L–1, lower-shear blood viscosity was highest for the eastern grey kangaroo. RBC deformability was greatly reduced for the Tasmanian devil. Eastern grey kangaroo blood had the highest RBC aggregation, whereas Tasmanian devil RBC did not aggregate. The surface charge of RBC for marsupials was ~15% lower than that of humans. The dependence of oxygen-delivery effectiveness on haemoglobin concentration (i.e. oxygen content) and blood viscosity was quantitated by calculating the haematocrit to blood viscosity ratio and was 15–25% lower for marsupials compared with humans. Our results suggest that environmental pressures since the marsupial–monotreme divergence have influenced the development of vastly different strategies to maintain a match between oxygen demand and delivery.
The effect of environmental variables on the activity patterns of the southern hairy-nosed wombat (Lasiorhinus latifrons) in captivity: onset, duration and cessation of activity
Authors: Hogan Lindsay A. , Johnston Steve D. , Lisle Allan T. , Horsup Alan B. , Janssen Tina , Phillips Clive J. C.
Published: July 2011

The influence of scotoperiod, ambient temperature and humidity on the activity of captive wombats was examined to differentiate environmental influence from that pertaining to food availability. The activity of 12 wombats (Lasiorhinus latifrons) housed at Rockhampton Zoo was remotely monitored by digital video-surveillance for one year, with environmental variables simultaneously recorded via dataloggers. Mean proportion of total daily time spent active was 18.2 ± 1.8%. Mean daily time spent active varied seasonally according to changes in temperature and humidity. Mean daily activity was greater during winter (301 ± 17 min) and spring (295 ± 16 min), than summer (234 ± 16 min) and autumn (238 ± 15 min) with differences due to a decrease in the number and length of activity bouts in summer and autumn; presumably these results reflect a need to maintain heat balance associated with exposure to elevated temperatures. Activity was positively correlated with temperature during winter (r = 0.60) and spring (r = 0.52) but negatively correlated during summer (r = –0.58) and autumn (r = –0.49), suggesting the existence of a thermoneutral zone where activity is maximised. We conclude that activity in captive wombats is influenced by environmental variables.
Spatial behaviour of yellow-footed rock-wallabies, Petrogale xanthopus, changes in response to active conservation management
Authors: Hayward Matt W. , Bellchambers Keith , Herman Kerryn , Bentley Joss , Legge Sarah
Published: July 2011

Competition for food is predicted to influence faunal movement patterns as animals have to range further to satisfy their nutrient requirements. Research between 1979 and 1984 found that yellow-footed rock-wallabies, Petrogale xanthopus, in Middle Gorge, Buckaringa Sanctuary, had home ranges (134–169 ha in winter) that were much larger than predicted, which was attributed to competing livestock and cropping. We studied the ranging behaviour of this population using GPS telemetry after the cessation of farming and following several years of fox, Vulpes vulpes, and goat, Capra hircus, control to determine whether the reduction in competition and predation pressure has affected movement patterns of this endangered species. Mean winter range size of the four GPS-collared rock-wallabies was 4.3 ha (kernel or 5.5-ha MCP), which is a much smaller area than the rock-wallabies used before farming ceased and fox and goat control was implemented. The rock-wallabies primarily used the mid- to lower slopes of the gorge country and preferred redgum creeks and gorge habitats. The rock-wallabies exhibited a crepuscular activity pattern. We hypothesise that the difference in movements has arisen because the rock-wallabies are no longer competing for resources with introduced herbivores, and are able to meet their forage requirements from a smaller area.
Maternal strategies of the Australian sea lion (Neophoca cinerea) at Dangerous Reef, South Australia
Authors: Lowther Andrew D. , Goldsworthy Simon D.
Published: July 2011

Maternal strategies of otariid seals reflect the optimisation between resource exploitation and offspring provisioning driven across spatially separated foraging and nursing grounds. Intercolony variation in the expression of maternal strategies may represent temporal and spatial differences in resource availability, intraspecies competition or differences in life-history traits. The current study describes maternal strategies of the Australian sea lion at the largest breeding colony of the species (Dangerous Reef) and a comparative analysis was performed with data collected 16 years earlier at Seal Bay (Kangaroo Island). Significant differences in maternal strategies were characterised by lower milk lipid content (21.0 versus 28.9%), abbreviated periods onshore (0.93 versus 1.63 days) and slower pup growth rates (0.09–0.12 kg day–1) at Dangerous Reef. These data suggest flexibility in the expression of maternal investment between breeding sites and support the hypothesis of localised adaptation
Tantalising tongues: male carpet pythons use chemoreception to differentiate among females
Authors: Bryant G. L. , Bateman P. W. , Fleming P. A.
Published: July 2011

For animals sparsely distributed across a landscape, finding and identifying a receptive female during a short breeding period can be a challenge for males. Many snakes appear to rely on the production of sex-specific pheromones to synchronise the timing of reproductive behaviour. The rare Australian south-west carpet python (Morelia spilota imbricata) displays non-aggressive mating aggregations of up to six males around a receptive female, suggesting that males are responding to some chemical signal that enables multiple males simultaneously to identify and locate the female. We investigated chemoreceptive response (tongue-flicking) of 10 male pythons under laboratory conditions to 12 (randomly ordered) treatments each presented for three minutes. Cutaneous chemicals (dissolved in hexane solvent) were collected on cotton buds from the skin of six female pythons and male responses to these were compared with six control treatments. Male pythons produced a greater number of tongue flicks during the first minute of each trial, with fewer in minutes 2 and 3. Male chemoreceptive response in the third minute varied significantly between treatments and was only maintained for trials presenting cutaneous chemicals collected from the three relatively largest female pythons. This experiment suggests that male carpet pythons can use chemoreception to obtain information about their social environment, identifying pheromone cues from large, potentially fecund females. This ability would be adaptive for male mate-selection behaviour and is likely to also reduce costs of searching behaviour.
Oscillatory patterns in temporal lobe reveal context reinstatement during memory search
Authors: Manning Jeremy R. , Polyn Sean M. , Baltuch Gordon H. , Litt Brian , Kahana Michael J.
Published: July 2011

Psychological theories of memory posit that when people recall a past event, they not only recover the features of the event itself, but also recover information associated with other events that occurred nearby in time. The events surrounding a target event, and the thoughts they evoke, may be considered to represent a context for the target event, helping to distinguish that event from similar events experienced at different times. The ability to reinstate this contextual information during memory search has been considered a hallmark of episodic, or event-based, memory. We sought to determine whether context reinstatement may be observed in electrical signals recorded from the human brain during episodic recall. Analyzing electrocorticographic recordings taken as 69 neurosurgical patients studied and recalled lists of words, we uncovered a neural signature of context reinstatement. Upon recalling a studied item, we found that the recorded patterns of brain activity were not only similar to the patterns observed when the item was studied, but were also similar to the patterns observed during study of neighboring list items, with similarity decreasing reliably with positional distance. The degree to which individual patients displayed this neural signature of context reinstatement was correlated with their tendency to recall neighboring list items successively. These effects were particularly strong in temporal lobe recordings. Our findings show that recalling a past event evokes a neural signature of the temporal context in which the event occurred, thus pointing to a neural basis for episodic memory.
Structural basis for RNA 3′-end recognition by Hfq
Authors: Sauer Evelyn , Weichenrieder Oliver
Published: July 2011

The homohexameric (L)Sm protein Hfq is a central mediator of small RNA-based gene regulation in bacteria. Hfq recognizes small regulatory RNAs (sRNAs) specifically, despite their structural diversity. This specificity could not be explained by previously described RNA-binding modes of Hfq. Here we present a distinct and preferred mode of Hfq–RNA interaction that involves the direct recognition of a uridine-rich RNA 3′ end. This feature is common in bacterial RNA transcripts as a consequence of Rho-independent transcription termination and hence likely contributes significantly to the general recognition of sRNAs by Hfq. Isothermal titration calorimetry shows nanomolar affinity between
Salmonella typhimurium
Hfq and a hexauridine substrate. We determined a crystal structure of the complex that reveals a constricted RNA backbone conformation in the proximal RNA-binding site of Hfq, allowing for a direct protein contact of the 3′ hydroxyl group. A free 3′ hydroxyl group is crucial for the high-affinity interaction with Hfq also in the context of a full-length sRNA substrate, RybB. The capacity of Hfq to occupy and sequester the RNA 3′ end has important implications for the mechanisms by which Hfq is thought to affect sRNA stability, turnover, and regulation.
Single-shot observation of growing streamers using an ultrafast camera
Authors: Takahashi E , Kato S , Furutani H , Sasaki A , Kishimoto Y , Takada K , Matsumura S , Sasaki H
Published: July 2011

A recently developed ultrafast camera that can acquire 108 frames per second was used to investigate positive streamer discharge. It enabled single-shot evaluation of streamer evolution without the need to consider shot-to-shot reproducibility. This camera was used to investigate streamers in argon. Growing branches, the transition when a streamer forms a return stroke, and related phenomena were clearly observed.
Magnetic nanostructures for advanced technologies: fabrication, metrology and challenges
Authors: Lau June W , Shaw Justin M
Published: July 2011

Magnetic nanostructures are an integral part to many state-of-the-art and emerging technologies. However, the complete path from parts (the nanostructures) to the manufacturing of the end products is not always obvious to students of magnetism. The paper follows this path of the magnetic nanostructure, and explains some of the steps along the way: What are the technologies that employ magnetic nanostructures? How are these nanostructures made? What is the physics behind the functional parts? How are the magnetic properties measured? Finally, we present, in our view, a list of challenges hindering progress in these technologies.
Electric field induced changes in the coercivity of a thin-film ferromagnet
Authors: Fowley C , Rode K , Oguz K , Kurt H , Coey J M D
Published: July 2011

Data are presented which indicate a modification of magnetic anisotropy in the MgO/CoFeB/Pd and MgO/CoFeB/Pt systems, using electric fields of order 500 MV m−1 (0.5 V nm−1) applied across a thermally grown SiO2 as a gate dielectric. The effect is most prominent at low temperature (12 K) and is manifested as a small change in coercivity. The sign of the effect depends on the choice of both capping layer and annealing temperature. The results suggest that both interfaces play a role in the appearance of perpendicular magnetic anisotropy in these thin-film stacks, and not just the interface with MgO.
Direct generation of core/shell nanoparticles from double-pulse laser ablation in a background gas
Authors: Jo Young Kyong , Wen Sy-Bor
Published: July 2011

In this study, a double-pulse laser ablation scheme is proposed to generate core/shell nanoparticles (CS-NPs). Compared with other existing methods for the generation of CS-NPs, the new scheme figures with its simple and in situ approach and can be applied to a wider variety of materials. Several types of CS-NPs are successfully generated with this new scheme (i.e. Sn/glass, Zn/glass, Zn/Si, Ge/Si, Cu/Zn CS-NPs). Four key factors affecting the generation of CS-NPs with this new scheme are also examined, namely (a) surface tensions of materials constructing the CS-NPs and its Gibbs free energy, (b) contribution of background gases (He and Ar), (c) contribution of the delay time between two lasers pulses and (d) contribution of laser energy on the formation of CS-NPs.
Development of gamma-ray diagnostics for ITER
Authors: Chugunov I.N. , Shevelev A.E. , Gin D.B. , Kiptily V.G. , Gorini G. , Nocente M. , Tardocchi M. , Doinikov D.N. , Naidenov V.O. , Khilkevitch E.M.
Published: July 2011

Gamma-ray spectrometry is a diagnostic tool for fast ions in large tokamak plasmas. The information provided allows us to identify and simultaneously distinguish the presence of fast α-particles and other ions (H, D, T, 3He) to obtain information on their energy distribution and relative densities, in addition to performing a tomographic radial profile reconstruction of the γ-emission sources. The lack of vertical diagnostic ports in ITER makes the implementation of tomographic neutron and γ-ray systems more complicated. The use of a vertical divertor port for the implementation of a vertical viewpoint is currently suggested. The strong magnetic field (∼2 T) found there makes it hard to use conventional multi-dynode photomultipliers as light detectors. Instead, the use of micro-channel plate photomultipliers is suggested here. Investigations of the magnetic field impact on the performance of the γ-spectrometer with a micro-channel photomultiplier are carried out. A high-speed pulse height analysis technique, which allows us to trace gain changes in the photomultiplier tube, is developed at the Ioffe Institute. The tests demonstrate the feasibility of γ-spectrometric measurements in the divertor port provided that micro-channel photomultiplier detectors and the developed high-speed technique are used.
Low cycle fatigue properties of reduced activation ferritic/martensitic steels after high-dose neutron irradiation
Authors: Gaganidze E. , Petersen C. , Aktaa J. , Povstyanko A. , Prokhorov V. , Diegele E. , Lässer R.
Published: July 2011

This paper focuses on the low cycle fatigue (LCF) behaviour of reduced activation ferritic/martensitic steels irradiated to a displacement damage dose of up to 70 dpa at 330–337 °C in the BOR 60 reactor within the ARBOR 2 irradiation programme. The influence of neutron irradiation on the fatigue behaviour was determined for the as-received EUROFER97, pre-irradiation heat-treated EUROFER97 HT and F82H-mod steels. Strain-controlled push–pull loading was performed using miniaturized cylindrical specimens at a constant temperature of 330 °C with total strain ranges between 0.8% and 1.1%. Comparison of the LCF behaviour of irradiated and reference unirradiated specimens was performed for both the adequate total and inelastic strains. Neutron irradiation-induced hardening may have various effects on the fatigue behaviour of the steels. The reduction of inelastic strain in the irradiated state compared with the reference unirradiated state at common total strain amplitudes may increase fatigue lifetime. The increase in the stress at the adequate inelastic strain, by contrast, may accelerate fatigue damage accumulation. Depending on which of the two effects mentioned dominates, neutron irradiation may either extend or reduce the fatigue lifetime compared with the reference unirradiated state. The results obtained for EUROFER97 and EUROFER97 HT confirm these considerations. Most of the irradiated specimens show fatigue lifetimes comparable to those of the reference unirradiated state at adequate inelastic strains. Some irradiated specimens, however, show lifetime reduction or increase in comparison with the reference state at adequate inelastic strains.
Quantum dynamics of quantum bits
Authors: Nguyen Bich Ha
Published: July 2011

The theory of coherent oscillations of the matrix elements of the density matrix of the two-state system as a quantum bit is presented. Different calculation methods are elaborated in the case of a free quantum bit. Then the most appropriate methods are applied to the study of the density matrices of the quantum bits interacting with a classical pumping radiation field as well as with the quantum electromagnetic field in a single-mode microcavity. The theory of decoherence of a quantum bit in Markovian approximation is presented. The decoherence of a quantum bit interacting with monoenergetic photons in a microcavity is also discussed. The content of the present work can be considered as an introduction to the study of the quantum dynamics of quantum bits.
Low temperature growth and properties of ZnO nanorod arrays
Authors: Wu Xiang , Chen Huibo , Gong Lihong , Qu Fengyu , Zheng Yufeng
Published: July 2011

In this paper, well aligned ZnO nanorod arrays were synthesized by a simple hydrothermal route at a low temperature. The diameters of the as-synthesized products were 20–60 nm and the lengths were as much as several micrometers. The surfaces and tops of the nanorods were smooth. The as-grown nanorod arrays were investigated by x-ray powder diffraction (XRD), scanning electron microscope (SEM), transmission electron microscope (TEM), photoluminescence (PL) spectroscopy and contact angle (CA) analysis. The as-grown nanorods were single crystalline structures with a wurtzite phase, and grew along the [0001] direction. The PL spectrum with only one strong peak at 383 nm shows good intrinsic emission.
Single-walled carbon nanotubes synthesized by chemical vapor deposition of C2H2 over an Al2O3 supported mixture of Fe, Mo, Co catalysts
Authors: Cao Thi Thanh , Ngo Thi Thanh Tam , Nguyen Van Chuc , Than Xuan Tinh , Nguyen Ba Thang , Phan Ngoc Minh
Published: July 2011

Single-walled carbon nanotubes (SWCNTs) have been successfully synthesized by chemical vapor deposition (CVD) using acetylene (C2H2) gas as a carbon source and a mixture of Fe/Mo/Co on an Al
2
O
3 support as a catalyst. The effects of the weight percentage (wt%) of metals in the Fe/Mo/Co/Al
2
O
3 catalysts, growth time, gas flow rate and growth temperature on SWCNT growth were studied in detail. The optimum growth conditions were found to be a growth time of 60 min, a growth temperature of 750 °C, Ar/H
2/C
2
H
2 flow rates of 420/100/14 sccm and a catalyst composition of Fe/Mo/Co/Al
2
O
3=5/3/1/80 (wt%). The morphologies and structures of the grown SWCNTs were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Raman spectroscopy techniques.
Ankrd2/ARPP is a novel Akt2 specific substrate and regulates myogenic differentiation upon cellular exposure to H2O2
Authors: Cenni Vittoria , Bavelloni Alberto , Beretti Francesca , Tagliavini Francesca , Manzoli Lucia , Lattanzi Giovanna , Maraldi Nadir M. , Cocco Lucio , Marmiroli Sandra
Published: July 2011

Activation of Akt-mediated signaling pathways is crucial for survival, differentiation, and regeneration of muscle cells. A proteomic-based search for novel substrates of Akt was therefore undertaken in C2C12 murine muscle cells exploiting protein characterization databases in combination with an anti–phospho-Akt substrate antibody. A Scansite database search predicted Ankrd2 (Ankyrin repeat domain protein 2, also known as ARPP) as a novel substrate of Akt. In vitro and in vivo studies confirmed that Akt phosphorylates Ankrd2 at Ser-99. Moreover, by kinase assay with recombinant Akt1 and Akt2, as well as by single-isoform silencing, we demonstrated that Ankrd2 is a specific substrate of Akt2. Ankrd2 is typically found in skeletal muscle cells, where it mediates the transcriptional response to stress conditions. In an attempt to investigate the physiological implications of Ankrd2 phosphorylation by Akt2, we found that oxidative stress induced by H2O2 triggers this phosphorylation. Moreover, the forced expression of a phosphorylation-defective mutant form of Ankrd2 in C2C12 myoblasts promoted a faster differentiation program, implicating Akt-dependent phosphorylation at Ser-99 in the negative regulation of myogenesis in response to stress conditions.
Insights into EB1 structure and the role of its C-terminal domain for discriminating microtubule tips from the lattice
Authors: Buey Rubén M. , Mohan Renu , Leslie Kris , Walzthoeni Thomas , Missimer John H. , Menzel Andreas , Bjelić Saša , Bargsten Katja , Grigoriev Ilya , Smal Ihor , Meijering Erik , Aebersold Ruedi , Akhmanova Anna , Steinmetz Michel O.
Published: July 2011

End-binding proteins (EBs) comprise a conserved family of microtubule plus end–tracking proteins. The concerted action of calponin homology (CH), linker, and C-terminal domains of EBs is important for their autonomous microtubule tip tracking, regulation of microtubule dynamics, and recruitment of numerous partners to microtubule ends. Here we report the detailed structural and biochemical analysis of mammalian EBs. Small-angle X-ray scattering, electron microscopy, and chemical cross-linking in combination with mass spectrometry indicate that EBs are elongated molecules with two interacting CH domains, an arrangement reminiscent of that seen in other microtubule- and actin-binding proteins. Removal of the negatively charged C-terminal tail did not affect the overall conformation of EBs; however, it increased the dwell times of EBs on the microtubule lattice in microtubule tip–tracking reconstitution experiments. An even more stable association with the microtubule lattice was observed when the entire negatively charged C-terminal domain of EBs was replaced by a neutral coiled-coil motif. In contrast, the interaction of EBs with growing microtubule tips was not significantly affected by these C-terminal domain mutations. Our data indicate that long-range electrostatic repulsive interactions between the C-terminus and the microtubule lattice drive the specificity of EBs for growing microtubule ends.
Regulation of cyclin-dependent kinase 4 translation through CUG-binding protein 1 and microRNA-222 by polyamines
Authors: Xiao Lan , Cui Yu-Hong , Rao Jaladanki N. , Zou Tongtong , Liu Lan , Smith Alexis , Turner Douglas J. , Gorospe Myriam , Wang Jian-Ying
Published: July 2011

The amino acid–derived polyamines are organic cations that are essential for growth in all mammalian cells, but their exact roles at the molecular level remain largely unknown. Here we provide evidence that polyamines promote the translation of cyclin-dependent kinase 4 (CDK4) by the action of CUG-binding protein 1 (CUGBP1) and microRNA-222 (miR-222) in intestinal epithelial cells. Both CUGBP1 and miR-222 were found to bind the CDK4 mRNA coding region and 3′-untranslated region and repressed CDK4 translation synergistically. Depletion of cellular polyamines increased cytoplasmic CUGBP1 abundance and miR-222 levels, induced their associations with the CDK4 mRNA, and inhibited CDK4 translation, whereas increasing the levels of cellular polyamines decreased CDK4 mRNA interaction with CUGBP1 and miR-222, in turn inducing CDK4 expression. Polyamine-deficient cells exhibited an increased colocalization of tagged CDK4 mRNA with processing bodies; this colocalization was abolished by silencing CUGBP1 and miR-222. Together, our findings indicate that polyamine-regulated CUGBP1 and miR-222 modulate CDK4 translation at least in part by altering the recruitment of CDK4 mRNA to processing bodies.
Translocation channel gating kinetics balances protein translocation efficiency with signal sequence recognition fidelity
Authors: Trueman Steven F. , Mandon Elisabet C. , Gilmore Reid
Published: July 2011

The transition between the closed and open conformations of the Sec61 complex permits nascent protein insertion into the translocation channel. A critical event in this structural transition is the opening of the lateral translocon gate that is formed by four transmembrane (TM) spans (TM2, TM3, TM7, and TM8 in Sec61p) to expose the signal sequence–binding site. To gain mechanistic insight into lateral gate opening, mutations were introduced into a lumenal loop (L7) that connects TM7 and TM8. The sec61 L7 mutants were found to have defects in both the posttranslational and cotranslational translocation pathways due to a kinetic delay in channel gating. The translocation defect caused by L7 mutations could be suppressed by the prl class of sec61 alleles, which reduce the fidelity of signal sequence recognition. The prl mutants are proposed to act by destabilizing the closed conformation of the translocation channel. Our results indicate that the equilibrium between the open and closed conformations of the protein translocation channel maintains a balance between translocation activity and signal sequence recognition fidelity.
Microtubule assembly in meiotic extract requires glycogen
Authors: Groen Aaron C. , Coughlin Margaret , Mitchison Timothy J.
Published: July 2011

The assembly of microtubules during mitosis requires many identified components, such as γ-tubulin ring complex (γ-TuRC), components of the Ran pathway (e.g., TPX2, HuRP, and Rae1), and XMAP215/chTOG. However, it is far from clear how these factors function together or whether more factors exist. In this study, we used biochemistry to attempt to identify active microtubule nucleation protein complexes from Xenopus meiotic egg extracts. Unexpectedly, we found both microtubule assembly and bipolar spindle assembly required glycogen, which acted both as a crowding agent and as metabolic source glucose. By also reconstituting microtubule assembly in clarified extracts, we showed microtubule assembly does not require ribosomes, mitochondria, or membranes. Our clarified extracts will provide a powerful tool for activity-based biochemical fractionations for microtubule assembly.
The RNA-binding protein ELAVL1/HuR is essential for mouse spermatogenesis, acting both at meiotic and postmeiotic stages
Authors: Chi Mai Nguyen , Auriol Jacques , Jégou Bernard , Kontoyiannis Dimitris L. , Turner James M.A. , de Rooij Dirk G. , Morello Dominique
Published: July 2011

Posttranscriptional mechanisms are crucial to regulate spermatogenesis. Accurate protein synthesis during germ cell development relies on RNA binding proteins that control the storage, stability, and translation of mRNAs in a tightly and temporally regulated manner. Here, we focused on the RNA binding protein Embryonic Lethal Abnormal Vision (ELAV) L1/Human antigen R (HuR) known to be a key regulator of posttranscriptional regulation in somatic cells but the function of which during gametogenesis has never been investigated. In this study, we have used conditional loss- and gain-of-function approaches to address this issue in mice. We show that targeted deletion of HuR specifically in germ cells leads to male but not female sterility. Mutant males are azoospermic because of the extensive death of spermatocytes at meiotic divisions and failure of spermatid elongation. The latter defect is also observed upon HuR overexpression. To elucidate further the molecular mechanisms underlying spermatogenesis defects in HuR-deleted and -overexpressing testes, we undertook a target gene approach and discovered that heat shock protein (HSP)A2/HSP70-2, a crucial regulator of spermatogenesis, was down-regulated in both situations. HuR specifically binds hspa2 mRNA and controls its expression at the translational level in germ cells. Our study provides the first genetic evidence of HuR involvement during spermatogenesis and reveals Hspa2 as a target for HuR.
The reconstructed ancestral subunit a functions as both V-ATPase isoforms Vph1p and Stv1p inSaccharomyces cerevisiae
Authors: Finnigan Gregory C. , Hanson-Smith Victor , Houser Benjamin D. , Park Hae J. , Stevens Tom H.
Published: July 2011

The vacuolar-type, proton-translocating ATPase (V-ATPase) is a multisubunit enzyme responsible for organelle acidification in eukaryotic cells. Many organisms have evolved V-ATPase subunit isoforms that allow for increased specialization of this critical enzyme. Differential targeting of the V-ATPase to specific subcellular organelles occurs in eukaryotes from humans to budding yeast. In Saccharomyces cerevisiae, the two subunit a isoforms are the only difference between the two V-ATPase populations. Incorporation of Vph1p or Stv1p into the V-ATPase dictates the localization of the V-ATPase to the vacuole or late Golgi/endosome, respectively. A duplication event within fungi gave rise to two subunit a genes. We used ancestral gene reconstruction to generate the most recent common ancestor of Vph1p and Stv1p (Anc.a) and tested its function in yeast. Anc.a localized to both the Golgi/endosomal network and vacuolar membrane and acidified these compartments as part of a hybrid V-ATPase complex. Trafficking of Anc.a did not require retrograde transport from the late endosome to the Golgi that has evolved for retrieval of the Stv1p isoform. Rather, Anc.a localized to both structures through slowed anterograde transport en route to the vacuole. Our results suggest an evolutionary model that describes the differential localization of the two yeast V-ATPase isoforms.
Deciphering the rules governing assembly order of mammalian septin complexes
Authors: Sellin Mikael E. , Sandblad Linda , Stenmark Sonja , Gullberg Martin
Published: July 2011

Septins are conserved GTP-binding proteins that assemble into lateral diffusion barriers and molecular scaffolds. Vertebrate genomes contain 9–17 septin genes that encode both ubiquitous and tissue-specific septins. Expressed septins may assemble in various combinations through both heterotypic and homotypic G-domain interactions. However, little is known regarding assembly states of mammalian septins and mechanisms directing ordered assembly of individual septins into heteromeric units, which is the focus of this study. Our analysis of the septin system in cells lacking or overexpressing selected septins reveals interdependencies coinciding with previously described homology subgroups. Hydrodynamic and single-particle data show that individual septins exist solely in the context of stable six- to eight-subunit core heteromers, all of which contain SEPT2 and SEPT6 subgroup members and SEPT7, while heteromers comprising more than six subunits also contain SEPT9. The combined data suggest a generic model for how the temporal order of septin assembly is homology subgroup-directed, which in turn determines the subunit arrangement of native heteromers. Because mammalian cells normally express multiple members and/or isoforms of some septin subgroups, our data also suggest that only a minor fraction of native heteromers are arranged as perfect palindromes.
Mi-2/NuRD complex function is required for normal S phase progression and assembly of pericentric heterochromatin
Authors: Sims Jennifer K. , Wade Paul A.
Published: July 2011

During chromosome duplication, it is essential to replicate not only the DNA sequence, but also the complex nucleoprotein structures of chromatin. Pericentric heterochromatin is critical for silencing repetitive elements and plays an essential structural role during mitosis. However, relatively little is understood about its assembly and maintenance during replication. The Mi2/NuRD chromatin remodeling complex tightly associates with actively replicating pericentric heterochromatin, suggesting a role in its assembly. Here we demonstrate that depletion of the catalytic ATPase subunit CHD4/Mi-2β in cells with a dampened DNA damage response results in a slow-growth phenotype characterized by delayed progression through S phase. Furthermore, we observe defects in pericentric heterochromatin maintenance and assembly. Our data suggest that chromatin assembly defects are sensed by an ATM-dependent intra–S phase chromatin quality checkpoint, resulting in a temporal block to the transition from early to late S phase. These findings implicate Mi-2β in the maintenance of chromatin structure and proper cell cycle progression.
Mannose-6-phosphate regulates destruction of lipid-linked oligosaccharides
Authors: Gao Ningguo , Shang Jie , Huynh Dang , Manthati Vijaya L. , Arias Carolina , Harding Heather P. , Kaufman Randal J. , Mohr Ian , Ron David , Falck John R. , Lehrman Mark A.
Published: July 2011

Mannose-6-phosphate (M6P) is an essential precursor for mannosyl glycoconjugates, including lipid-linked oligosaccharides (LLO; glucose3mannose9GlcNAc2-P-P-dolichol) used for protein N-glycosylation. In permeabilized mammalian cells, M6P also causes specific LLO cleavage. However, the context and purpose of this paradoxical reaction are unknown. In this study, we used intact mouse embryonic fibroblasts to show that endoplasmic reticulum (ER) stress elevates M6P concentrations, leading to cleavage of the LLO pyrophosphate linkage with recovery of its lipid and lumenal glycan components. We demonstrate that this M6P originates from glycogen, with glycogenolysis activated by the kinase domain of the stress sensor IRE1-α. The apparent futility of M6P causing destruction of its LLO product was resolved by experiments with another stress sensor, PKR-like ER kinase (PERK), which attenuates translation. PERK's reduction of N-glycoprotein synthesis (which consumes LLOs) stabilized steady-state LLO levels despite continuous LLO destruction. However, infection with herpes simplex virus 1, an N-glycoprotein-bearing pathogen that impairs PERK signaling, not only caused LLO destruction but depleted LLO levels as well. In conclusion, the common metabolite M6P is also part of a novel mammalian stress-signaling pathway, responding to viral stress by depleting host LLOs required for N-glycosylation of virus-associated polypeptides. Apparently conserved throughout evolution, LLO destruction may be a response to a variety of environmental stresses.
Anillin promotes astral microtubule-directed cortical myosin polarization
Authors: Tse Yu Chung , Piekny Alisa , Glotzer Michael
Published: July 2011

Assembly of a cytokinetic contractile ring is a form of cell polarization in which the equatorial cell cortex becomes differentiated from the polar regions. Microtubules direct cytokinetic polarization via the central spindle and astral microtubules. The mechanism of central spindle–directed furrow formation is reasonably well understood, but the aster-directed pathway is not. In aster-directed furrowing, cytoskeletal factors accumulate to high levels at sites distal to the asters and at reduced levels at cortical sites near the asters. In this paper, we demonstrate that the cytoskeletal organizing protein anillin (ANI-1) promotes the formation of an aster-directed furrow in Caenorhabditis elegans embryos. Microtubule-directed nonmuscle myosin II polarization is aberrant in embryos depleted of ANI-1. In contrast, microtubule-directed polarized ANI-1 localization is largely unaffected by myosin II depletion. Consistent with a role in the induction of cortical asymmetry, ANI-1 also contributes to the polarization of arrested oocytes. Anillin has an evolutionarily conserved capacity to associate with microtubules, possibly providing an inhibitory mechanism to promote polarization of the cell cortex.
An evolutionarily conserved Rit GTPase–p38 MAPK signaling pathway mediates oxidative stress resistance
Authors: Cai Weikang , Rudolph Jennifer L. , Harrison Susan M. W. , Jin Ling , Frantz Aubrey L. , Harrison Douglas A. , Andres Douglas A.
Published: July 2011

Ras-related small GTP-binding proteins control a wide range of cellular processes by regulating a variety of effector pathways, including prominent roles in the control of mitogen-activated protein kinase (MAPK) cascades. Although the regulatory role(s) for many Ras family GTPases are well established, the physiological function for the Rit/Rin subfamily has been lacking. Here, using both knockout mice and Drosophila models, we demonstrate an evolutionarily conserved role for Rit subfamily GTPases (mammalian Rit and Rin, and the Drosophila RIC homologue) in governing survival in response to oxidative stress. Primary embryonic fibroblasts derived from Rit knockout mice display increased apoptosis and selective disruption of MAPK signaling following reactive oxygen species (ROS) exposure but not in response to endoplasmic reticulum stress or DNA damage. These deficits include a reduction in ROS-mediated stimulation of a p38-MK2-HSP27 signaling cascade that controls Akt activation, directing Bad phosphorylation to promote cell survival. Furthermore, D-RIC null flies display increased susceptibility to environmental stresses and reduced stress-dependent p38 signaling, extending the Rit-p38 survival pathway to Drosophila. Together, our studies establish the Rit GTPases as critical regulators of an evolutionarily conserved, p38 MAPK–dependent signaling cascade that functions as an important survival mechanism for cells in response to oxidative stress.
spacodiR: structuring of phylogenetic diversity in ecological communities
Authors: Eastman Jonathan M. , Paine C. E. Timothy , Hardy Olivier J.
Published: July 2011

Motivation:  spacodiR is a cross-platform package, written for the R environment, for studying partitioning of diversity among natural communities in space and time. Complementing and extending existing software, spacodiR allows for hypothesis testing and parameter estimation in studying spatial structuring of species-, phylogenetic- and trait diversities.

Availability: Integrated with other software in the R environment and with well documented and demonstrated functions, spacodiR is an open-source package and available at http://cran.r-project.org.

Contact:  jonathan.eastman@gmail.com; ohardy@ulb.ac.be
Altered protein secretion of Chlamydia trachomatis in persistently infected human endocervical epithelial cells
Authors: Wang Jin , Frohlich Kyla M. , Buckner Lyndsey , Quayle Alison J. , Luo Miao , Feng Xiaogeng , Beatty Wandy , Hua Ziyu , Rao Xiancai , Lewis Maria E. , Sorrells Kelly , Santiago Kerri , Zhong Guangming , Shen Li
Published: July 2011

Chlamydia
trachomatis is the most common bacterial infection of the human reproductive tract globally; however, the mechanisms underlying the adaptation of the organism to its natural target cells, human endocervical epithelial cells, are not clearly understood. To secure its intracellular niche, C. trachomatis must modulate the host cellular machinery by secreting virulence factors into the host cytosol to facilitate bacterial growth and survival. Here we used primary human endocervical epithelial cells and HeLa cells infected with C. trachomatis to examine the secretion of bacterial proteins during productive growth and persistent growth induced by ampicillin. Specifically, we observed a decrease in secretable chlamydial protease-like activity factor (CPAF) in the cytosol of host epithelial cells exposed to ampicillin with no evident reduction of CPAF product by C. trachomatis. In contrast, the expression of CopN and Tarp was downregulated, suggesting that C. trachomatis responds to ampicillin exposure by selectively altering the expression of secretable proteins. In addition, we observed a greater accumulation of outer-membrane vesicles from C. trachomatis in persistently infected cells. Taken together, these results suggest that the regulation of both gene expression and the secretion of chlamydial virulence proteins is involved in the adaptation of the bacteria to a persistent infection state in human genital epithelial cells.
An optimized in vitro blood–brain barrier model reveals bidirectional transmigration of African trypanosome strains
Authors: Untucht Christopher , Rasch Janine , Fuchs Elena , Rohde Manfred , Bergmann Simone , Steinert Michael
Published: July 2011

The transmigration of African trypanosomes across the human blood–brain barrier (BBB) is the critical step during the course of human African trypanosomiasis. The parasitesTrypanosoma brucei gambienseandT. b. rhodesienseare transmitted to humans during the bite of tsetse flies. Trypanosomes multiply within the bloodstream and finally invade the central nervous system (CNS), which leads to the death of untreated patients. This project focused on the mechanisms of trypanosomal traversal across the BBB. In order to establish a suitablein vitroBBB model for parasite transmigration, different human cell lines were used, including ECV304, HBMEC and HUVEC, as well as C6 rat astrocytes. Validation of the BBB models withEscherichia coliHB101 andE. coliK1 revealed that a combination of ECV304 cells seeded on Matrigel as a semi-synthetic basement membrane and C6 astrocytes resulted in an optimal BBB model system. The BBB model showed selective permeability for the pathogenicE. coliK1 strain, and African trypanosomes were able to traverse the optimized ECV304–C6 BBB efficiently. Furthermore, coincubation indicated that paracellular macrophage transmigration does not facilitate trypanosomal BBB traversal. An inverse assembly of the BBB model demonstrated that trypanosomes were also able to transmigrate the optimized ECV304–C6 BBB backwards, indicating the relevance of the CNS as a possible reservoir of a relapsing parasitaemia.
Fallacies and false premises—a critical assessment of the arguments for the recognition of paraphyletic taxa in botany
Authors: Schmidt‐Lebuhn Alexander N.
Published: July 2011

One of the central controversies in contemporary taxonomy and systematics revolves around whether to accept or to reject paraphyletic taxa. The present review is the result of a survey of the ongoing discussion in botany over the past ca. 15 years, and attempts to systematically and critically assess all individual arguments presented for the formal recognition of paraphyletic groups in the classification of life. Where arguments are found to be without merit, rebuttals are presented in the hope of excluding them from further discussion, which can then concentrate on those that have merit. Where arguments are found to be sound, their implications and possible solutions are discussed. The controversy around paraphyletic taxa can be broken down into three questions: whether their rejection or acceptance would lead to a classification better reflecting patterns of biological diversity and evolutionary history; whether their rejection or acceptance would lead to a more practical, useful and predictive classification; and whether their rejection is compatible with ranked and binary Linnaean taxonomy. All available arguments for paraphyletic taxa relating to the first question are demonstrated to be based on various logical fallacies or false premises, especially misunderstandings of the principles of phylogenetic systematics. The issue of usefulness is harder to resolve, as different classifications serve different needs. It is presumably unavoidable but also preferable that phylogenetic and non‐phylogenetic ways of classifying species continue to coexist, serving different needs. Finally, an insistence on monophyletic taxa is found to be incompatible with binary taxonomy under a set of very specific circumstances and assumptions whose presence and accuracy are not universally accepted.

© The Willi Hennig Society 2011.