bluuebunny/crossref_metadata_2025 huggingface dataset:
ADP-ribosylation of human defensin HNP-1 results in the replacement of the modified arginine with the noncoded amino acid ornithine
Authors: Stevens Linda A. , Levine Rodney L. , Gochuico Bernadette R. , Moss Joel
Published: November 2009

Defensins (e.g., human neutrophil peptides, or HNPs) contribute to innate immunity through diverse actions, including microbial killing; high concentrations are present in the lung in response to inflammation. Arginines are critical for HNP activity, which is decreased by their replacement with ornithine. ADP-ribosyltransferases (ARTs) catalyze transfer of ADP-ribose from NAD to an acceptor arginine in a protein substrate, whereas ADP-ribosylarginine hydrolases release ADP-ribose. ART1 on the surface of airway epithelial cells ADP-ribosylated HNP-1 specifically on arginines 14 and 24, with ADP-ribosylation altering biological activity. Di- and mono-ADP-ribosylated HNP-1 were isolated from bronchoalveolar lavage fluid (BALF) of patients with asthma and idiopathic pulmonary fibrosis (IPF), suggesting a role for ADP-ribosylation in disease. In the present study, we observed that ART1-catalyzed ADP-ribosylation of HNP-1 in vitro generated a product with ADP-ribose on arginine 24, and ornithine replacing arginine at position 14. We hypothesized that ADP-ribosylarginine is susceptible to a nonenzymatic hydrolytic reaction yielding ornithine. On incubation of di- or mono-ADP-ribosyl-HNP-1 at 37 °C, ADP-ribosylarginine was partially replaced by ornithine, whereas ornithine was not detected by amino acid analysis and mass spectrometry of unmodified HNP-1 incubated under the same conditions. Further, ornithine was produced from the model compound, ADP-ribosylarginine. BALF from an IPF patient contained ADP-ribosyl-HNP-ornithine as well as mono- and di-ADP-ribosylated HNP-1, consistent with in vivo conversion of arginine to ornithine. Targeted ADP-ribosylation of specific arginines by transferases, resulting in their replacement with ornithine, is an alternative pathway for regulation of protein function through posttranslational modification.
Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
Authors: McGuffin Liam J. , Roche Daniel B.
Published: November 2009

Motivation: The accurate prediction of the quality of 3D models is a key component of successful protein tertiary structure prediction methods. Currently, clustering- or consensus-based Model Quality Assessment Programs (MQAPs) are the most accurate methods for predicting 3D model quality; however, they are often CPU intensive as they carry out multiple structural alignments in order to compare numerous models. In this study, we describe ModFOLDclustQ—a novel MQAP that compares 3D models of proteins without the need for CPU intensive structural alignments by utilizing the Q measure for model comparisons. The ModFOLDclustQ method is benchmarked against the top established methods in terms of both accuracy and speed. In addition, the ModFOLDclustQ scores are combined with those from our older ModFOLDclust method to form a new method, ModFOLDclust2, that aims to provide increased prediction accuracy with negligible computational overhead.

Results: The ModFOLDclustQ method is competitive with leading clustering-based MQAPs for the prediction of global model quality, yet it is up to 150 times faster than the previous version of the ModFOLDclust method at comparing models of small proteins (<60 residues) and over five times faster at comparing models of large proteins (>800 residues). Furthermore, a significant improvement in accuracy can be gained over the previous clustering-based MQAPs by combining the scores from ModFOLDclustQ and ModFOLDclust to form the new ModFOLDclust2 method, with little impact on the overall time taken for each prediction.

Availability: The ModFOLDclustQ and ModFOLDclust2 methods are available to download from http://www.reading.ac.uk/bioinf/downloads/

Contact:  l.j.mcguffin@reading.ac.uk
Targeting PML‐RARα and Oncogenic Signaling Pathways by Chinese Herbal Mixture Tien-Hsien Liquid in Acute Promyelocytic Leukemia NB4 Cells
Authors: Yao Chih-Jung , Yang Chia-Ming , Chuang Shuang-En , Yan Jiann-Long , Liu Chun-Yen , Chen Suz-Wen , Yan Kun-Huang , Lai Tung-Yuan , Lai Gi-Ming
Published: November 2009

Tien-Hsien Liquid (THL) is a Chinese herbal mixture that has been used worldwide as complementary treatment for cancer patients in the past decade. Recently, THL has been shown to induce apoptosis in various types of solid tumor cells in vitro. However, the underlying molecular mechanisms have not yet been well elucidated. In this study, we explored the effects of THL on acute promyelocytic leukemia (APL) NB4 cells, which could be effectively treated by some traditional Chinese remedies containing arsenic trioxide. The results showed THL could induce G2/M arrest and apoptosis in NB4 cells. Accordingly, the decrease of cyclin A and B1 were observed in THL‐treated cells. The THL‐induced apoptosis was accompanied with caspase‐3 activation and decrease of PML‐RARα fusion protein. Moreover, DNA methyltransferase 1 and oncogenic signaling pathways such as Akt/mTOR, Stat3 and ERK were also down‐regulated by THL. By using ethyl acetate extraction and silica gel chromatography, an active fraction of THL named as EAS5 was isolated. At about 0.5–1% of the dose of THL, EAS5 appeared to have most of THL‐induced multiple molecular targeting effects in NB4 cells. Based on the findings of these multi‐targeting effects, THL might be regarding as a complementary and alternative therapeutic agent for refractory APL.
The predation of farmed salmon by South American sea lions (Otaria flavescens) in southern Chile
Authors: Vilata Juan , Oliva Doris , Sepúlveda Maritza
Published: November 2009

Vilata, J., Oliva, D., and Sepúlveda, M. 2010. The predation of farmed salmon by South American sea lions (Otaria flavescens) in southern Chile. – ICES Journal of Marine Science, 67: 475–482. The South American sea lion Otaria flavescens is abundant off southern Chile. Because Chilean salmon farming has experienced an explosive growth in the past two decades, interactions between O. flavescens and this industry have increased. Fieldwork, including in situ behavioural observations, was carried out at three salmon farms off southern Chile from May to July 2008. The aim was to analyse possible patterns in the interactions and to evaluate whether they were influenced by the endogenous circa-rhythms of the species, prey size, tidal flux, and the use of an acoustic harassment device (AHD). The results showed that the attacks by O. flavescens followed seasonal patterns, with salmon predated more in autumn and winter, and daily patterns, with more interactions at night. In addition, attacks were more frequent on larger salmon, suggesting the existence of a prey-size preference. More sea lions were sighted at the ebb and flow tide peaks, when currents are stronger, suggesting that currents linked to tidal flux might facilitate the access of the sea lions to the farmed salmon. Although the use of AHDs appeared positive at one site, there is a strong suspicion that their efficacy may be site-specific.
Deformation micromechanisms of collagen fibrils under uniaxial tension
Authors: Tang Yuye , Ballarini Roberto , Buehler Markus J. , Eppell Steven J.
Published: November 2009

Collagen, an essential building block of connective tissues, possesses useful mechanical properties due to its hierarchical structure. However, little is known about the mechanical properties of collagen fibril, an intermediate structure between the collagen molecule and connective tissue. Here, we report the results of systematic molecular dynamics simulations to probe the mechanical response of initially unflawed finite size collagen fibrils subjected to uniaxial tension. The observed deformation mechanisms, associated with rupture and sliding of tropocollagen molecules, are strongly influenced by fibril length, width and cross-linking density. Fibrils containing more than approximately 10 molecules along their length and across their width behave as representative volume elements and exhibit brittle fracture. Shorter fibrils experience a more graceful ductile-like failure. An analytical model is constructed and the results of the molecular modelling are used to find curve-fitted expressions for yield stress, yield strain and fracture strain as functions of fibril structural parameters. Our results for the first time elucidate the size dependence of mechanical failure properties of collagen fibrils. The associated molecular deformation mechanisms allow the full power of traditional material and structural engineering theory to be applied to our understanding of the normal and pathological mechanical behaviours of collagenous tissues under load.
Alishewanella agri sp. nov., isolated from landfill soil
Authors: Kim Min-Soo , Jo Seon Kyung , Roh Seong Woon , Bae Jin-Woo
Published: November 2009

Strain BL06Twas isolated from landfill soil in Pohang, Korea. Strain BL06Tis Gram-negative, aerobic, non-motile and rod-shaped. For growth, the NaCl range is 0–6 % (w/v), the temperature range is 10–44 °C and the pH range is 5.5–12.0. Based on the 16S rRNA gene and gyrase B (gyrB) gene sequences, phylogenetic analysis showed that strain BL06Tis associated with the genusAlishewanellaand related closely to the type strains ofAlishewanellaspecies (98.8 % 16S rRNA gene sequence similarity toAlishewanella aestuarii, 98.7 % toAlishewanella fetalisand 98.5 % toAlishewanella jeotgali). Physiological and biochemical tests verified that strain BL06Tis genotypically and phenotypically different from previously described species in the genusAlishewanella. DNA–DNA hybridization experiments showed that relatedness between the genomic DNA of strain BL06Tand type strains of otherAlishewanellaspecies is <41 %. These findings suggest strongly that the strain represents a novel species, despite high 16S rRNA gene sequence similarity between strain BL06Tand related strains. Therefore, strain BL06T(=KCTC 22400T=JCM 15597T) is proposed to represent a novel species in the genusAlishewanella, namedAlishewanella agrisp. nov.
Vagococcus penaei sp. nov., isolated from spoilage microbiota of cooked shrimp (Penaeus vannamei)
Authors: Jaffrès Emmanuel , Prévost Hervé , Rossero Albert , Joffraud Jean-Jacques , Dousset Xavier
Published: November 2009

A polyphasic taxonomic study, using phenotypic, phylogenetic and genotypic characterization, was performed on five Gram-stain-positive, catalase-negative, coccus-shaped Vagococcus-like bacteria isolated from the spoilage microbiota of cooked shrimp. Comparative 16S rRNA gene sequence analysis indicated that the isolates belonged to the genus Vagococcus. The five isolates shared 100% 16S rRNA gene sequence similarity, and representative strain CD276T formed a branch that was distinct from the type strains of the six recognized species of the genus Vagococcus (Vagococcus fluvialis CCUG 32704T, V. salmoninarum NCFB 2777T, V. lutrae CCUG 39187T, V. fessus M2661/98/1T, V. carniphilus ATCC BAA-340T and V. elongatus PPC9T). The taxonomic position of strain CD276T was clarified using DNA–DNA hybridization, pulsed-field gel electrophoresis of whole-genome DNA, G+C content determination, cell-wall peptidoglycan typing, fatty acid analysis and biochemical characterization. On the basis of this evidence, a novel species, Vagococcus penaei sp. nov., is proposed. The type strain is CD276T (=LMG 24833T =CIP 109914T).
Flavobacterium glycines sp. nov., a facultative methylotroph isolated from the rhizosphere of soybean
Authors: Madhaiyan Munusamy , Poonguzhali Selvaraj , Lee Jung-Sook , Lee Keun Chul , Sundaram Subbiah
Published: November 2009

An aerobic, yellow-pigmented, facultatively methylotrophic, Gram-staining-negative, non-spore-forming bacterium, designated strain Gm-149T, was isolated from the rhizosphere of cultivated soybean in India. Cells were motile by gliding. The predominant cellular fatty acids were iso-C15 : 0, summed feature 3 (comprising iso-C15 : 0 2-OH and/or C16 : 1
ω7c), C16 : 0 3-OH and anteiso-C15 : 0, and the major isoprenoid quinone was MK-6. The G+C content of the genomic DNA of strain Gm-149T was 35.6 mol%. Comparative 16S rRNA gene sequence analysis showed that strain Gm-149T formed a distinct phyletic line within the genus Flavobacterium. Based on levels of pairwise 16S rRNA gene sequence similarity, strain Gm-149T was related most closely to the type strain of Flavobacterium daejeonense (97.1 %), but the level of DNA–DNA relatedness between these two strains was about 11.2 %. On the basis of phenotypic and genotypic data, strain Gm-149T is considered to represent a novel species of the genus Flavobacterium, for which the name Flavobacterium glycines sp. nov. is proposed. The type strain is Gm-149T (=ICMP 17618T=NBRC 105008T).
Paenibacillus prosopidis sp. nov., isolated from the nodules of Prosopis farcta
Authors: Valverde Angel , Fterich Amira , Mahdhi Mosbah , Ramírez-Bahena Martha-Helena , Caviedes Miguel A. , Mars Mohamed , Velázquez Encarna , Rodriguez-Llorente Ignacio D.
Published: November 2009

A bacterial strain, designated PW21T, was isolated from root nodules ofProsopis farctain Tunisia. Phylogenetic analysis based on 16S rRNA gene sequences placed the isolate into the genusPaenibacillus, with its closest relatives beingPaenibacillus glycanilyticusDS-1TandPaenibacillus castaneaeCh-32Twith identity values of 96.9 %. DNA–DNA hybridization measurements showed values of less than 25 % with respect to these two species. The isolate was a Gram-variable, motile and sporulating rod. Catalase activity was positive and oxidase activity was weakly positive. Aesculin, CM-cellulose, xylan and starch were hydrolysed but casein and gelatin were not. Acetoin production was weakly positive and nitrate reduction was negative. Urease production was negative. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the predominant menaquinone and anteiso-C15 : 0, iso-C16 : 0and iso-C15 : 0were the major fatty acids. Major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, a glycolipid, six phospholipids, an unidentified lipid and two unknown aminophosphoglycolipids.meso-Diaminopimelic acid was not detected in the peptidoglycan. The DNA G+C content of the isolate was 52.9 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain PW21Tshould be considered to represent a novel species of the genusPaenibacillus, for which the namePaenibacillus prosopidissp. nov. is proposed. The type strain is PW21T(=LMG 25259T=CECT 7506T=DSM 22405T).
Bacillus rigui sp. nov., isolated from wetland fresh water
Authors: Baik Keun Sik , Lim Chae Hong , Park Seong Chan , Kim Eun Mi , Rhee Moon Soo , Seong Chi Nam
Published: November 2009

Two Gram-stain-positive strains, WPCB074Tand WPCB165, were isolated from fresh water collected from the Woopo wetland (Republic of Korea). Both strains were strictly aerobic, motile, endospore-forming rods. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strains WPCB074Tand WPCB165 belonged to the genusBacillusand that strain WPCB074Twas most closely related toBacillus solisalsiYC1T(98.4 % sequence similarity),B. barbaricusV2-BIII-A2T(97.7 %),B. macauensisZFHKF-1T(96.9 %),B. arsenicusCon a/3T(96.4 %) andB. gelatiniLMG 21880T(95.1 %). The 16S rRNA gene sequences of strains WPCB074Tand WPCB165 differed at one position (99.9 % similarity), suggesting that these two strains constitute a single species. DNA–DNA relatedness between strain WPCB074Tand the type strains ofB. solisalsi,B. barbaricus,B. macauensis,B. arsenicusandB. gelatiniwere 26, 17, 20, 14 and 7 %, respectively. Strain WPCB074Twas characterized by having cell-wall peptidoglycan based onmeso-diaminopimelic acid, MK-7 as the predominant menaquinone and iso-C15 : 0and anteiso-C15 : 0as the major fatty acids. The DNA G+C content of strain WPCB074Twas 41.9 mol%. On the basis of phenotypic properties, phylogeny and genomic distinctiveness, strain WPCB074Trepresents a novel species of the genusBacillusfor which the nameBacillus riguisp. nov. is proposed. The type strain is WPCB074T(=KCTC 13278T=JCM 16348T).
Methanoculleus hydrogenitrophicus sp. nov., a methanogenic archaeon isolated from wetland soil
Authors: Tian Jianqing , Wang Yanfen , Dong Xiuzhu
Published: November 2009

An obligately anaerobic, methanogenic archaeon, strain HCT, was isolated from soil of the Zoige wetland on the Tibetan plateau, China. The strain was isolated through construction of an artificial butyrate-degrading consortium in co-culture with a syntrophic bacterium, ‘Syntrophomonas erecta subsp. sporosyntropha’ JCM 13344. Cells of strain HCT were irregular coccoids, 0.8–2 μm in diameter, that occurred singly and utilized only H2/CO2 for growth and methane production. Growth occurred at 18–45 °C (optimum around 37 °C). The pH for growth was 5.0–8.5 (optimal growth around pH 6.6). The G+C content of the genomic DNA was 60.2 mol%. 16S rRNA gene sequence analysis indicated that strain HCT was affiliated to the genus Methanoculleus, with sequence similarities of 94.8–97.2 % to existing members. However, strain HCT was distinguished from described Methanoculleus species by not using formate for growth or methane formation and not requiring acetate as a growth factor. On the basis of phylogenetic analysis and phenotypic characteristics, the novel species Methanoculleus hydrogenitrophicus sp. nov. is proposed, with strain HCT (=CGMCC 1.5146T =JCM 16311T) as the type strain.
Pontibaca methylaminivorans gen. nov., sp. nov., a member of the family Rhodobacteraceae
Authors: Kim Kwang Kyu , Lee Jung-Sook , Lee Keun Chul , Oh Hee-Mock , Kim Song-Gun
Published: November 2009

The alphaproteobacterial strains GRP21T and PH34, which were isolated from coastal sediment of the East Sea, Korea, were subjected to a polyphasic taxonomic investigation. The strains were Gram-negative, non-motile, non-spore-forming, oval-shaped rods that produced creamy-white colonies on tryptic soy agar, required NaCl for growth, contained Q-10 as the predominant ubiquinone, contained 16 : 0, 18 : 1ω7c and 19 : 0 cyclo ω8c as major fatty acids and had polar lipid profiles consisting of phosphatidylcholine, phosphatidylglycerol, an unknown aminolipid, an unknown phospholipid and three unknown lipids. Phylogenetic analysis, based on 16S rRNA gene sequencing, showed that the strains were most closely related to Donghicola eburneus KCTC 12735T, with 94.5 % sequence similarity, but formed a separate lineage within the family Rhodobacteraceae. The combined genotypic and phenotypic data supported the conclusion that the strains represent a novel genus and species, for which the name Pontibaca methylaminivorans gen. nov., sp. nov. is proposed. The type strain of Pontibaca methylaminivorans is GRP21T (=KCTC 22497T =DSM 21219T).
The Arabidopsis Tandem Zinc Finger Protein AtTZF1 Traffics between the Nucleus and Cytoplasmic Foci and Binds Both DNA and RNA
Authors: Pomeranz Marcelo C. , Hah Cyrus , Lin Pei-Chi , Kang Shin Gene , Finer John J. , Blackshear Perry J. , Jang Jyan-Chyun
Published: November 2009

Processing bodies (PBs) are specialized cytoplasmic foci where mRNA turnover and translational repression can take place. Stress granules are related cytoplasmic foci. The CCCH tandem zinc finger proteins (TZFs) play pivotal roles in gene expression, cell fate specification, and various developmental processes. Human TZF binds AU-rich elements at the 3′ untranslated region and recruits decapping, deadenylation, and exonucleolytic enzymes to PBs for RNA turnover. Recent genetic studies indicate that plant TZFs are involved in gene regulation and hormone-mediated environmental responses. It is unknown if plant TZFs can bind RNA and be localized to PBs or stress granules. The Arabidopsis (Arabidopsis thaliana) AtTZF1/AtCTH/AtC3H23 was identified as a sugar-sensitive gene in a previous microarray study. It is characterized by a TZF motif that is distinct from the human TZF. Higher plants such as Arabidopsis and rice (Oryza sativa) each have a gene family containing this unique TZF motif. Here, we show that AtTZF1 can traffic between the nucleus and cytoplasmic foci. AtTZF1 colocalizes with markers of PBs, and the morphology of these cytoplasmic foci resembles that of mammalian PBs and stress granules. AtTZF1-associated cytoplasmic foci are dynamic and tissue specific. They can be induced by dark and wound stresses and are preferentially present in actively growing tissues and stomatal precursor cells. Since AtTZF1 can bind both DNA and RNA in vitro, it raises the possibility that AtTZF1 might be involved in DNA and/or RNA regulation.
Functional Analyses of the CLAVATA2-Like Proteins and Their Domains That Contribute to CLAVATA2 Specificity
Authors: Wang Guodong , Long Yuchen , Thomma Bart P.H.J. , de Wit Pierre J.G.M. , Angenent Gerco C. , Fiers Martijn
Published: November 2009

The Arabidopsis (Arabidopsis thaliana) CLAVATA2 (CLV2) gene encodes a leucine-rich repeat receptor-like protein (RLP) that is involved in controlling the stem cell population size in the shoot apical meristem. Our previous genome-wide functional analysis of 57 AtRLP genes revealed only a few phenotypes for mutant alleles, despite screening a wide range of growth and developmental stages and assaying sensitivity to various stress responses, including susceptibility toward pathogens. To gain further insight into the biological role of AtRLPs, in particular CLV2-related AtRLP genes, we tested their ability to complement the clv2 mutant phenotype. We found that out of four close CLV2 homologs tested, AtRLP2 and AtRLP12 could functionally complement the clv2 mutant when expressed under the control of the CLV2 promoter. This indicates that the functional specificity of these three genes is determined at the level of their transcriptional regulation. Single and double mutant combinations with impaired AtRLP2 and/or AtRLP12 did not show an aberrant phenotype, suggesting that other genes are redundant with these CLV2-like genes. To understand which protein domains are essential for CLV2 function and which parts are interchangeable between related CLV2-like proteins, we performed domain-deletion and domain-swap experiments. These experiments revealed that CLV2 remains functional without the island domain, whereas the C1 and C3 regions of the leucine-rich repeat domain are essential for functionality. Analysis of domain-swap constructs showed that the C3-G region of CLV2 can be replaced by that of AtRLP38, although it could not complement the clv2 mutant under control of the CLV2 promoter. This suggests that the C3-G region is conserved among related AtRLP members, whereas the C1 domain may determine the functional specificity of CLV2.
Nicotiana attenuataSIPK, WIPK, NPR1, and Fatty Acid-Amino Acid Conjugates Participate in the Induction of Jasmonic Acid Biosynthesis by Affecting Early Enzymatic Steps in the Pathway
Authors: Kallenbach Mario , Alagna Fiammetta , Baldwin Ian Thomas , Bonaventure Gustavo
Published: November 2009

Wounding and herbivore attack elicit the rapid (within minutes) accumulation of jasmonic acid (JA) that results from the activation of previously synthesized biosynthetic enzymes. Recently, several regulatory factors that affect JA production have been identified; however, how these regulators affect JA biosynthesis remains at present unknown. Here we demonstrate that Nicotiana attenuata salicylate-induced protein kinase (SIPK), wound-induced protein kinase (WIPK), nonexpressor of PR-1 (NPR1), and the insect elicitor N-linolenoyl-glucose (18:3-Glu) participate in mechanisms affecting early enzymatic steps of the JA biosynthesis pathway. Plants silenced in the expression of SIPK and NPR1 were affected in the initial accumulation of 13-hydroperoxy-linolenic acid (13-OOH-18:3) after wounding and 18:3-Glu elicitation by mechanisms independent of changes in 13-lipoxygenase activity. Moreover, 18:3-Glu elicited an enhanced and rapid accumulation of 13-OOH-18:3 that depended partially on SIPK and NPR1 but was independent of increased 13-lipoxygenase activity. Together, the results suggested that substrate supply for JA production was altered by 18:3-Glu elicitation and SIPK- and NPR1-mediated mechanisms. Consistent with a regulation at the level of substrate supply, we demonstrated by virus-induced gene silencing that a wound-repressed plastidial glycerolipase (NaGLA1) plays an essential role in the induction of de novo JA biosynthesis. In contrast to SIPK and NPR1, mechanisms mediated by WIPK did not affect the production of 13-OOH-18:3 but were critical to control the conversion of this precursor into 12-oxo-phytodienoic acid. These differences could be partially accounted for by reduced allene oxide synthase activity in WIPK-silenced plants.
Novel and Expanded Roles for MAPK Signaling inArabidopsisStomatal Cell Fate Revealed by Cell Type–Specific Manipulations
Authors: Lampard Gregory R. , Lukowitz Wolfgang , Ellis Brian E. , Bergmann Dominique C.
Published: November 2009

Mitogen-activated protein kinase (MAPK) signaling networks regulate numerous eukaryotic biological processes. In Arabidopsis thaliana, signaling networks that contain MAPK kinases MKK4/5 and MAPKs MPK3/6 function in abiotic and biotic stress responses and regulate embryonic and stomatal development. However, how single MAPK modules direct specific output signals without cross-activating additional downstream processes is largely unknown. Studying relationships between MAPK components and downstream signaling outcomes is difficult because broad experimental manipulation of these networks is often lethal or associated with multiple phenotypes. Stomatal development in Arabidopsis follows a series of discrete, stereotyped divisions and cell state transitions. By expressing a panel of constitutively active MAPK kinase (MAPKK) variants in discrete stomatal lineage cell types, we identified a new inhibitory function of MKK4 and MKK5 in meristemoid self-renewal divisions. Furthermore, we established roles for MKK7 and MKK9 as both negative and (unexpectedly) positive regulators during the major stages of stomatal development. This has expanded the number of known MAPKKs that regulate stomatal development and allowed us to build plausible and testable subnetworks of signals. This in vivo cell type–specific assay can be adapted to study other protein families and thus may reveal insights into other complex signal transduction pathways in plants.
A relaxed lattice option pricing model: implied skewness and kurtosis
Authors: Ji Dasheng , Wade Brorsen B.
Published: November 2009

Purpose

The purpose of this paper is to develop an option pricing model applicable to US options. The lognormality assumption that has typically been imposed with past binomial and trinomial option pricing models is relaxed. The relaxed lattice model is then used to determine skewness and kurtosis of distributions of futures prices implied from option prices.

Design/methodology/approach

The relaxed lattice is based on Gaussian quadrature. The markets studied include corn, soybeans, and wheat. Skewness and kurtosis are implied by minimizing the squared deviations of actual option premia from predicted premia.

Findings

Positive skewness is the major source of nonnormality, but both skewness and kurtosis are important as the trinomial model that considers kurtosis has greater accuracy than the binomial model. The out‐of‐sample forecasting accuracy of the relaxed lattice models is better than the Black‐Scholes model in most, but not all cases.

Research limitations/implications

The model might benefit from using option prices from more than one day. The implied skewness and kurtosis were quite variable and using more data might reduce this variability.

Practical implications

Empirical results mostly show positive implied skewness, which suggests extreme price rises were more likely than extreme price decreases.

Originality/value

The relaxed lattice is a new model and the results about implied higher moments are new for these commodities. There are competing models available that should be able to get similar accuracy, so one key advantage of the new approach is its simplicity and ease of use.
Women farmers' access to credit from rural banks in Ghana
Authors: Akudugu Mamudu A. , Egyir Irene S. , Mensah‐Bonsu Akwasi
Published: November 2009

Purpose

The purpose of this paper is to examine women farmers' access to credit from rural banks (RBs) in the Upper East region of Ghana. The paper examines the nature of credit supply by the RBs to their customers and the proportion that goes to women over a ten year period. It proposes the modelling of socio‐economic, technical and institutional factors influencing women farmers' access to credit from financial institutions in general and rural banks (RBs) in particular. The paper aims to expand the frontiers of rural and agricultural financing as well as the integration of gender interest in the financial sectors of developing countries.

Design/methodology/approach

In total, 200 women farmers were randomly selected and information on socio‐economic, technical and institutional issues solicited from them. Ratio analyses were carried out and the logistic regression used to model the socio‐economic, technical and institutional factors that have influence on access to credit from RBs by women farmers.

Findings

The paper provides empirical evidence of close gender parity in terms of credit supply by RBs in Ghana. About 44 per cent of the credit portfolios of RBs in Ghana go to women and the remaining 56 per cent goes to men. Education, application procedures, access to land, income level, farm size, membership to economic associations, savings, type of crop grown, interest rate and distance to RBs are the socio‐economic, technical and institutional factors that influence women farmers' access to credit.

Research limitations/implications

The paper is limited to only women farmers. There is the need for further research that considers men and women so as to establish whether or not there is gender insensitivity by financial institutions in Ghana and other developing countries.

Practical implications

This paper provides empirical implications for the development of a vibrant financial sector in developing countries that provide equal access to men and women, rural and urban dwellers as well as actors in the formal and informal sectors.

Originality/value

This paper brings to light the issues of access to productive resources such as production credit by women in developing countries, particularly Ghana.
Factors affecting precautionary savings of self‐employed farm households
Authors: Mishra Ashok K. , Chang Hung‐Hao
Published: November 2009

Purpose

The purpose of this paper is to empirically investigate the effects of farm income variability, farm size, and other socio‐demographic characteristics on the precautionary saving behavior of farm households and to estimate the influences of the identified factors on the amount of savings by self‐employed farm households.

Design/methodology/approach

Using 2003 Agricultural Resource Management Survey (ARMS) data and a Double‐Hurdle procedure, the likelihood and the amount of savings by farm households are estimated.

Findings

An important empirical finding of this study is that variability in income plays an important role in explaining precautionary savings of US farm households. Findings suggest that farm households facing higher income risk save more and accumulate more wealth. It is indicated that several farm, operator, household, and demographic attributes contribute to the precautionary savings of farm households. In particular, results show that educational attainment by operator and spouses have positive impact on the decision to save. In addition, results from this study show that farms that specialize in cash grain are likely to have precautionary savings.

Practical implications

Farm households today are virtually indistinguishable from non‐farm households in their levels of income and diversity of employment. As a result, government policies that influence general economic conditions have much more profound impacts on farm families. Federal support of farm income warrants continued scrutiny. This paper shows that greater income uncertainty increases savings and wealth of farm households. Therefore, farm policies that reduce income variability or uncertainty will have an impact on precautionary savings and wealth of farm households.

Originality/value

Several studies have investigated savings of households; however, these studies are limited to entire US population, older Americans, or non‐self‐employed individuals in the USA. Little is known about the savings behavior of self‐employed US farm households owing to a lack of household survey data and because of the complex relationship between the farm household and farm business in terms of resource allocation (both capital and labor).
Upper Midwest dairy farm revenue variation and insurance implications
Authors: Wolf Christopher A. , Roy Black J. , Hadrich Joleen C.
Published: November 2009

Purpose

The purpose of this paper is to examine the sources and magnitude of variation in accrual adjusted gross farm revenue and farm revenue net of feed purchases on Michigan dairy farms representative of Upper Midwest dairy farms. The paper aims to assess whether adjusted gross revenue‐type insurance instruments meet insurability conditions when applied to dairy farms.

Design/methodology/approach

Accrual adjusted dairy farm revenue and revenue net of feed purchased from Michigan dairy farm panel data from 1995 through 2006 were detrended and summarized. Variance decomposition was used to identify sources of variation in adjusted gross revenue and adjusted gross revenue less feed purchases. In‐sample insurance premiums were estimated and Monte Carlo simulations were used to adjust these premiums for out‐of‐sample considerations.

Findings

Milk price variation was the largest source of variation while milk production per cow varied little. Farms with smaller herds and those with larger percentages of farm revenue from crop sales had higher relative revenue variability and would trigger a higher frequency of indemnities under a whole farm revenue insurance contract.

Research limitations/implications

Because the data analyzed conclude in 2006, the volatility of the past couple of years is not reflected. Therefore, researchers are encouraged to test the proposed insurance feasibility further with more recent data.

Practical implications

The paper addresses considerations for the development and commercialization of a feasible dairy revenue insurance instrument.

Originality/value

This paper fulfils a need to understand magnitude and source of revenue variation on dairy farms and how insurance might mitigate negative consequences of this variation.
The importance of personal norms for purchasing organic milk
Authors: Klöckner Christian A. , Ohms Silvia
Published: November 2009

Purpose

The purpose of this paper is to apply a structured approach to understand the importance of personal ecological norms in purchasing organic food. The norm‐activation‐model by Schwartz is used to predict self‐reported and observed purchase behaviour of organic milk.

Design/methodology/approach

The paper reports the results of a field study with 63 customers of a German supermarket. A combination of covert observation and in‐store interviews was applied to obtain reliable data on actual shopping behaviour and its predictors.

Findings

The results show that the self‐reported and the observed purchase of organic milk is predicted by personal ecological norms, social norms, and perceived behavioural control. Personal norms are activated by awareness of need, awareness of consequences, perceived behavioural control, and social norms. People with strong personal norms use “organic production”, the “EU‐BIO‐Label” and “ingredients” as additional criteria during their decision process. For people with strong ecological norms the price difference between organic and conventional milk, the lack of knowledge about organic milk, and convenience are less important constraints. Finally, people with strong personal norms react more sensitively to proposed norm‐centred interventions.

Practical implications

The study offers insight into the processes of motivating behaviour and can therefore be used to design intervention strategies. Suggestions are developed in the closing part of the paper.

Originality/value

The study applies for the first time the norm‐activation‐model to the domain of purchasing organic milk and underlines the importance of normative influences for this decision.
Determining the factors affecting the consumers' willingness to pay higher prices for genetically unmodified products
Authors: Gokalp Goktolga Z. , Esengun Kemal
Published: November 2009

Purpose

The purpose of this paper is to determine the factors affecting the consumers' willingness to pay higher prices for genetically unmodified products.

Design/methodology/approach

Tomato was selected as a model crop. Data used in this study were gathered from questionnaires conducted in Tokat province of Turkey in April 2006. Questionnaires were accomplished via face‐to‐face interviews over 262 households. “Ordered logit model” was used in determining the factors that affect the willingness of consumers for higher prices for genetically unmodified products. Ordered models are those that limit dependent variables to certain intervals. According to the results, variables of household size, monthly household income, household's monthly food consumption expenditure and level of consumers' sensitivity over the issue affected the willingness to pay higher prices for genetically unmodified products.

Findings

Results of the study indicated that household size and monthly household income had negative effects on the willingness to pay extra, while monthly food expenditure and concern had positive effects.

Originality/value

The results of the study will be beneficial for the policy makers, producers, consumers and those conducting research in this area alike. Carrying out studies aimed at determining consumer preference, such as this, will help form consumer consciousness, especially in Turkey, to protect consumer health.
The UK pig cycle: a spectral analysis
Authors: Dawson Philip John
Published: November 2009

Purpose

The purpose of this paper is to identify cyclical patterns in the prices and production of UK pigmeat, 1989‐2008.

Design/methodology/approach

The approach takes the form of spectral analysis.

Findings

Results show evidence of both annual and seasonal cycles, but there is little evidence of a three‐to‐four‐year cycle. The likely cause of the latter's absence is increasing imports and a changing market structure.

Practical implications

Conventional wisdom is that the traditional pig cycle is of three‐to‐four years' duration and the UK's pig policy is based partly on its existence and that the design and implementation of UK pig policy are predicated on the basis of a traditional cycle is misplaced.

Originality/value

No previous or recent empirical investigation of the UK pig cycle exists, perhaps because its existence is considered to be axiomatic.
Indian cold chain: modeling the inhibitors
Authors: Joshi Rohit , Banwet Devinder Kumar , Shankar Ravi
Published: November 2009

Purpose

The cold chain has become an integral part of the supply chain of perishable items. Recent studies have shown a critical absence of a strong and dependable cold chain in developing economies. The purpose of this paper is to set out to identify and inter‐relate the inhibitors that significantly influence the efficiency of a cold chain in developing economies like India.

Design/methodology/approach

The synthesis and prioritization of inhibitors are done on the basis of an extensive literature review as well as consultation with academicians and industrial professionals. Using semi‐structured interviews and Fuzzy Interpretive Structure Modeling (FISM) approach, the research presents a hierarchy‐based model.

Findings

The end result is a model that establishes the relationships among the identified inhibitors with their respective dominance. The research shows that there exists a group of inhibitors having a high driving power and low dependence with strategic importance and requiring maximum attention and another group includes inhibitors that have high dependence and the consequential actions.

Research limitations/implications

At the time when cold chain is the key domain for the food sector, these findings will be immensely helpful for industry professionals, Government, non‐government, academia and the community in developing strategies and impounding the root causes responsible for the inefficient and weak cold chain in India. The Indian situation echoes to the situation in most of the developing economies and similar solutions can apply there also. These findings will be truly useful for organizations that are planning to operate food chains in developing nations.

Orignality/value

Presentation of inhibitors in hierarchy and their classification into driver and dependent categories with their respective dominance on the system is a unique effort in the area of cold chain management. This would help decision makers to better utilize the limited resources.
An exploratory RFID patent analysis
Authors: Taghaboni‐Dutta Fataneh , Trappey Amy J.C. , Trappey Charles V. , Wu Hsin‐Ying
Published: November 2009

Purpose

This paper aims to study the development of radio frequency identification (RFID) technology through an analysis of patents filed with and issued by the US Patent and Trademark Office. A close analysis of these clusters reveals the patent development strategies of two competing factions of RFID technology developers. This paper provides an analysis of the patents along with insights into the contents of the patents held by these two groups.

Design/methodology/approach

The analysis is based on Intermec Technologies and the RFID Patent Pool, the two major players in this domain. The comparison of Intermec Technologies and RFID Patent Pool is conducted using meta‐data analysis and patent content clustering. The methodology and approach includes data pre‐processing, key phrase extraction using term frequency‐inverse document frequency, ontology construction, key phrase correlation measurement, patent technology clustering and patent document clustering. Clusters are derived using the K‐means approach and a prototype Legal Knowledge Management Platform.

Findings

The findings support a strong link between intellectual property and competitive advantage – specifically Intermec Technologies, which have not joined the RFID Patent Pool. The patent search results show that Intermec Technologies hold basic RFID patents in the early stages of technology development, which has placed the company in a dominant position.

Research limitations/implications

The features of each cluster clearly depict the niches and specialties of companies and provide a historical framework of RFID technology development.

Practical implications

The RFID patent analysis shows that if a company holds crucial patents in the early stages of a developing technology which relate to the fundamental key aspects of the technology, then the company will be more likely to maintain a leading and dominant position in that industry segment (i.e. RFID in this study).

Originality/value

This research uses patent content cluster analysis to explain the rationale behind an alliance strategy decision.
Education and continuing professional development for Indonesian academic librarians
Authors: Maesaroh Imas , Genoni Paul
Published: November 2009

Purpose

This paper aims to report base‐line data on the current levels of education, skills, and knowledge of Indonesian academic librarians, and provides an insight into their continuing professional development. The paper also seeks to report: the current level of qualifications of librarians working in Indonesian academic libraries; and the current level and type of continuing professional development and work place training in Indonesian academic libraries.

Design/methodology/approach

This paper includes the results of a questionnaire delivered to all librarians working in Indonesian public universities. The survey instrument was based on that used in the NEXUS survey distributed to Australian library and information studies (LIS) professionals in 2006. The paper includes a comparison of survey results on key indicators for Indonesian and Australian library and information staff.

Findings

The research reports comparative shortcomings in the level and standard of education available to Indonesian academic librarians. The issue of continuing professional development is more complex, with quite high levels of participation in some types of training reported by the Indonesian respondents, but generally lower levels of satisfaction with that training than reported by their Australian counterparts.

Research limitations/implications

Some of the conclusions made comparing the situations in Indonesia and Australia are tentative due to the different understandings of key terms and concepts in the two countries. The data reported in the paper are quantitative and comprehensive findings require further qualitative research.

Practical implications

The results have implications for the future development of library education in Indonesia, and workplace training for Indonesian academic librarians.

Originality/value

The research reported is the first to collect large‐scale data relating to LIS workforce education and continuing professional development from a developing country.
Competency‐based service reviews and workforce planning at Deakin University library
Authors: Cardwell Paul
Published: November 2009

Purpose

This paper seeks to describe an approach to staff development and workforce planning which is implemented as part of a process of internal reviews of service areas within an academic library.

Design/methodology/approach

The paper describes the factors leading to the development of such a process within the Deakin University Library.

Findings

A number of different factors – internal to the library, at the university level and in the wider environment – have driven the need for such reviews and influenced their design. The approach developed focuses on comparing current workforce capabilities (competencies and resource levels) with the set of competencies and resources required to deliver the projected services to the standards required. This account highlights the links between the review process and the implementation of a library‐wide staff development framework.

Practical implications

A number of practical implications may be drawn: the value of a flexible approach taking into account the local and institutional environment; the critical importance of organizational needs driving individual staff development and the benefits of mapping links from strategic goals to staff development.

Originality/value

The paper focuses on an emerging process for service delivery in an academic library.