bluuebunny/crossref_metadata_2025 huggingface dataset:
Phytoplasma protein effector SAP11 enhances insect vector reproduction by manipulating plant development and defense hormone biosynthesis
Authors: Sugio Akiko , Kingdom Heather N. , MacLean Allyson M. , Grieve Victoria M. , Hogenhout Saskia A.
Published: November 2011

Phytoplasmas are insect-transmitted phytopathogenic bacteria that can alter plant morphology and the longevity and reproduction rates and behavior of their insect vectors. There are various examples of animal and plant parasites that alter the host phenotype to attract insect vectors, but it is unclear how these parasites accomplish this. We hypothesized that phytoplasmas produce effectors that modulate specific targets in their hosts leading to the changes in plant development and insect performance. Previously, we sequenced and mined the genome of Aster Yellows phytoplasma strain Witches’ Broom (AY-WB) and identified 56 candidate effectors. Here, we report that the secreted AY-WB protein 11 (SAP11) effector modulates plant defense responses to the advantage of the AY-WB insect vector
Macrosteles quadrilineatus
. SAP11 binds and destabilizes
Arabidopsis
CINCINNATA (CIN)-related TEOSINTE BRANCHED1, CYCLOIDEA, PROLIFERATING CELL FACTORS 1 and 2 (TCP) transcription factors, which control plant development and promote the expression of lipoxygenase (
LOX
) genes involved in jasmonate (JA) synthesis. Both the
Arabidopsis
SAP11 lines and AY-WB–infected plants produce less JA on wounding. Furthermore, the AY-WB insect vector produces more offspring on AY-WB–infected plants, SAP11 transgenic lines, and plants impaired in CIN-TCP and JA synthesis. Thus, SAP11-mediated destabilization of CIN-TCPs leads to the down-regulation of
LOX2
expression and JA synthesis and an increase in
M. quadrilineatus
progeny. Phytoplasmas are obligate inhabitants of their plant host and insect vectors, in which the latter transmits AY-WB to a diverse range of plant species. This finding demonstrates that pathogen effectors can reach beyond the pathogen–host interface to modulate a third organism in the biological interaction.
Separation of stem cell maintenance and transposon silencing functions of Piwi protein
Authors: Klenov Mikhail S. , Sokolova Olesya A. , Yakushev Evgeny Y. , Stolyarenko Anastasia D. , Mikhaleva Elena A. , Lavrov Sergey A. , Gvozdev Vladimir A.
Published: November 2011

Piwi-interacting RNAs (piRNAs) and Piwi proteins have the evolutionarily conserved function of silencing of repetitive genetic elements in germ lines. The founder of the Piwi subfamily,
Drosophila
nuclear Piwi protein, was also shown to be required for the maintenance of germ-line stem cells (GSCs). Hence, null mutant
piwi
females exhibit two types of abnormalities, overexpression of transposons and severely underdeveloped ovaries. It remained unknown whether the failure of GSC maintenance is related to transposon derepression or if GSC self-renewal and piRNA silencing are two distinct functions of the Piwi protein. We have revealed a mutation,

piwi
Nt

, removing the nuclear localization signal of the Piwi protein.

piwi
Nt

females retain the ability of GSC self-renewal and a near-normal number of egg chambers in the ovarioles but display a drastic transposable element derepression and nuclear accumulation of their transcripts in the germ line.

piwi
Nt

mutants are sterile most likely because of the disturbance of piRNA-mediated transposon silencing. Analysis of chromatin modifications in the

piwi
Nt

ovaries indicated that Piwi causes chromatin silencing only of certain types of transposons, whereas others are repressed in the nuclei without their chromatin modification. Thus, Piwi nuclear localization that is required for its silencing function is not essential for the maintenance of GSCs. We suggest that the Piwi function in GSC self-renewal is independent of transposon repression and is normally realized in the cytoplasm of GSC niche cells.
Endonuclease VIII-like 3 (Neil3) DNA glycosylase promotes neurogenesis induced by hypoxia-ischemia
Authors: Sejersted Yngve , Hildrestrand Gunn A. , Kunke David , Rolseth Veslemøy , Krokeide Silje Z. , Neurauter Christine G. , Suganthan Rajikala , Atneosen-Åsegg Monica , Fleming Aaron M. , Saugstad Ola D. , Burrows Cynthia J. , Luna Luisa , Bjørås Magnar
Published: November 2011

Neural stem/progenitor cell proliferation and differentiation are required to replace damaged neurons and regain brain function after hypoxic-ischemic events. DNA base lesions accumulating during hypoxic-ischemic stress are removed by DNA glycosylases in the base-excision repair pathway to prevent cytotoxicity and mutagenesis. Expression of the DNA glycosylase endonuclease VIII-like 3 (Neil3) is confined to regenerative subregions in the embryonic and perinatal brains. Here we show profound neuropathology in Neil3-knockout mice characterized by a reduced number of microglia and loss of proliferating neuronal progenitors in the striatum after hypoxia-ischemia. In vitro expansion of Neil3-deficient neural stem/progenitor cells revealed an inability to augment neurogenesis and a reduced capacity to repair for oxidative base lesions in single-stranded DNA. We propose that Neil3 exercises a highly specialized function through accurate molecular repair of DNA in rapidly proliferating cells.
Vβ2 natural killer T cell antigen receptor-mediated recognition of CD1d-glycolipid antigen
Authors: Patel Onisha , Pellicci Daniel G. , Uldrich Adam P. , Sullivan Lucy C. , Bhati Mugdha , McKnight Melissa , Richardson Stewart K. , Howell Amy R. , Mallevaey Thierry , Zhang Jingjing , Bedel Romain , Besra Gurdyal S. , Brooks Andrew G. , Kjer-Nielsen Lars , McCluskey James , Porcelli Steven A. , Gapin Laurent , Rossjohn Jamie , Godfrey Dale I.
Published: November 2011

Natural killer T cell antigen receptors (NKT TCRs) recognize lipid-based antigens (Ags) presented by CD1d. Although the TCR α-chain is invariant, NKT TCR Vβ exhibits greater diversity, with one (Vβ11) and three (Vβ8, Vβ7, and Vβ2) Vβ chains in humans and mice, respectively. With the exception of the Vβ2 NKT TCR, NKT TCRs possess canonical tyrosine residues within complementarity determining region (CDR) 2β that are critical for CD1d binding. Thus, how Vβ2 NKT TCR docks with CD1d-Ag was unclear. Despite the absence of the CDR2β-encoded tyrosine residues, we show that the Vβ2 NKT TCR engaged CD1d-Ag in a similar manner and with a comparable affinity and energetic footprint to the manner observed for the Vβ8.2 and Vβ7 NKT TCRs. Accordingly, the germline–encoded regions of the TCR β-chain do not exclusively dictate the innate NKT TCR-CD1d-Ag docking mode. Nevertheless, clear fine specificity differences for the CD1d-Ag existed between the Vβ2 NKT TCR and the Vβ8.2 and Vβ7 NKT TCRs, with the Vβ2 NKT TCR exhibiting greater sensitivity to modifications to the glycolipid Ag. Furthermore, within the Vβ2 NKT TCR-CD1d-αGalCer complex, the CDR2β loop mediated fewer contacts with CD1d, whereas the CDR1β and CDR3β loops contacted CD1d to a much greater extent compared with most Vβ11, Vβ8.2, and Vβ7 NKT TCRs. Accordingly, there is a greater interplay between the germline– and nongermline–encoded loops within the TCR β-chain of the Vβ2 NKT TCR that enables CD1d-Ag ligation.
Heat shock protein 70 kDa chaperone/DnaJ cochaperone complex employs an unusual dynamic interface
Authors: Ahmad Atta , Bhattacharya Akash , McDonald Ramsay A. , Cordes Melissa , Ellington Benjamin , Bertelsen Eric B. , Zuiderweg Erik R. P.
Published: November 2011

The heat shock protein 70 kDa (Hsp70)/DnaJ/nucleotide exchange factor system assists in intracellular protein (re)folding. Using solution NMR, we obtained a three-dimensional structure for a 75-kDa Hsp70–DnaJ complex in the ADP state, loaded with substrate peptide. We establish that the J domain (residues 1–70) binds with its positively charged helix II to a negatively charged loop in the Hsp70 nucleotide-binding domain. The complex shows an unusual “tethered” binding mode which is stoichiometric and saturable, but which has a dynamic interface. The complex represents part of a triple complex of Hsp70 and DnaJ both bound to substrate protein. Mutagenesis data indicate that the interface is also of relevance for the interaction of Hsp70 and DnaJ in the ATP state. The solution complex is completely different from a crystal structure of a disulfide-linked complex of homologous proteins [Jiang, et al. (2007)
Mol Cell
28:422–433].
RNAi screening reveals requirement for host cell secretory pathway in infection by diverse families of negative-strand RNA viruses
Authors: Panda Debasis , Das Anshuman , Dinh Phat X. , Subramaniam Sakthivel , Nayak Debasis , Barrows Nicholas J. , Pearson James L. , Thompson Jesse , Kelly David L. , Ladunga Istvan , Pattnaik Asit K.
Published: November 2011

Negative-strand (NS) RNA viruses comprise many pathogens that cause serious diseases in humans and animals. Despite their clinical importance, little is known about the host factors required for their infection. Using vesicular stomatitis virus (VSV), a prototypic NS RNA virus in the family
Rhabdoviridae
, we conducted a human genome-wide siRNA screen and identified 72 host genes required for viral infection. Many of these identified genes were also required for infection by two other NS RNA viruses, the lymphocytic choriomeningitis virus of the
Arenaviridae
family and human parainfluenza virus type 3 of the
Paramyxoviridae
family. Genes affecting different stages of VSV infection, such as entry/uncoating, gene expression, and assembly/release, were identified. Depletion of the proteins of the coatomer complex I or its upstream effectors ARF1 or GBF1 led to detection of reduced levels of VSV RNA. Coatomer complex I was also required for infection of lymphocytic choriomeningitis virus and human parainfluenza virus type 3. These results highlight the evolutionarily conserved requirements for gene expression of diverse families of NS RNA viruses and demonstrate the involvement of host cell secretory pathway in the process.
Terminal protein-primed amplification of heterologous DNA with a minimal replication system based on phage Φ29
Authors: Mencía Mario , Gella Pablo , Camacho Ana , de Vega Miguel , Salas Margarita
Published: November 2011

The DNA amplification performed by terminal protein-primed replication systems has not yet been developed for its general use to produce high amounts of DNA linked to terminal protein (TP). Here we present a method to amplify in vitro heterologous DNAs using the Φ29 DNA replication machinery and producing DNA with TP covalently attached to the 5′ end. The amplification requires four Φ29 proteins, DNA polymerase, TP, single-stranded DNA binding protein and double-stranded DNA binding protein (p6). The DNA to be amplified is inserted between two sequences that are the Φ29 DNA replication origins, consisting of 191 and 194 bp from the left and right ends of the phage genome, respectively. The replication origins do not need to have TP covalently attached beforehand to be functional in amplification and they can be joined to the DNA to be amplified by cloning or ligation. The facts that two functional origins were required at the ends of a linear template DNA and that the kinetics of DNA synthesis was very similar to that obtained using the TP-containing Φ29 genome as template support the proposal that genuine amplification is taking place. Amplification factors of 30-fold have been obtained. Possible applications of DNAs produced by this method are discussed.
Algorithm discovery by protein folding game players
Authors: Khatib Firas , Cooper Seth , Tyka Michael D. , Xu Kefan , Makedon Ilya , Popović Zoran , Baker David , Players Foldit
Published: November 2011

Foldit is a multiplayer online game in which players collaborate and compete to create accurate protein structure models. For specific hard problems, Foldit player solutions can in some cases outperform state-of-the-art computational methods. However, very little is known about how collaborative gameplay produces these results and whether Foldit player strategies can be formalized and structured so that they can be used by computers. To determine whether high performing player strategies could be collectively codified, we augmented the Foldit gameplay mechanics with tools for players to encode their folding strategies as “recipes” and to share their recipes with other players, who are able to further modify and redistribute them. Here we describe the rapid social evolution of player-developed folding algorithms that took place in the year following the introduction of these tools. Players developed over 5,400 different recipes, both by creating new algorithms and by modifying and recombining successful recipes developed by other players. The most successful recipes rapidly spread through the Foldit player population, and two of the recipes became particularly dominant. Examination of the algorithms encoded in these two recipes revealed a striking similarity to an unpublished algorithm developed by scientists over the same period. Benchmark calculations show that the new algorithm independently discovered by scientists and by Foldit players outperforms previously published methods. Thus, online scientific game frameworks have the potential not only to solve hard scientific problems, but also to discover and formalize effective new strategies and algorithms.
CD95 triggers Orai1-mediated localized Ca2+entry, regulates recruitment of protein kinase C (PKC) β2, and prevents death-inducing signaling complex formation
Authors: Khadra Nadine , Bresson-Bepoldin Laurence , Penna Aubin , Chaigne-Delalande Benjamin , Ségui Bruno , Levade Thierry , Vacher Anne-Marie , Reiffers Josy , Ducret Thomas , Moreau Jean-François , Cahalan Michael D. , Vacher Pierre , Legembre Patrick
Published: November 2011

The death receptor CD95 plays a pivotal role in immune surveillance and immune tolerance. Binding of CD95L to CD95 leads to recruitment of the adaptor protein Fas-associated death domain protein (FADD), which in turn aggregates caspase-8 and caspase-10. Efficient formation of the CD95/FADD/caspase complex, known as the death-inducing signaling complex (DISC), culminates in the induction of apoptosis. We show that cells exposed to CD95L undergo a reorganization of the plasma membrane in which the Ca2+release-activated Ca2+channel Orai1 and the endoplasmic reticulum-resident activator stromal interaction molecule 1 colocalize with CD95 into a micrometer-sized cluster in which the channel elicits a polarized entry of calcium. Orai1 knockdown and expression of a dominant negative construct (Orai1E106A) reveal that on CD95 engagement, the Orai1-driven localized Ca2+influx is fundamental to recruiting the Ca2+-dependent protein kinase C (PKC) β2 to the DISC. PKCβ2 in turn transiently holds the complex in an inactive status, preventing caspase activation and transmission of the apoptotic signal. This study identifies a biological role of Ca2+and the Orai1 channel that drives a transient negative feedback loop, introducing a lag phase in the early steps of the CD95 signal. We suggest that these localized events provide a time of decision to prevent accidental cell death.
Modulation of the feedback-related negativity by instruction and experience
Authors: Walsh Matthew M. , Anderson John R.
Published: November 2011

A great deal of research focuses on how humans and animals learn from trial-and-error interactions with the environment. This research has established the viability of reinforcement learning as a model of behavioral adaptation and neural reward valuation. Error-driven learning is inefficient and dangerous, however. Fortunately, humans learn from nonexperiential sources of information as well. In the present study, we focused on one such form of information, instruction. We recorded event-related potentials as participants performed a probabilistic learning task. In one experiment condition, participants received feedback only about whether their responses were rewarded. In the other condition, they also received instruction about reward probabilities before performing the task. We found that instruction eliminated participants’ reliance on feedback as evidenced by their immediate asymptotic performance in the instruction condition. In striking contrast, the feedback-related negativity, an event-related potential component thought to reflect neural reward prediction error, continued to adapt with experience in both conditions. These results show that, whereas instruction may immediately control behavior, certain neural responses must be learned from experience.
Existence of a novel clathrin-independent endocytic pathway in yeast that depends on Rho1 and formin
Authors: Prosser Derek C. , Drivas Theodore G. , Maldonado-Báez Lymarie , Wendland Beverly
Published: November 2011

Yeast is a powerful model organism for dissecting the temporal stages and choreography of the complex protein machinery during endocytosis. The only known mechanism for endocytosis in yeast is clathrin-mediated endocytosis, even though clathrin-independent endocytic pathways have been described in other eukaryotes. Here, we provide evidence for a clathrin-independent endocytic pathway in yeast. In cells lacking the clathrin-binding adaptor proteins Ent1, Ent2, Yap1801, and Yap1802, we identify a second endocytic pathway that depends on the GTPase Rho1, the downstream formin Bni1, and the Bni1 cofactors Bud6 and Spa2. This second pathway does not require components of the better-studied endocytic pathway, including clathrin and Arp2/3 complex activators. Thus, our results reveal the existence of a second pathway for endocytosis in yeast, which suggests similarities with the RhoA-dependent endocytic pathways of mammalian cells.
A deep-level analysis of Ni–Au/AlN/(1 1 1) p+-Si metal–insulator–semiconductor capacitors
Authors: Simoen E , Visalli D , Van Hove M , Leys M , Borghs G
Published: November 2011

Deep levels formed by the growth of a 200 nm AlN buffer layer on highly B-doped (1 1 1) Czochralski Si substrates are investigated by deep-level transient spectroscopy on metal–insulator–semiconductor capacitors. The spectra reveal both a high density of interface states and a high concentration of extended defects in the silicon substrate. Annealing of the AlN buffer for 2840 s in NH3/H2 at 1130 °C, corresponding to the thermal budget for further growth of the AlGaN/GaN layers for high-voltage power devices, results in a reduction of the density of interface states and a transformation of the near-interface bulk defects. At the same time, it is found that annealing reduces the tensile strain and the bow of the AlN/Si substrates.
Investigation of ion implantation induced intermixing in InP based quaternary quantum wells
Authors: Du S C , Fu L , Tan H H , Jagadish C
Published: November 2011

In this work, proton and arsenic ion implantation induced intermixing in AlInGaAs/InGaAs quantum wells (QWs) has been studied and compared with InGaAsP/InGaAs QWs. The different interdiffusion results obtained from the two QW structures are compared and discussed based on thermal annealing studies, different implantation ion species, dynamic annealing effects of barrier layers, as well as interdiffusion mechanisms.
Systematical, experimental investigations on LiMgZ (Z = P, As, Sb) wide band gap semiconductors
Authors: Beleanu Andreea , Mondeshki Mihail , Juan Quin , Casper Frederick , Felser Claudia , Porcher Florence
Published: November 2011

This work reports on the experimental investigation of wide band gap compounds LiMgZ (Z = P, As, Sb), which are promising candidates for opto-electronics and anode materials for lithium batteries. The compounds crystallize in the cubic (C1
b
) MgAgAs structure (space group
). The polycrystalline samples are synthesized by solid-state reaction methods. X-ray and neutron diffraction measurements show homogeneous, single-phased samples. The electronic properties are studied using the direct current method. Additionally, UV–Vis diffuse reflectance spectra are recorded in order to investigate the band gap nature. The measurements show that all compounds exhibit semiconducting behaviour with direct band gaps of 1.0–2.3 eV depending on the Z element. A decrease in the peak widths in the static 7Li nuclear magnetic resonance spectra with increasing temperature is observed, which can be directly related to an increase in Li ion mobility.
Exploring the doping effects of Ag in p-type PbSe compounds with enhanced thermoelectric performance
Authors: Wang Shanyu , Zheng Gang , Luo Tingting , She Xiaoyu , Li Han , Tang Xinfeng
Published: November 2011

In this study, we prepared a series of Ag-doped PbSe bulk materials by a melting–quenching process combined with a subsequent spark plasma sintering process, and systematically investigated the doping effects of Ag on the thermoelectric properties. Ag substitution in the Pb site does not introduce resonant levels near the valence band edge or detectable change in the density of state in the vicinity of the Fermi level, but moves the Fermi level down and increases the carrier concentration to a maximum value of ∼4.7 × 1019 cm−3 which is still insufficient for heavily doped PbSe compounds. Nonetheless, the non-monotonic variation in carrier concentration with increasing Ag content indicates that Ag doping reaches the solution limit at ∼1.0% and the excessive Ag presumably acts as donors in the materials. Moreover, the large energy gap of the PbSe-based material wipes off significant ‘roll-over’ in the Seebeck coefficient at elevated temperatures which gives rise to high power factors, being comparable to p-type Te analogues. Consequently, the maximum ZT reaches ∼1.0 for the 1.5% Ag-doped samples with optimized carrier density, which is ∼70% improvement in comparison with an undoped sample and also superior to the commercialized p-type PbTe materials.
Asymptotic periodicity of grade associated to multigraded modules
Authors: Hayasaka Futoshi
Published: November 2011

Let

R
R

be a Noetherian

N

r

\mathbb {N}^r

-graded ring generated in degrees

d

1

,
…
,

d

r

\textbf {d}_1, \dots , \textbf {d}_r

which are linearly independent vectors over

R

\mathbb {R}

, and let

a

\mathfrak a

be an ideal in

R

0

R_\textbf {0}

. In this paper, we investigate the asymptotic behavior of the grade of the ideal

a

\mathfrak a

on the homogeneous components

M

n

M_\textbf {n}

of a finitely generated

Z

r

\mathbb {Z}^r

-graded

R
R

-module

M
M

and show that the periodicity occurs in a cone.
Development of an Assay for Rapid Detection and Quantification of Verticillium dahliae in Soil
Authors: Bilodeau Guillaume J. , Koike Steven T. , Uribe Pedro , Martin Frank N.
Published: November 2011

Verticillium dahliae is responsible for Verticillium wilt on a wide range of hosts, including strawberry, on which low soil inoculum densities can cause significant crop loss. Determination of inoculum density is currently done by soil plating but this can take 6 to 8 weeks to complete and delay the grower's ability to make planting decisions. To provide a faster means for estimating pathogen populations in the soil, a multiplexed TaqMan real-time polymerase chain reaction (PCR) assay based on the ribosomal DNA (rDNA) intergenic spacer (IGS) was developed for V. dahliae. The assay was specific for V. dahliae and included an internal control for evaluation of inhibition due to the presence of PCR inhibitors in DNA extracted from soil samples. An excellent correlation was observed in regression analysis (R2 = 0.96) between real-time PCR results and inoculum densities determined by soil plating in a range of field soils with pathogen densities as low as 1 to 2 microsclerotia/g of soil. Variation in copy number of the rDNA was also evaluated among isolates by SYBR Green real-time PCR amplification of the V. dahliae-specific amplicon compared with amplification of several single-copy genes and was estimated to range from ≈24 to 73 copies per haploid genome, which translated into possible differences in results among isolates of ≈1.8 cycle thresholds. Analysis of the variation in results of V. dahliae quantification among extractions of the same soil sample indicated that assaying four replicate DNA extractions for each field sample would provide accurate results. A TaqMan assay also was developed to help identify colonies of V. tricorpus on soil plates.
The TOPLESS Interactome: A Framework for Gene Repression in Arabidopsis
Authors: Causier Barry , Ashworth Mary , Guo Wenjia , Davies Brendan
Published: November 2011

Transcription factors activate or repress target gene expression or switch between activation and repression. In animals and yeast, Groucho/Tup1 corepressor proteins are recruited by diverse transcription factors to induce context-specific transcriptional repression. Two groups of Groucho/Tup1-like corepressors have been described in plants. LEUNIG and LEUNIG_HOMOLOG constitute one group and TOPLESS (TPL) and the four TPL-related (TPR) corepressors form the other. To discover the processes in which TPL and the TPR corepressors operate, high-throughput yeast two-hybrid approaches were used to identify interacting proteins. We found that TPL/TPR corepressors predominantly interact directly with specific transcription factors, many of which were previously implicated in transcriptional repression. The interacting transcription factors reveal that the TPL/TPR family has been coopted multiple times to modulate gene expression in diverse processes, including hormone signaling, stress responses, and the control of flowering time, for which we also show biological validation. The interaction data suggest novel mechanisms for the involvement of TPL/TPR corepressors in auxin and jasmonic acid signaling. A number of short repression domain (RD) sequences have previously been identified in Arabidopsis (Arabidopsis thaliana) transcription factors. All known RD sequences were enriched among the TPL/TPR interactors, and novel TPL-RD interactions were identified. We show that the presence of RD sequences is essential for TPL/TPR recruitment. These data provide a framework for TPL/TPR-dependent transcriptional repression. They allow for predictions about new repressive transcription factors, corepressor interactions, and repression mechanisms and identify a wide range of plant processes that utilize TPL/TPR-mediated gene repression.
Gravistimulation Changes the Accumulation Pattern of the CsPIN1 Auxin Efflux Facilitator in the Endodermis of the Transition Zone in Cucumber Seedlings
Authors: Watanabe Chiaki , Fujii Nobuharu , Yanai Kenichi , Hotta Takuya , Kim Dai-Hee , Kamada Motoshi , Sasagawa-Saito Yuko , Nishimura Takeshi , Koshiba Tomokazu , Miyazawa Yutaka , Kim Kyung-Min , Takahashi Hideyuki
Published: November 2011

Cucumber (Cucumis sativus) seedlings grown in a horizontal position develop a specialized protuberance (or peg) on the lower side of the transition zone between the hypocotyl and the root. This occurs by suppressing peg formation on the upper side via a decrease in auxin resulting from a gravitational response. However, the gravity-stimulated mechanism of inducing asymmetric auxin distribution in the transition zone is poorly understood. The gravity-sensing tissue responsible for regulating auxin distribution in the transition zone is thought to be the endodermal cell. To characterize the gravity-stimulated mechanism, the auxin efflux facilitator PIN-FORMED1 (CsPIN1) in the endodermis was identified and the localization of CsPIN1 proteins during the gravimorphogenesis of cucumber seedlings was examined. Immunohistochemical analysis revealed that the accumulation pattern of CsPIN1 protein in the endodermal cells of the transition zone of cucumber seedlings grown horizontally differed from that of plants grown vertically. Gravistimulation for 30 min prompted changes in the accumulation pattern of CsPIN1 protein in the endodermis as well as the asymmetric distribution of auxin in the transition zone. Furthermore, 2,3,5-triiodobenzoic acid inhibited the differential distribution of auxin as well as changes in the accumulation pattern of CsPIN1 in the endodermis of the transition zone during gravistimulation. These results suggest that the altered pattern of CsPIN1 accumulation in the endodermis in response to gravistimulation influences lateral auxin transport through the endodermis, resulting in asymmetric auxin distribution in the transition zone.
Genetic diversity and population structure of five Ethiopian chicken ecotypes
Authors: Goraga Z. , Weigend S. , Brockmann G.
Published: November 2011

This study aimed to analyse the genetic diversity and population structure of five Ethiopian chicken ecotypes (N = 155), which were compared with six commercial purebreds (N = 180). For the analysis of genetic diversity, 26 AVIANDIV microsatellite markers were used. The number of alleles in Ethiopian ecotypes ranged from 2 to 19 per locus, with a mean of 6.1. The average observed heterozygosity within ecotype varied between 0.53 and 0.57. The overall heterozygote deficiency (FIT) in Ethiopian ecotypes was 0.124 ± 0.037. Over 68% of FIT was because of within‐ecotype deficiency (FIS). In the phylogenetic tree, Ethiopian ecotypes clustered into two groups. The analysis of the relationship between populations using the structure program provided further evidence for the occurrence of at least two subgroups in the Ethiopian ecotypes. Findings of this study may provide the background for future studies to identify the origin of the two gene pools representing the Ethiopian chicken ecotypes and to characterize the gene variants influencing economically important traits.
Comparison of SNPs and microsatellites for assessing the genetic structure of chicken populations
Authors: Gärke C. , Ytournel F. , Bed’hom B. , Gut I. , Lathrop M. , Weigend S. , Simianer H.
Published: November 2011

Many studies in human genetics compare informativeness of single‐nucleotide polymorphisms (SNPs) and microsatellites (single sequence repeats; SSR) in genome scans, but it is difficult to transfer the results directly to livestock because of different population structures. The aim of this study was to determine the number of SNPs needed to obtain the same differentiation power as with a given standard set of microsatellites. Eight chicken breeds were genotyped for 29 SSRs and 9216 SNPs. After filtering, only 2931 SNPs remained. The differentiation power was evaluated using two methods: partitioning of the Euclidean distance matrix based on a principal component analysis (PCA) and a Bayesian model‐based clustering approach. Generally, with PCA‐based partitioning, 70 SNPs provide a comparable resolution to 29 SSRs. In model‐based clustering, the similarity coefficient showed significantly higher values between repeated runs for SNPs compared to SSRs. For the membership coefficients, reflecting the proportion to which a fraction segment of the genome belongs to the ith cluster, the highest values were obtained for 29 SSRs and 100 SNPs respectively. With a low number of loci (29 SSRs or ≤100 SNPs), neither marker types could detect the admixture in the Gödöllö Nhx population. Using more than 250 SNPs allowed a more detailed insight into the genetic architecture. Thus, the admixed population could be detected. It is concluded that breed differentiation studies will substantially gain power even with moderate numbers of SNPs.
Identification and characterization of C106R, a novel mutation in the DNA‐binding domain of GCMB, in a family with autosomal‐dominant hypoparathyroidism
Authors: Yi Hyon‐Seung , Eom Young Sil , Park Ie Byung , Lee Sangho , Hong Suntaek , Jüppner Harald , Mannstadt Michael , Lee Sihoon
Published: November 2011

Overview  Glial cells missing B (GCMB) is a transcription factor that is expressed in the parathyroid hormone (PTH)‐secreting cells of the parathyroid glands. Several mutations in GCMB have been reported to cause hypoparathyroidism (HP). We identified a family with two individuals in two generations (mother and son), who are affected by autosomal‐dominant hypoparathyroidism (AD‐HP). A novel heterozygous mutation in exon 2 of GCMB was identified in both affected individuals that changes cysteine at position 106 of the putative DNA‐binding domain of GCMB to arginine (C106R).

Methods  We performed mutational analysis of the genes encoding GCMB, pre‐pro PTH, GATA3 and CaSR using polymerase chain reaction (PCR)‐amplified genomic DNA. The identified GCMB mutant was characterized by functional studies including nuclear localization, electrophoretic mobility shift assays (EMSA) and luciferase reporter assays, and homology modelling was performed to generate a three‐dimensional structural model for the DNA‐binding domain of GCMB to predict the structural consequences of the identified mutation.

Results  The C106R mutant of GCMB failed to interact with the DNA consensus recognition motif, as determined by EMSA. Furthermore, in comparison with wild‐type GCMB, the C106R mutant demonstrated reduced transactivation in luciferase reporter assays; however, the mutant GCMB failed to reduce the activity of the wild‐type protein. Consistent with the EMSA findings, homology modelling analysis suggested that replacement of cysteine 106 with arginine would interfere with DNA binding.

Conclusions  We have identified a novel GCMB mutation that may explain AD‐HP in our family. However, the exact mechanism by which this heterozygous mutation leads to the disease in the described family remains to be elucidated.
Predicting the onset of Addison’s disease: ACTH, renin, cortisol and 21‐hydroxylase autoantibodies
Authors: Baker Peter R. , Nanduri Priyaanka , Gottlieb Peter A. , Yu Liping , Klingensmith Georgeanna J. , Eisenbarth George S. , Barker Jennifer M.
Published: November 2011

Context  Autoantibodies to 21‐hydroxylase (21OH‐AA) precede onset of autoimmune Addison’s disease (AD). Progression to AD can take months to years, and early detection of metabolic decompensation may prevent morbidity and mortality.

Objective  To define optimal methods of predicting progression to overt AD (defined by subnormal peak cortisol response to Cosyntropin) in 21OH‐AA+ individuals.

Design, Setting and Participants  Individuals were screened for 21OH‐AA at the Barbara Davis Center from 1993 to 2011. Subjects positive for 21OH‐AA (n = 87) were tested, and the majority prospectively followed for the development of Addison’s disease, including seven diagnosed with AD upon 21OH‐AA discovery (discovered), seven who progressed to AD (progressors) and 73 nonprogressors.

Main Outcome Measured  Plasma renin activity (PRA), ACTH, baseline cortisol, peak cortisol and 21OH‐AA were measured at various time points relative to diagnosis of AD or last AD‐free follow‐up.

Results  Compared with nonprogressors, in the time period 2 months–2 years prior to the onset of AD, progressors were significantly more likely to have elevated ACTH (11–22 pm, P < 1E‐4), with no significant differences in mean PRA (P = 0·07) or baseline cortisol (P = 0·08), and significant but less distinct differences seen with 21OH‐AA levels (P < 1E‐4) and poststimulation cortisol levels (P = 6E‐3).

Conclusion  Moderately elevated ACTH is a more useful early indicator of impending AD than 21OH‐AA, PRA or peak cortisol, in the 2 months–2 years preceding the onset of AD.
Intensity of pituitary adenoma on T2‐weighted magnetic resonance imaging predicts the response to octreotide treatment in newly diagnosed acromegaly
Authors: Heck Ansgar , Ringstad Geir , Fougner Stine L. , Casar‐Borota Olivera , Nome Terje , Ramm‐Pettersen Jon , Bollerslev Jens
Published: November 2011

Background  Primary, preoperative medical treatment is an option in selected patients with acromegaly, but a subset of patients respond poorly. Valid prediction of response to somatostatin analogues (SA) might thus alter treatment stratification. The aims of this study were to assess whether T2 signal intensity could determine long‐term response to first‐line SA treatment and to assess clinical and biochemical baseline characteristics, as well as histological subtype in relation to the magnetic resonance imaging (MRI) appearances.

Methods  In 45 newly diagnosed patients, T2‐weighted signal intensity of the tumour was classified into hypo‐, iso‐ or hyperintense. Biochemical and clinical baseline variables for the three groups were compared. In 25 patients primarily treated with long‐acting SA for a median of 6 months [interquartile range (IQR):155–180 days], GH and IGF‐1 reduction was assessed, and in 34 cases, immunohistochemical granulation pattern was evaluated.

Results  The results showed that 12 (27%) adenomas were hypointense, 15 (33%) isointense and 18 (40%) hyperintense. Median IGF‐1 [ratio IGF‐1/ULN; (upper limit of normal)] was 3·5 (2·3–4·9), 2·9 (2·6–3·8) and 1·9 (1·3–2·6), respectively (P = 0·006 for difference between groups). Median GH values (μg/l) of a 3‐ to 5‐point profile were 17·5 (6·1–35), 9·3 (6·0–32·5) and 4·1 (1·5–8·3), (P = 0·025).

Median IGF‐1 reduction (% of baseline) after first‐line SA treatment was 51 (49–70), 36 (19–74) and 13 (5–42) (P = 0·03); median reduction in GH (% of baseline) was 86 (72–94), 78 (62–85) and 46 (1–70) (P = 0·02).

T2 hyperintensity was associated with sparse granulation pattern on immunohistochemistry.

Conclusion  In patients with acromegaly, T2 signal intensity at diagnosis correlates with histological features and predicts biochemical outcome of first‐line SA treatment.
Forecasting climate change impacts to plant community composition in the Sonoran Desert region
Authors: Munson Seth M. , Webb Robert H. , Belnap Jayne , Andrew Hubbard J. , Swann Don E. , Rutman Sue
Published: November 2011

Hotter and drier conditions projected for the southwestern United States can have a large impact on the abundance and composition of long‐lived desert plant species. We used long‐term vegetation monitoring results from 39 large plots across four protected sites in the Sonoran Desert region to determine how plant species have responded to past climate variability. This cross‐site analysis identified the plant species and functional types susceptible to climate change, the magnitude of their responses, and potential climate thresholds. In the relatively mesic mesquite savanna communities, perennial grasses declined with a decrease in annual precipitation, cacti increased, and there was a reversal of the Prosopis velutina expansion experienced in the 20th century in response to increasing mean annual temperature (MAT). In the more xeric Arizona Upland communities, the dominant leguminous tree, Cercidium microphyllum, declined on hillslopes, and the shrub Fouquieria splendens decreased, especially on south‐ and west‐facing slopes in response to increasing MAT. In the most xeric shrublands, the codominant species Larrea tridentata and its hemiparasite Krameria grayi decreased with a decrease in cool season precipitation and increased aridity, respectively. This regional‐scale assessment of plant species response to recent climate variability is critical for forecasting future shifts in plant community composition, structure, and productivity.
Social networking for adolescents with severe haemophilia
Authors: KHAIR K. , HOLLAND M. , CARRINGTON S.
Published: November 2011

Summary.  Access to modern treatments allows adolescents with haemophilia to manage their haemophilia at home, with improved treatment outcomes and quality of life, but has reduced peer support and the potential for experiential learning from older peers. Social networking, aided by modern communication technologies, may offer health benefits through peer support. We sought to assess whether or not disease‐specific social networking could benefit adolescents with severe haemophilia. A total of 150 adolescents (aged 10–18) with severe haemophilia A or B from 11 UK treatment centres or those who had attended focus groups to explore the potential for a social network designed specifically for their use were surveyed. Teenage boys with severe haemophilia in the UK who responded to an online and paper questionnaire (n = 47; 31% response rate) rarely knew of or socialized with others with haemophilia outside their families. Two‐thirds of respondents said they would like to meet others. For 70% of boys, parents were the major source of information about haemophilia, yet more than half said they often had trouble finding answers to their questions. These boys frequently used online social networks to chat with friends. Adolescents with severe haemophilia frequently have limited contact with others and many wish to have greater contact. They may benefit from peer support and experiential learning gained through online social networking. The SixVibe restricted access social network is to be launched in 2011. It includes features designed to promote and facilitate the development of peer‐to peer disease management skills for adolescents with severe haemophilia.
Effects of food ration on SMR: influence of food consumption on individual variation in metabolic rate in juvenile coho salmon (Onchorhynchus kisutch)
Authors: Van Leeuwen Travis E. , Rosenfeld Jordan S. , Richards Jeffrey G.
Published: November 2011

1. Consistency of differences in standard metabolic rate (SMR) between individual juvenile salmonids and the apparently limited ability of individuals to regulate their SMR has led many researchers to conclude that differences in individual SMR are fixed (i.e. genetic).

2. To test for the effects of food ration on individual performance and metabolism, SMR was estimated by measuring oxygen consumption using flow‐through respirometry on individually separated young of the year coho salmon (Oncorhynchus kisutch) placed on varying food rations over a period of 44 days.

3. Results demonstrate that the quantity of food consumed directly affects SMR of juvenile coho salmon, independent of specific dynamic action (SDA, an elevation in metabolic rate from the increased energy demands associated with digestion immediately following a meal) and indicates that higher food consumption is a cause of elevated SMR rather than a consequence of it. Juvenile coho salmon therefore demonstrated an ability to regulate their SMR according to food availability and ultimately food consumption.

4. This study indicates that food consumption may play a pivotal role in understanding individual variation in SMR independent of inherent genetic differences. We suggest that studies involving SMR need to be cautious about the effects of intra‐individual differences in food consumption in communal tanks or in different microhabitats in the wild as disproportionate food consumption may contribute more to variation in SMR than intrinsic (genetic) factors.

5. In general, our results suggest that evolutionary changes in SMR are likely a response to selection on food consumption and growth, rather than SMR itself.
Full compliance with harvest regulations yields ecological benefits: Northern Gulf of California case study
Authors: Ainsworth Cameron H. , Morzaria‐Luna Hem Nalini , Kaplan Isaac C. , Levin Phillip S. , Fulton Elizabeth A.
Published: November 2011

1. The Northern Gulf of California is an ecologically important marine area with a high degree of biodiversity, endemism and productivity. Mounting conservation concerns have prompted researchers to propose new management regulations, restricting fishing and protecting sensitive species. Compliance with existing regulations is poor. Rules that are currently in place, if followed, may go a long way towards achieving the ecological goals of management.

2. We conduct a review of existing fisheries regulations in this area. Then, using a spatially explicit marine ecosystem model (Atlantis), we estimate the benefits of compliance with existing fisheries regulations.

3. Under a full compliance scenario, we find large increases in protected species biomass within 25 years and a slowed rate of ecosystem degradation because of fishing. However, full compliance costs the fishing industry about 30% of its annual revenue.

4. We parse out the benefits offered by management instruments (including spatial management protections, seasonal fishery closures, gear restrictions, cessation of illegal fishing and vessel buy‐out programmes) and conclude that a suite of measures is needed to address major conservation objectives.

5. Synthesis and applications. This exercise quantifies the benefits of improved fisheries enforcement and provides a benchmark by which the value of future regulatory amendments can be assessed. Where compliance with existing regulations is poor, conservation goals may be better served by strengthening enforcement than by enacting new rules and legislation.
Restoration of the fire–grazing interaction in Artemisia filifolia shrubland
Authors: Winter Stephen L. , Fuhlendorf Samuel D. , Goad Carla L. , Davis Craig A. , Hickman Karen R. , Leslie Jr David M.
Published: November 2011

1. Patterns of landscape heterogeneity are crucial to the maintenance of biodiversity in shrublands and grasslands, yet management practices in these ecosystems typically seek to homogenize landscapes. Furthermore, there is limited understanding of how the interaction of ecological processes, such as fire and grazing, affects patterns of heterogeneity at different spatial scales.

2. We conducted research in Artemisia filifolia (Asteraceae) shrublands located in the southern Great Plains of North America to determine the effect of restoring the fire–grazing interaction on vegetation structure. Data were collected for 3 years in replicated pastures grazed by cattle Bos taurus where the fire–grazing interaction had been restored (fire and grazing = treatment pastures) and in pastures that were grazed but remained unburned (grazing only, no fire = control pastures). The effect of the fire–grazing interaction on heterogeneity (variance) of vegetation structure was assessed at scales from 12·5 m2 to 609 ha.

3. Most measurements of vegetation structure within treatment pastures differed from control pastures for 1–3 years after being burned but were thereafter similar to the values found in unburned control pastures.

4. Treatment pastures were characterized by a lower amount of total heterogeneity and a lower amount of heterogeneity through time.

5. Heterogeneity of vegetation structure tended to decrease as the scale of measurement increased in both treatment and control pastures. There was deviation from this trend, however, in the treatment pastures that exhibited much higher heterogeneity at the patch scale (mean patch size = 202 ha) of measurement, the scale at which patch fires were conducted.

6.
Synthesis and applications. Vegetation structure in A. filifolia shrublands of our study was readily altered by the fire–grazing interaction but also demonstrated substantial resilience to these effects. The fire–grazing interaction also changed the total amount of heterogeneity characterizing this system, the scale at which heterogeneity in this system was expressed and the amount of heterogeneity expressed through time. Land managers seeking to impose a shifting mosaic of heterogeneity on this vegetation type can do so by restoring the fire–grazing interaction with potential conservation benefits similar to what has been achieved in other ecosystems where historic cycles of disturbance and rest have been restored.