bluuebunny/crossref_metadata_2025 huggingface dataset:
Piglet performance and immunity is determined by the parity of both the birth dam and the rearing dam
Authors: Miller Y. J. , Collins A. M. , Emery D. , Begg D. J. , Smits R. J. , Holyoake P. K.
Published: October 2012

Gilt progeny have lower weaning weights and higher post-weaning medication and mortality rates, indicating greater disease susceptibility, than do sow progeny. The present study aimed to identify explanatory innate or adaptive immunity differences between gilt and sow progeny and potential pre- or post-natal influences. Sixty-four dams were vaccinated twice pre-farrowing with tetanus toxoid (TT). Serum (pre-vaccination) and colostrum and/or milk samples were collected to determine concentrations of TT-specific immunoglobulin G (IgG), by using an enzyme-linked immunosorbent assay (ELISA). Piglets were removed from their birth dam before suckling and fostered (not to their birth dam) to form 16 gilt and 16 sow litters, with five gilt-born and five sow-born piglets per litter. Piglets were vaccinated at weaning (4 weeks old) with either TT or saline (control). Sera and whole blood were collected from three gilt-born and three sow-born piglets per litter at 2, 4 and 7 weeks of age. Innate immunity was assessed indirectly on whole blood using an interferon gamma (IFN-γ) immune cell stimulation assay and a phagocytic assay. Piglets were weighed at birth, 4, 10, 17 and 22 weeks of age. There was no difference (P > 0.05) in the concentration of TT-specific IgG in colostrum and milk from gilts and older-parity sows, suggesting a similar ability to transfer IgG antibodies to a novel antigen. Birth dam parity did not affect piglets’ TT-specific IgG concentrations pre-weaning (P > 0.05) suggesting similar ability to absorb passively acquired IgG. Sow-reared piglets, however, had lower (P < 0.05) concentrations of TT-specific IgG than did gilt-reared piglets, possibly due to haemodilution in the faster-growing sow progeny. Gilt-born progeny had a reduced IgG response post-weaning to TT vaccination relative to sow-born progeny (P < 0.05), indicating adaptive immunity differences. Birth dam parity did not affect (P > 0.05) innate immunity (number/responsiveness of cells). Rearing dam parity influenced phagocytic activity pre- and post-weaning (gilt-reared > sow-reared; P < 0.05), possibly due to increased pathogen challenge. Birthweight was affected by birth dam parity (sow-born > gilt-born; P < 0.05) while rearing dam parity determined weaning weight (sow-reared > gilt-reared; P < 0.05), with no difference evident at 22 weeks. The results of the present study suggest that gilt-born progeny may be more susceptible to disease post-weaning than sow-born progeny due to their lower birthweight and reduced humoral immune responsiveness. The rearing dam may also affect disease susceptibility in progeny due to slower pre-weaning growth, lower weaning weights and increased pathogen challenge, both pre- and post-weaning.
CuII Complexes of Isomeric Ligands Derived from 2-Pyridine-carboxaldehyde and m- or p-Xylylenediamine: An Intermolecularly ?-Stacked Dinuclear Species and a Trinuclear Circular Helicate that Encapsulates a Chloride Ion
Authors: Lee Young Hoon , Woo Arim , Won Mi Seon , Cho Jeong Hwan , Clegg Jack K. , Hayami Shinya , Thuéry Pierre , Lindoy Leonard F. , Kim Yang
Published: October 2012

Di- and trinuclear CuII complexes [Cu2L1(2,2′-bipyridine)2Cl2]Cl2·11H2O and [Cu3(L2)3Cl3]Cl3·1.25MeOH·4H2O incorporating the isomeric Schiff base ligands 1,1′-(1,4-phenylene)bis(N-(pyridin-2-ylmethylene)methanamine) (L1) and 1,1′-(1,4-phenylene)bis(N-(pyridin-2-ylmethylene)methanamine) (L2), each incorporating two separated α-diimine coordination domains, have been synthesised and their X-ray crystal structures and variable temperature magnetic properties determined. The X-ray crystal structure of [Cu2L1(2,2′-bipyridine)2Cl2]Cl2·11H2O shows that each CuII centre is bound to two nitrogen atoms from L1, two from a bipyridine ligand, and a chloride anion. Intramolecular π-stacking interactions are present between the central phenyl ring of L1 and both rings of each bipyridine ligand. The structure of [Cu3(L2)3Cl3]Cl3·1.25MeOH·4H2O shows an unusual trinuclear circular helicate arrangement with approximate C3-symmetry. A chloride anion is encapsulated in the structure being bound by six non-classical hydrogen bond interactions. Variable temperature magnetic susceptibility measurements indicated the presence of weak antiferromagnetic behaviour for [Cu2L1(2,2′-bipyridine)2Cl2]Cl2·11H2O and weak ferromagnetic behaviour for [Cu3(L2)3Cl3]Cl3·1.25MeOH·4H2O.
GROWSCREEN-Rhizo is a novel phenotyping robot enabling simultaneous measurements of root and shoot growth for plants grown in soil-filled rhizotrons
Authors: Nagel Kerstin A. , Putz Alexander , Gilmer Frank , Heinz Kathrin , Fischbach Andreas , Pfeifer Johannes , Faget Marc , Blossfeld Stephan , Ernst Michaela , Dimaki Chryssa , Kastenholz Bernd , Kleinert Ann-Katrin , Galinski Anna , Scharr Hanno , Fiorani Fabio , Schurr Ulrich
Published: October 2012

Root systems play an essential role in ensuring plant productivity. Experiments conducted in controlled environments and simulation models suggest that root geometry and responses of root architecture to environmental factors should be studied as a priority. However, compared with aboveground plant organs, roots are not easily accessible by non-invasive analyses and field research is still based almost completely on manual, destructive methods. Contributing to reducing the gap between laboratory and field experiments, we present a novel phenotyping system (GROWSCREEN-Rhizo), which is capable of automatically imaging roots and shoots of plants grown in soil-filled rhizotrons (up to a volume of ~18 L) with a throughput of 60 rhizotrons per hour. Analysis of plants grown in this setup is restricted to a certain plant size (up to a shoot height of 80 cm and root-system depth of 90 cm). We performed validation experiments using six different species and for barley and maize, we studied the effect of moderate soil compaction, which is a relevant factor in the field. First, we found that the portion of root systems that is visible through the rhizotrons’ transparent plate is representative of the total root system. The percentage of visible roots decreases with increasing average root diameter of the plant species studied and depends, to some extent, on environmental conditions. Second, we could measure relatively minor changes in root-system architecture induced by a moderate increase in soil compaction. Taken together, these findings demonstrate the good potential of this methodology to characterise root geometry and temporal growth responses with relatively high spatial accuracy and resolution for both monocotyledonous and dicotyledonous species. Our prototype will allow the design of high-throughput screening methodologies simulating environmental scenarios that are relevant in the field and will support breeding efforts towards improved resource use efficiency and stability of crop yields.
The art of growing plants for experimental purposes: a practical guide for the plant biologist
Authors: Poorter Hendrik , Fiorani Fabio , Stitt Mark , Schurr Uli , Finck Alex , Gibon Yves , Usadel Björn , Munns Rana , Atkin Owen K. , Tardieu François , Pons Thijs L.
Published: October 2012

Every year thousands of experiments are conducted using plants grown under more-or-less controlled environmental conditions. The aim of many such experiments is to compare the phenotype of different species or genotypes in a specific environment, or to study plant performance under a range of suboptimal conditions. Our paper aims to bring together the minimum knowledge necessary for a plant biologist to set up such experiments and apply the environmental conditions that are appropriate to answer the questions of interest. We first focus on the basic choices that have to be made with regard to the experimental setup (e.g. where are the plants grown; what rooting medium; what pot size). Second, we present practical considerations concerning the number of plants that have to be analysed considering the variability in plant material and the required precision. Third, we discuss eight of the most important environmental factors for plant growth (light quantity, light quality, CO2, nutrients, air humidity, water, temperature and salinity); what critical issues should be taken into account to ensure proper growth conditions in controlled environments and which specific aspects need attention if plants are challenged with a certain a-biotic stress factor. Finally, we propose a simple checklist that could be used for tracking and reporting experimental conditions.
Pot size matters: a meta-analysis of the effects of rooting volume on plant growth
Authors: Poorter Hendrik , Bühler Jonas , van Dusschoten Dagmar , Climent José , Postma Johannes A.
Published: October 2012

The majority of experiments in plant biology use plants grown in some kind of container or pot. We conducted a meta-analysis on 65 studies that analysed the effect of pot size on growth and underlying variables. On average, a doubling of the pot size increased biomass production by 43%. Further analysis of pot size effects on the underlying components of growth suggests that reduced growth in smaller pots is caused mainly by a reduction in photosynthesis per unit leaf area, rather than by changes in leaf morphology or biomass allocation. The appropriate pot size will logically depend on the size of the plants growing in them. Based on various lines of evidence we suggest that an appropriate pot size is one in which the plant biomass does not exceed 1 g L–1. In current research practice ~65% of the experiments exceed that threshold. We suggest that researchers need to carefully consider the pot size in their experiments, as small pots may change experimental results and defy the purpose of the experiment.
MicroRNA-223 is neuroprotective by targeting glutamate receptors
Authors: Harraz Maged M. , Eacker Stephen M. , Wang Xueqing , Dawson Ted M. , Dawson Valina L.
Published: October 2012

Stroke is a major cause of mortality and morbidity worldwide. Extracellular glutamate accumulation leading to overstimulation of the ionotropic glutamate receptors mediates neuronal injury in stroke and in neurodegenerative disorders. Here we show that miR-223 controls the response to neuronal injury by regulating the functional expression of the glutamate receptor subunits GluR2 and NR2B in brain. Overexpression of miR-223 lowers the levels of GluR2 and NR2B by targeting 3′-UTR target sites (TSs) in GluR2 and NR2B, inhibits NMDA-induced calcium influx in hippocampal neurons, and protects the brain from neuronal cell death following transient global ischemia and excitotoxic injury. MiR-223 deficiency results in higher levels of NR2B and GluR2, enhanced NMDA-induced calcium influx, and increased miniature excitatory postsynaptic currents in hippocampal neurons. In addition, the absence of MiR-223 leads to contextual, but not cued memory deficits and increased neuronal cell death following transient global ischemia and excitotoxicity. These data identify miR-223 as a major regulator of the expression of GluR2 and NR2B, and suggest a therapeutic role for miR-223 in stroke and other excitotoxic neuronal disorders.
Synthesis between demic and cultural diffusion in the Neolithic transition in Europe
Authors: Fort Joaquim
Published: October 2012

There is a long-standing controversy between two models of the Neolithic transition. The demic model assumes that the Neolithic range expansion was mainly due to the spread of populations, and the cultural model considers that it was essentially due to the spread of ideas. Here we integrate the demic and cultural models in a unified framework. We show that cultural diffusion explains ∼40% of the spread rate of the Neolithic transition in Europe, as implied by archaeological data. Thus, cultural diffusion cannot be neglected, but demic diffusion was the most important mechanism in this major historical process at the continental scale. This quantitative approach can be useful also in regional analysis, the description of Neolithic transitions in other continents, and models of many human spread phenomena.
Late Cretaceous restructuring of terrestrial communities facilitated the end-Cretaceous mass extinction in North America
Authors: Mitchell Jonathan S. , Roopnarine Peter D. , Angielczyk Kenneth D.
Published: October 2012

The sudden environmental catastrophe in the wake of the end-Cretaceous asteroid impact had drastic effects that rippled through animal communities. To explore how these effects may have been exacerbated by prior ecological changes, we used a food-web model to simulate the effects of primary productivity disruptions, such as those predicted to result from an asteroid impact, on ten Campanian and seven Maastrichtian terrestrial localities in North America. Our analysis documents that a shift in trophic structure between Campanian and Maastrichtian communities in North America led Maastrichtian communities to experience more secondary extinction at lower levels of primary production shutdown and possess a lower collapse threshold than Campanian communities. Of particular note is the fact that changes in dinosaur richness had a negative impact on the robustness of Maastrichtian ecosystems against environmental perturbations. Therefore, earlier ecological restructuring may have exacerbated the impact and severity of the end-Cretaceous extinction, at least in North America.
DNA damage and eIF4G1 in breast cancer cells reprogram translation for survival and DNA repair mRNAs
Authors: Badura Michelle , Braunstein Steve , Zavadil Jiri , Schneider Robert J.
Published: October 2012

The cellular response to DNA damage is mediated through multiple pathways that regulate and coordinate DNA repair, cell cycle arrest, and cell death. We show that the DNA damage response (DDR) induced by ionizing radiation (IR) is coordinated in breast cancer cells by selective mRNA translation mediated by high levels of translation initiation factor eIF4G1 (eukaryotic initiation factor 4γ1). Increased expression of eIF4G1, common in breast cancers, was found to selectively increase translation of mRNAs involved in cell survival and the DDR, preventing autophagy and apoptosis [
Survivin
, hypoxia inducible factor 1α (
HIF1
α
), X-linked inhibitor of apoptosis (
XIAP
)], promoting cell cycle arrest [growth arrest and DNA damage protein 45a (
GADD45a
), protein 53 (
p53
), ATR-interacting protein (
ATRIP
), Check point kinase 1 (
Chk1
)] and DNA repair [p53 binding protein 1 (
53BP1
), breast cancer associated proteins 1, 2 (
BRCA1/2
), Poly-ADP ribose polymerase (
PARP
), replication factor c2–5 (
Rfc2-5
), ataxia telangiectasia mutated gene 1 (
ATM
), meiotic recombination protein 11 (
MRE-11
), and others]. Reduced expression of eIF4G1, but not its homolog eIF4G2, greatly sensitizes cells to DNA damage by IR, induces cell death by both apoptosis and autophagy, and significantly delays resolution of DNA damage foci with little reduction of overall protein synthesis. Although some mRNAs selectively translated by higher levels of eIF4G1 were found to use internal ribosome entry site (IRES)-mediated alternate translation, most do not. The latter group shows significantly reduced dependence on eIF4E for translation, facilitated by an enhanced requirement for eIF4G1. Increased expression of eIF4G1 therefore promotes specialized translation of survival, growth arrest, and DDR mRNAs that are important in cell survival and DNA repair following genotoxic DNA damage.
Genetic activation of BK currents in vivo generates bidirectional effects on neuronal excitability
Authors: Montgomery Jenna R. , Meredith Andrea L.
Published: October 2012

Large-conductance calcium-activated potassium channels (BK) are potent negative regulators of excitability in neurons and muscle, and increasing BK current is a novel therapeutic strategy for neuro- and cardioprotection, disorders of smooth muscle hyperactivity, and several psychiatric diseases. However, in some neurons, enhanced BK current is linked with seizures and paradoxical increases in excitability, potentially complicating the clinical use of agonists. The mechanisms that switch BK influence from inhibitory to excitatory are not well defined. Here we investigate this dichotomy using a gain-of-function subunit (BK
R207Q
) to enhance BK currents. Heterologous expression of BK
R207Q
generated currents that activated at physiologically relevant voltages in lower intracellular Ca
2+
, activated faster, and deactivated slower than wild-type currents. We then used BK
R207Q
expression to broadly augment endogenous BK currents in vivo, generating a transgenic mouse from a circadian clock-controlled
Period1
gene fragment (
Tg-BK

R207Q

). The specific impact on excitability was assessed in neurons of the suprachiasmatic nucleus (SCN) in the hypothalamus, a cell type where BK currents regulate spontaneous firing under distinct day and night conditions that are defined by different complements of ionic currents. In the SCN,
Tg-BK

R207Q

expression converted the endogenous BK current to fast-activating, while maintaining similar current-voltage properties between day and night. Alteration of BK currents in
Tg-BK

R207Q

SCN neurons increased firing at night but decreased firing during the day, demonstrating that BK currents generate bidirectional effects on neuronal firing under distinct conditions.
Ideal, catch, and slip bonds in cadherin adhesion
Authors: Rakshit Sabyasachi , Zhang Yunxiang , Manibog Kristine , Shafraz Omer , Sivasankar Sanjeevi
Published: October 2012

Classical cadherin cell-cell adhesion proteins play key morphogenetic roles during development and are essential for maintaining tissue integrity in multicellular organisms. Classical cadherins bind in two distinct conformations, X-dimer and strand-swap dimer; during cellular rearrangements, these adhesive states are exposed to mechanical stress. However, the molecular mechanisms by which cadherins resist tensile force and the pathway by which they convert between different conformations are unclear. Here, we use single molecule force measurements with an atomic force microscope (AFM) to show that E-cadherin, a prototypical classical cadherin, forms three types of adhesive bonds: catch bonds, which become longer lived in the presence of tensile force; slip bonds, which become shorter lived when pulled; and ideal bonds that are insensitive to mechanical stress. We show that X-dimers form catch bonds, whereas strand-swap dimers form slip bonds. Our data suggests that ideal bonds are formed as X-dimers convert to strand-swap binding. Catch, slip, and ideal bonds allow cadherins to withstand tensile force and tune the mechanical properties of adhesive junctions.
NMR structure of a lytic polysaccharide monooxygenase provides insight into copper binding, protein dynamics, and substrate interactions
Authors: Aachmann Finn L. , Sørlie Morten , Skjåk-Bræk Gudmund , Eijsink Vincent G. H. , Vaaje-Kolstad Gustav
Published: October 2012

Lytic polysaccharide monooxygenases currently classified as carbohydrate binding module family 33 (CBM33) and glycoside hydrolase family 61 (GH61) are likely to play important roles in future biorefining. However, the molecular basis of their unprecedented catalytic activity remains largely unknown. We have used NMR techniques and isothermal titration calorimetry to address structural and functional aspects of CBP21, a chitin-active CBM33. NMR structural and relaxation studies showed that CBP21 is a compact and rigid molecule, and the only exception is the catalytic metal binding site. NMR data further showed that His28 and His114 in the catalytic center bind a variety of divalent metal ions with a clear preference for Cu2+(Kd= 55 nM; from isothermal titration calorimetry) and higher preference for Cu1+(Kd∼ 1 nM; from the experimentally determined redox potential for CBP21-Cu2+of 275 mV using a thermodynamic cycle). Strong binding of Cu1+was also reflected in a reduction in the pKavalues of the histidines by 3.6 and 2.2 pH units, respectively. Cyanide, a mimic of molecular oxygen, was found to bind to the metal ion only. These data support a model where copper is reduced on the enzyme by an externally provided electron and followed by oxygen binding and activation by internal electron transfer. Interactions of CBP21 with a crystalline substrate were mapped in a2H/1H exchange experiment, which showed that substrate binding involves an extended planar binding surface, including the metal binding site. Such a planar catalytic surface seems well-suited to interact with crystalline substrates.
Structural asymmetry in the magnesium channel CorA points to sequential allosteric regulation
Authors: Pfoh Roland , Li Angela , Chakrabarti Nilmadhab , Payandeh Jian , Pomès Régis , Pai Emil F.
Published: October 2012

Magnesium ions (Mg
2+
) are essential for life, but the mechanisms regulating their transport into and out of cells remain poorly understood. The CorA-Mrs2-Alr1 superfamily of Mg
2+
channels represents the most prevalent group of proteins enabling Mg
2+
ions to cross membranes.
Thermotoga maritima
CorA (TmCorA) is the only member of this protein family whose complete 3D fold is known. Here, we report the crystal structure of a mutant in the presence and absence of divalent ions and compare it with previous divalent ion-bound TmCorA structures. With Mg
2+
present, this structure shows binding of a hydrated Mg
2+
ion to the periplasmic Gly-Met-Asn (GMN) motif, revealing clues of ion selectivity in this unique channel family. In the absence of Mg
2+
, TmCorA displays an unexpected asymmetric conformation caused by radial and lateral tilts of protomers that leads to bending of the central, pore-lining helix. Molecular dynamics simulations support these movements, including a bell-like deflection. Mass spectrometric analysis confirms that major proteolytic cleavage occurs within a region that is selectively exposed by such a bell-like bending motion. Our results point to a sequential allosteric model of regulation, where intracellular Mg
2+
binding locks TmCorA in a symmetric, transport-incompetent conformation and loss of intracellular Mg
2+
causes an asymmetric, potentially influx-competent conformation of the channel.
Brønsted basicity of the air–water interface
Authors: Mishra Himanshu , Enami Shinichi , Nielsen Robert J. , Stewart Logan A. , Hoffmann Michael R. , Goddard William A. , Colussi Agustín J.
Published: October 2012

Differences in the extent of protonation of functional groups lying on either side of water–hydrophobe interfaces are deemed essential to enzymatic catalysis, molecular recognition, bioenergetic transduction, and atmospheric aerosol–gas exchanges. The sign and range of such differences, however, remain conjectural. Herein we report experiments showing that gaseous carboxylic acids RCOOH(g) begin to deprotonate on the surface of water significantly more acidic than that supporting the dissociation of dissolved acids RCOOH(aq). Thermodynamic analysis indicates that > 6 H
2
O molecules must participate in the deprotonation of RCOOH(g) on water, but quantum mechanical calculations on a model air–water interface predict that such event is hindered by a significant kinetic barrier unless OH
−
ions are present therein. Thus, by detecting RCOO
−
we demonstrate the presence of OH
−
on the aerial side of on pH > 2 water exposed to RCOOH(g). Furthermore, because in similar experiments the base (Me)
3
N(g) is protonated only on pH < 4 water, we infer that the outer surface of water is Brønsted neutral at pH ∼3 (rather than at pH 7 as bulk water), a value that matches the isoelectric point of bubbles and oil droplets in independent electrophoretic experiments. The OH
−
densities sensed by RCOOH(g) on the aerial surface of water, however, are considerably smaller than those at the (>1 nm) deeper shear planes probed in electrophoresis, thereby implying the existence of OH
−
gradients in the interfacial region. This fact could account for the weak OH
−
signals detected by surface-specific spectroscopies.
Plasmodium falciparum
responds to amino acid starvation by entering into a hibernatory state
Authors: Babbitt Shalon E. , Altenhofen Lindsey , Cobbold Simon A. , Istvan Eva S. , Fennell Clare , Doerig Christian , Llinás Manuel , Goldberg Daniel E.
Published: October 2012

The human malaria parasite
Plasmodium falciparum
is auxotrophic for most amino acids. Its amino acid needs are met largely through the degradation of host erythrocyte hemoglobin; however the parasite must acquire isoleucine exogenously, because this amino acid is not present in adult human hemoglobin. We report that when isoleucine is withdrawn from the culture medium of intraerythrocytic
P. falciparum
, the parasite slows its metabolism and progresses through its developmental cycle at a reduced rate. Isoleucine-starved parasites remain viable for 72 h and resume rapid growth upon resupplementation. Protein degradation during starvation is important for maintenance of this hibernatory state. Microarray analysis of starved parasites revealed a 60% decrease in the rate of progression through the normal transcriptional program but no other apparent stress response.
Plasmodium
parasites do not possess a TOR nutrient-sensing pathway and have only a rudimentary amino acid starvation-sensing eukaryotic initiation factor 2α (eIF2α) stress response. Isoleucine deprivation results in GCN2-mediated phosphorylation of eIF2α, but kinase-knockout clones still are able to hibernate and recover, indicating that this pathway does not directly promote survival during isoleucine starvation. We conclude that
P. falciparum
, in the absence of canonical eukaryotic nutrient stress-response pathways, can cope with an inconsistent bloodstream amino acid supply by hibernating and waiting for more nutrient to be provided.
Structural mechanism of RuBisCO activation by carbamylation of the active site lysine
Authors: Stec Boguslaw
Published: October 2012

Ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is a crucial enzyme in carbon fixation and the most abundant protein on earth. It has been studied extensively by biochemical and structural methods; however, the most essential activation step has not yet been described. Here, we describe the mechanistic details of Lys carbamylation that leads to RuBisCO activation by atmospheric CO
2
. We report two crystal structures of nitrosylated RuBisCO from the red algae
Galdieria sulphuraria
with O
2
and CO
2
bound at the active site.
G. sulphuraria
RuBisCO is inhibited by cysteine nitrosylation that results in trapping of these gaseous ligands. The structure with CO
2
defines an elusive, preactivation complex that contains a metal cation Mg
2+
surrounded by three H
2
O/OH molecules. Both structures suggest the mechanism for discriminating gaseous ligands by their quadrupole electric moments. We describe conformational changes that allow for intermittent binding of the metal ion required for activation. On the basis of these structures we propose the individual steps of the activation mechanism. Knowledge of all these elements is indispensable for engineering RuBisCO into a more efficient enzyme for crop enhancement or as a remedy to global warming.
Rubisco small-subunit α-helices control pyrenoid formation inChlamydomonas
Authors: Meyer Moritz T. , Genkov Todor , Skepper Jeremy N. , Jouhet Juliette , Mitchell Madeline C. , Spreitzer Robert J. , Griffiths Howard
Published: October 2012

The pyrenoid is a subcellular microcompartment in which algae sequester the primary carboxylase, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). The pyrenoid is associated with a CO2-concentrating mechanism (CCM), which improves the operating efficiency of carbon assimilation and overcomes diffusive limitations in aquatic photosynthesis. Using the model algaChlamydomonas reinhardtii, we show that pyrenoid formation, Rubisco aggregation, and CCM activity relate to discrete regions of the Rubisco small subunit (SSU). Specifically, pyrenoid occurrence was shown to be conditioned by the amino acid composition of two surface-exposed α-helices of the SSU: higher plant-like helices knock out the pyrenoid, whereas native algal helices establish a pyrenoid. We have also established that pyrenoid integrity was essential for the operation of an active CCM. With the algal CCM being functionally analogous to the terrestrial C4pathway in higher plants, such insights may offer a route toward transforming algal and higher plant productivity for the future.
Transcriptome-wide analyses of CstF64–RNA interactions in global regulation of mRNA alternative polyadenylation
Authors: Yao Chengguo , Biesinger Jacob , Wan Ji , Weng Lingjie , Xing Yi , Xie Xiaohui , Shi Yongsheng
Published: October 2012

Cleavage stimulation factor 64 kDa (CstF64) is an essential pre-mRNA 3′ processing factor and an important regulator of alternative polyadenylation (APA). Here we characterized CstF64–RNA interactions in vivo at the transcriptome level and investigated the role of CstF64 in global APA regulation through individual nucleotide resolution UV crosslinking and immunoprecipitation sequencing and direct RNA sequencing analyses. We observed highly specific CstF64–RNA interactions at poly(A) sites (PASs), and we provide evidence that such interactions are widely variable in affinity and may be differentially required for PAS recognition. Depletion of CstF64 by RNAi has a relatively small effect on the global APA profile, but codepletion of the CstF64 paralog CstF64τ leads to greater APA changes, most of which are characterized by the increased relative use of distal PASs. Finally, we found that CstF64 binds to thousands of dormant intronic PASs that are suppressed, at least in part, by U1 small nuclear ribonucleoproteins. Taken together, our findings provide insight into the mechanisms of PAS recognition and identify CstF64 as an important global regulator of APA.
Functional remodeling of RNA processing in replacement chloroplasts by pathways retained from their predecessors
Authors: Dorrell Richard G. , Howe Christopher J.
Published: October 2012

Chloroplasts originate through the endosymbiotic integration of a host and a photosynthetic symbiont, with processes established within the host for the biogenesis and maintenance of the nascent chloroplast. It is thought that several photosynthetic eukaryotes have replaced their original chloroplasts with others derived from different source organisms in a process termed “serial endosymbiosis of chloroplasts.” However, it is not known whether replacement chloroplasts are affected by the biogenesis and maintenance pathways established to support their predecessors. Here, we investigate whether pathways established during a previous chloroplast symbiosis function in the replacement chloroplasts of the dinoflagellate alga
Karenia mikimotoi
. We show that chloroplast transcripts in
K. mikimotoi
are subject to 3′ polyuridylylation and extensive sequence editing. We confirm that these processes do not occur in free-living relatives of the replacement chloroplast lineage, but are otherwise found only in the ancestral, red algal-derived chloroplasts of dinoflagellates and their closest relatives. This indicates that these unusual RNA-processing pathways have been retained from the original symbiont lineage and made use of by the replacement chloroplast. Our results constitute an addition to current theories of chloroplast evolution in which chloroplast biogenesis may be radically remodeled by pathways remaining from previous symbioses.
Biologically inspired LED lens from cuticular nanostructures of firefly lantern
Authors: Kim Jae-Jun , Lee Youngseop , Kim Ha Gon , Choi Ki-Ju , Kweon Hee-Seok , Park Seongchong , Jeong Ki-Hun
Published: October 2012

Cuticular nanostructures found in insects effectively manage light for light polarization, structural color, or optical index matching within an ultrathin natural scale. These nanostructures are mainly dedicated to manage incoming light and recently inspired many imaging and display applications. A bioluminescent organ, such as a firefly lantern, helps to out-couple light from the body in a highly efficient fashion for delivering strong optical signals in sexual communication. However, the cuticular nanostructures, except the light-producing reactions, have not been well investigated for physical principles and engineering biomimetics. Here we report a unique observation of high-transmission nanostructures on a firefly lantern and its biological inspiration for highly efficient LED illumination. Both numerical and experimental results clearly reveal high transmission through the nanostructures inspired from the lantern cuticle. The nanostructures on an LED lens surface were fabricated by using a large-area nanotemplating and reconfigurable nanomolding with heat-induced shear thinning. The biologically inspired LED lens, distinct from a smooth surface lens, substantially increases light transmission over visible ranges, comparable to conventional antireflection coating. This biological inspiration can offer new opportunities for increasing the light extraction efficiency of high-power LED packages.
Epistasis in tomato color mutations involves regulation of
phytoene synthase 1
expression by
cis
-carotenoids
Authors: Kachanovsky David E. , Filler Shdema , Isaacson Tal , Hirschberg Joseph
Published: October 2012

Tomato (
Solanum lycopersicum
) fruit accumulate the red carotenoid pigment lycopene. The recessive mutation
yellow-flesh
(locus
r
) in tomato eliminates fruit carotenoids by disrupting the activity of the fruit-specific phytoene synthase (PSY1), the first committed step in the carotenoid biosynthesis pathway. Fruits of the recessive mutation
tangerine
(
t
) appear orange due to accumulation of 7,9,7′,9′-tetra-
cis
-lycopene (prolycopene) as a result of a mutation in the carotenoid
cis
–
trans
isomerase. It was established 60 y ago that
tangerine
is epistatic to
yellow-flesh
. This uncharacteristic epistasis interaction defies a paradigm in biochemical genetics arguing that mutations that disrupt enzymes acting early in a biosynthetic pathway are epistatic to other mutations that block downstream steps in the same pathway. To explain this conundrum, we have investigated the interaction between
tangerine
and
yellow-flesh
at the molecular level. Results presented here indicate that allele
r

2997

of
yellow-flesh
eliminates transcription of
PSY1
in fruits. In a genetic background of
tangerine
, transcription of
PSY1
is partially restored to a level sufficient for producing phytoene and downstream carotenoids. Our results revealed the molecular mechanism underlying the epistasis of
t
over
r
and suggest the involvement of
cis
-carotenoid metabolites in a feedback regulation of
PSY1
gene expression.
Critical role of calcitonin gene-related peptide receptors in cortical spreading depression
Authors: Tozzi Alessandro , de Iure Antonio , Di Filippo Massimiliano , Costa Cinzia , Caproni Stefano , Pisani Antonio , Bonsi Paola , Picconi Barbara , Cupini Letizia M. , Materazzi Serena , Geppetti Pierangelo , Sarchielli Paola , Calabresi Paolo
Published: October 2012

Cortical spreading depression (CSD) is a key pathogenetic step in migraine with aura. Dysfunctions of voltage-dependent and receptor-operated channels have been implicated in the generation of CSD and in the pathophysiology of migraine. Although a known correlation exists between migraine and release of the calcitonin gene-related peptide (CGRP), the possibility that CGRP is involved in CSD has not been examined in detail. We analyzed the pharmacological mechanisms underlying CSD and investigated the possibility that endogenous CGRP contributes to this phenomenon. CSD was analyzed in rat neocortical slices by imaging of the intrinsic optical signal. CSD was measured as the percentage of the maximal surface of a cortical slice covered by the propagation of intrinsic optical signal changes during an induction episode. Reproducible CSD episodes were induced through repetitive elevations of extracellular potassium concentration. AMPA glutamate receptor antagonism did not inhibit CSD, whereas NMDA receptor antagonism did inhibit CSD. Blockade of voltage-dependent sodium channels by TTX also reduced CSD. CSD was also decreased by the antiepileptic drug topiramate, but not by carbamazepine. Interestingly, endogenous CGRP was released in the cortical tissue in a calcium-dependent manner during CSD, and three different CGRP receptor antagonists had a dose-dependent inhibitory effect on CSD, suggesting a critical role of CGRP in this phenomenon. Our findings show that both glutamate NMDA receptors and voltage-dependent sodium channels play roles in CSD. They also demonstrate that CGRP antagonism reduces CSD, supporting the possible use of drugs targeting central CGRP receptors as antimigraine agents.
Role of an esterase in flavor volatile variation within the tomato clade
Authors: Goulet Charles , Mageroy Melissa H. , Lam Nghi B. , Floystad Abbye , Tieman Denise M. , Klee Harry J.
Published: October 2012

Tomato flavor is dependent upon a complex mixture of volatiles including multiple acetate esters. Red-fruited species of the tomato clade accumulate a relatively low content of acetate esters in comparison with the green-fruited species. We show that the difference in volatile ester content between the red- and green-fruited species is associated with insertion of a retrotransposon adjacent to the most enzymatically active member of a family of esterases. This insertion causes higher expression of the esterase, resulting in the reduced levels of multiple esters that are negatively correlated with human preferences for tomato. The insertion was evolutionarily fixed in the red-fruited species, suggesting that high expression of the esterase and consequent low ester content may provide an adaptive advantage in the ancestor of the red-fruited species. These results illustrate at a molecular level how closely related species exhibit major differences in volatile production by altering a volatile-associated catabolic activity.
Internal signal correlates neural populations and biases perceptual decision reports
Authors: Carnevale Federico , de Lafuente Victor , Romo Ranulfo , Parga Néstor
Published: October 2012

In perceptual decision-making tasks the activity of neurons in frontal and posterior parietal cortices covaries more with perceptual reports than with the physical properties of stimuli. This relationship is revealed when subjects have to make behavioral choices about weak or uncertain stimuli. If knowledge about stimulus onset time is available, decision making can be based on accumulation of sensory evidence. However, the time of stimulus onset or even its very presence is often ambiguous. By analyzing firing rates and correlated variability of frontal lobe neurons while monkeys perform a vibrotactile detection task, we show that behavioral outcomes are crucially affected by the state of cortical networks before stimulus onset times. The results suggest that sensory detection is partly due to a purely internal signal whereas the stimulus, if finally applied, adds a contribution to this initial processing later on. The probability to detect or miss the stimulus can thus be explained as the combined effect of this variable internal signal and the sensory evidence.
A functional promoter polymorphism of SLC2A4 is associated with aerobic endurance in a Chinese population
Authors: Xia Xiaohui , Hu Yang , Xu Liang , Chen Ting
Published: October 2012

The G/A mutation in SLC2A4 promoter, rs5418, was investigated to assess the relationship between the SLC2A4 gene and aerobic endurance in the muscle uptake of glucose. Genotypic/allelic frequencies of rs5418 in SLC2A4 in 102 top‐level long‐distance runners (53 men and 49 women) were compared with those of 206 healthy controls (118 men and 88 women) from the same ethnic background (Han Chinese). The functional significance of rs5418 was analysed using the dual‐luciferase reporter assay system. The A allele of SLC2A4 rs5418 was overrepresented in athletes (61.8%) compared with that in the controls (45.6%; P<0.05, power = 0.989), and the AA genotype in athletes (74.5%) was higher than that in the controls (66.0%; P<0.05, power = 0.999). The luciferase reporter vector containing the SLC2A4 promoter with rs5418‐A alleles produced significantly greater relative luciferase activity (19.49±4.41) than that with rs5418‐G alleles (13.04±4.45; P<0.05, power = 0.867). Our findings suggest that the AA genotype and A allele of SLC2A4 rs5418 were associated with top‐level endurance performance in the northern Han Chinese population. The molecular mechanism was based on the functional mutation that changed the activity of the promoter, thereby affecting gene expression.
Northern = smart and Southern = nice: The development of accent attitudes in the United States
Authors: Kinzler Katherine D. , DeJesus Jasmine M.
Published: October 2012

Adults evaluate others based on their speech, yet little is known of the developmental trajectory by which accent attitudes are acquired. Here we investigate the development of American children's attitudes about Northern- and Southern-accented American English. Children in Illinois (the “North”) and Tennessee (the “South”) evaluated the social desirability, personality characteristics, and geographic origins of Northern- and Southern-accented individuals. Five- to 6-year-old children in Illinois preferred the Northern-accented speakers as potential friends, yet did not demonstrate knowledge of any stereotypes about the different groups; 5–6-year-old children in Tennessee did not show a preference towards either type of speaker. Nine- to 10-year-old children in both Illinois and Tennessee evaluated the Northern-accented individuals as sounding “smarter” and “in charge”, and the Southern-accented individuals as sounding “nicer.” Thus, older children endorse similar stereotypes to those observed in adulthood. These accent attitudes develop in parallel across children in different regions and reflect both positive and negative assessments of a child's own group.
Conditional deletion of cytokine receptor chains reveals that IL-7 and IL-15 specify CD8 cytotoxic lineage fate in the thymus
Authors: McCaughtry Tom M. , Etzensperger Ruth , Alag Amala , Tai Xuguang , Kurtulus Sema , Park Jung-Hyun , Grinberg Alex , Love Paul , Feigenbaum Lionel , Erman Batu , Singer Alfred
Published: October 2012

The thymus generates T cells with diverse specificities and functions. To assess the contribution of cytokine receptors to the differentiation of T cell subsets in the thymus, we constructed conditional knockout mice in which IL-7Rα or common cytokine receptor γ chain (γc) genes were deleted in thymocytes just before positive selection. We found that γc expression was required to signal the differentiation of MHC class I (MHC-I)–specific thymocytes into CD8+ cytotoxic lineage T cells and into invariant natural killer T cells but did not signal the differentiation of MHC class II (MHC-II)–specific thymocytes into CD4+ T cells, even into regulatory Foxp3+CD4+ T cells which require γc signals for survival. Importantly, IL-7 and IL-15 were identified as the cytokines responsible for CD8+ cytotoxic T cell lineage specification in vivo. Additionally, we found that small numbers of aberrant CD8+ T cells expressing Runx3d could arise without γc signaling, but these cells were developmentally arrested before expressing cytotoxic lineage genes. Thus, γc-transduced cytokine signals are required for cytotoxic lineage specification in the thymus and for inducing the differentiation of MHC-I–selected thymocytes into functionally mature T cells.
Disorder and weak localization effects in Co2MnxTi1−xAl Heusler alloy thin films
Authors: Aftab M , Hassnain Jaffari G , Hasanain S K , Abbas Turab Ali , Ismat Shah S
Published: October 2012

The effects of disorder on the structural, magnetic and transport properties of stoichiometric Co2Mn
x
Ti1−x
Al (0 ⩽ x ⩽ 1) thin films are reported. All the compositions exhibited B2-type structure with the actual composition of each film, as determined by Rutherford backscattering spectroscopy (RBS), being close to the nominal value. The values of saturation magnetization increase with increasing Mn content in the films and are in general agreement with the values obtained using the Slater–Pauling rule and the actual (RBS determined) compositions. Electrical resistivity as a function of temperature shows a change from metallic-type behaviour for x ⩽ 0.25 to a semiconducting type for x > 0.25. At lower temperatures (T < 25 K) metallic compositions show the presence of a resistivity minimum. The resistivity behaviour above low T upturn in metallic compositions follows a T
2 dependence that is explained in terms of electron–electron scattering and one-magnon scattering. The presence of a resistivity minimum and the crossover from metallic to semiconducting type resistivity are explained in terms of localization effects originating mainly in the Co antisite disorder in these alloy films.
Validation of a triangular quantum well model for GaN-based HEMTs used in pH and dipole moment sensing
Authors: Rabbaa S , Stiens J
Published: October 2012

Gallium nitride (GaN) is a relatively new semiconductor material that has the potential of replacing gallium arsenide (GaAs) in some of the more recent technological applications, for example chemical sensor applications. In this paper, we introduce a triangular quantum well model for an undoped AlGaN/GaN high electron mobility transistor (HEMT) structure used as a chemical and biological sensor for pH and dipole moment measurements of polar liquids. We have performed theoretical calculations related to the HEMT characteristics and we have compared them with experimental measurements carried out in many previous papers. These calculations include the current–voltage (I–V) characteristics of the device, the surface potential, the change in the drain current with the dipole moment and the drain current as a function of pH. The results exhibit good agreement with experimental measurements for different polar liquids and electrolyte solutions. It is also found that the drain current of the device exhibits a large linear variation with the dipole moment, and that the surface potential and the drain current depend strongly on the pH. Therefore, it can distinguish molecules with slightly different dipole moments and solutions with small variations in pH. The ability of the device to sense biomolecules (such as proteins) with very large dipole moments is investigated.
Fabrication of pure gold nanostructures by electron beam induced deposition with Au(CO)Cl precursor: deposition characteristics and primary beam scattering effects
Authors: Mulders J J L , Veerhoek J M , Bosch E G T , Trompenaars P H F
Published: October 2012

In the search for a direct write, high-purity electron beam induced deposition (EBID) process, a new gold precursor that is commonly available is investigated. This precursor, Au(CO)Cl, can indeed be used to produce a high-purity golden nanostructure (>95 at% Au), at a wide variety of electron beam parameters. The use of a mass spectrometer to determine the components of the actual precursor vapour showed that the Au(CO)Cl density in the vapour is very low (estimated at <0.1%), while the main component is CO. This indicates that the electron decomposition cross-section of the actual precursor is roughly two orders of magnitude higher than for common EBID precursors. A remarkable observation is a skirt deposition at positions between 5 and 200 µm away from the beam impact point. This skirt cannot be attributed to secondary electrons of type II (SE2), but results from local scattering of the primary beam on its way through the precursor gas. The skirt deposition is quantified experimentally and by modelling and must be present in all EBID processes with any precursor, delivered through a local supply system with fluxes in the range 1016–1019 molecules cm−2 s−1. It is shown that the skirt effect can be minimized by increasing the applied beam energy and by reducing the gas path length.