bluuebunny/crossref_metadata_2025 huggingface dataset:
Lack of adrenomedullin in the mouse brain results in behavioral changes, anxiety, and lower survival under stress conditions
Authors: Fernández Ana P. , Serrano Julia , Tessarollo Lino , Cuttitta Frank , Martínez Alfredo
Published: August 2008

The adrenomedullin (AM) gene,adm, is widely expressed in the central nervous system (CNS) and several functions have been suggested for brain AM. Until now, a formal confirmation of these actions using genetic models has been elusive since the systemicadmknockout results in embryo lethality. We have built a conditional knockout mouse model using the Cre/loxP approach. When crossed with transgenic mice expressing the Cre recombinase under the tubulin Tα-1 promoter, we obtained animals with no AM expression in the CNS but normal levels in other organs. These animals lead normal lives and do not present any gross morphological defect. Specific areas of the brain of animals lacking CNS AM contain hyperpolymerized tubulin, a consequence of AM downregulation. Behavioral analysis shows that mice with no AM in their brain have impaired motor coordination and are hyperactive and overanxious when compared to their wild-type littermates. Treatment with methylphenidate, haloperidol, and diazepam did not show differences between genotypes. Circulating levels of adrenocorticotropic hormone and corticosterone were similar in knockout and wild-type mice. Animals with no brain AM were less resistant to hypobaric hypoxia than wild-type mice, demonstrating the neuroprotective function of AM in the CNS. In conclusion, AM exerts a beneficial action in the brain by maintaining homeostasis both under normal and stress conditions.
Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont
Bacteroides fragilis
Authors: Coyne Michael J. , Chatzidaki-Livanis Maria , Paoletti Lawrence C. , Comstock Laurie E.
Published: August 2008

Bacteroides
species are the most abundant Gram-negative bacteria of the human colonic microbiota. These endogenous organisms are unique in that they synthesize an extensive number of phase-variable surface polysaccharides. Pathogenic bacteria phase vary expression of surface molecules for immune evasion, but the importance of the synthesis of multiple phase-variable polysaccharides to these commensal bacteria is unknown. We previously showed that a
Bacteroides fragilis
mutant unable to synthesize 4 of the 8 capsular polysaccharides and unable to glycosylate proteins properly is rapidly outcompeted by the wild-type strain for colonization of the gnotobiotic mouse intestine. In the present study, we constructed mutants defective only in capsule polysaccharide synthesis to define better the importance of these surface molecules to intestinal colonization. We discovered a key enzymatic activity required for synthesis of 7 of the 8 capsular polysaccharides. Deletion of its gene resulted in the first
B. fragilis
mutant able to synthesize only one phase-variable polysaccharide, and further mutation resulted in a stable acapsular mutant. We show that the acapsular mutant is rapidly outcompeted, but synthesis of a single polysaccharide is sufficient for the organism to colonize the gnotobiotic intestine competitively. These data demonstrate that initial colonization of the gnotobiotic mouse intestine by
B. fragilis
requires that the organism synthesize only a single polysaccharide and suggest that the synthesis of multiple phase-variable polysaccharides is important for the bacteria's long-term maintenance in the normally complex and competitive ecosystem.
Androgen receptor is a tumor suppressor and proliferator in prostate cancer
Authors: Niu Yuanjie , Altuwaijri Saleh , Lai Kuo-Pao , Wu Chun-Te , Ricke William A. , Messing Edward M. , Yao Jorge , Yeh Shuyuan , Chang Chawnshang
Published: August 2008

Targeting androgens/androgen receptor (AR) functions via androgen deprivation therapy (ADT) remains the standard treatment for prostate cancer. However, most tumors eventually recur despite ADT. Here we demonstrate that the prostate AR may function as both a suppressor and a proliferator to suppress or promote prostate cancer metastasis. Results from orthotopically recombining stromal WPMY1 cells with epithelial PC3 prostate cancer cells in mice demonstrated that restoring AR in epithelial PC3 cells or knockdown of AR in stromal WPMY1 cells suppressed prostate cancer metastasis. Knockdown of the AR in epithelial CWR22rv1 prostate cancer cells also resulted in increased cell invasion
in vitro
and
in vivo
. Restoring AR in PC3 cells (PC3-AR9) results in decreased invasion in bone lesion assays and
in vivo
mouse models. Mice lacking the prostate epithelial AR have increased apoptosis in epithelial luminal cells and increased proliferation in epithelial basal cells. The consequences of these two contrasting results led to the expansion of CK5/CK8-positive intermediate cells, and mice developed larger and more invasive metastatic tumors in lymph nodes and died earlier than wild-type littermates. Mechanistic dissection suggested that androgens/AR might directly or indirectly modulate metastasis-related genes and suppression of TGFβ1 signals results in the partial inhibition of AR-mediated metastasis. Collectively, our understanding of these opposing roles of prostatic AR may revolutionize the way we combat prostate cancer, and allow the development of new and better therapies by targeting only the proliferative role of AR.
Targeting the stromal androgen receptor in primary prostate tumors at earlier stages
Authors: Niu Yuanjie , Altuwaijri Saleh , Yeh Shuyuan , Lai Kuo-Pao , Yu Shengqiang , Chuang Kuang-Hsiang , Huang Shu-Pin , Lardy Henry , Chang Chawnshang
Published: August 2008

To differentiate roles of androgen receptor (AR) in prostate stromal and epithelial cells, we have generated inducible-(ind)ARKO-TRAMP and prostate epithelial-specific ARKO TRAMP (pes-ARKO-TRAMP) mouse models, in which the AR was knocked down in both prostate epithelium and stroma or was knocked out in the prostate epithelium, respectively. We found that loss of AR in both mouse models resulted in poorly differentiated primary tumors with expanded intermediate cell populations. Interestingly, knockdown of both epithelial and stromal AR in ind-ARKO-TRAMP mice at earlier stages resulted in smaller primary prostate tumors with lower proliferation rates, and knockout of AR in pes-ARKO-TRAMP mice resulted in larger primary prostate tumors with higher proliferation rates. The differential proliferation rates, yet with similarly expanded intermediate cell populations, indicated that the prostate stromal AR might play a more dominant role than the epithelial AR to promote primary tumor proliferation at an early stage of tumor. Tissue recombination of human prostate stromal cell lines (WPMY1-v or WPMY1-ARsi) with human prostate cancer epithelial cell lines (PC3-v or PC3-AR9) further demonstrated that the AR might function as a suppressor in epithelial cells and a proliferator in stromal cells in the primary prostate tumors. The dual roles of the AR in prostate epithelium and stroma may require us to reevaluate the target and timing of androgen-deprivation therapy for prostate cancer patients and may suggest a need to develop new drugs to selectively target stromal AR in the primary prostate tumors at earlier stages.
A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes
Authors: Hellwig Sabine , Bass Brenda L.
Published: August 2008

Although much has been learned about short noncoding RNAs, long noncoding transcripts are largely uncharacterized. Here, we describe
Caenorhabditis elegans rncs-1
, a highly base-paired, 800-nucleotide noncoding RNA expressed in hypodermis and intestine. Transcription of
rncs-1
is modulated in response to food supply. Although highly double-stranded, we show that
rncs-1
RNA is not a substrate for Dicer because of branched structures at its termini. However,
rncs-1
RNA inhibits Dicer cleavage of a second dsRNA
in vitro
, presumably by competition. We validate this observation
in vivo
by demonstrating that mRNA levels of several Dicer-regulated genes vary with changes in
rncs-1
expression. Certain viruses express dsRNA to compete with cellular dsRNA-mediated pathways, and our data suggest that
rncs-1
provides a cellular correlate of this phenomenon.
Rapid tolerization of virus-activated tumor-specific CD8
+
T cells in prostate tumors of TRAMP mice
Authors: Bai Ailin , Higham Eileen , Eisen Herman N. , Wittrup K. Dane , Chen Jianzhu
Published: August 2008

To study T cell responses to tumors in an autochthonous model, we expressed a CD8 T cell epitope SIYRYYGL (SIY) in the prostate of transgenic adenocarcinoma (TRAMP) mice (referred to as TRP-SIY), which spontaneously develop prostate cancer. Naïve SIY-specific CD8 T cells adoptively transferred into TRP-SIY mice became tolerized in the prostate draining lymph nodes. Vaccination of TRP-SIY mice intranasally with influenza virus that expresses the SIY epitope resulted in generation of SIY-specific effector T cells in the lung-draining lymph nodes. These effector T cells expressed TNFα and IFNγ, eliminated SIY peptide-loaded target cells
in vivo
, and infiltrated prostate tumors, where they rapidly lost the ability to produce effector cytokines. A population of these T cells persisted in prostate tumors but not in lymphoid organs and could be induced to re-express effector functions following cytokine treatment
in vitro
. These findings suggest that T cells of a given clone can be activated and tolerized simultaneously in different microenvironments of the same host and that effector T cells are rapidly tolerized in the tumors. Our model provides a system to study T cell-tumor interactions in detail and to test the efficacy of cancer immunotherapeutic strategies.
Energy-dependent fitness: A quantitative model for the evolution of yeast transcription factor binding sites
Authors: Mustonen Ville , Kinney Justin , Callan Curtis G. , Lässig Michael
Published: August 2008

We present a genomewide cross-species analysis of regulation for broad-acting transcription factors in yeast. Our model for binding site evolution is founded on biophysics: the binding energy between transcription factor and site is a quantitative phenotype of regulatory function, and selection is given by a fitness landscape that depends on this phenotype. The model quantifies conservation, as well as loss and gain, of functional binding sites in a coherent way. Its predictions are supported by direct cross-species comparison between four yeast species. We find ubiquitous compensatory mutations within functional sites, such that the energy phenotype and the function of a site evolve in a significantly more constrained way than does its sequence. We also find evidence for substantial evolution of regulatory function involving point mutations as well as sequence insertions and deletions within binding sites. Genes lose their regulatory link to a given transcription factor at a rate similar to the neutral point mutation rate, from which we infer a moderate average fitness advantage of functional over nonfunctional sites. In a wider context, this study provides an example of inference of selection acting on a quantitative molecular trait.
Autoinhibitory regulation of SCF-mediated ubiquitination by human cullin 1's C-terminal tail
Authors: Yamoah Kosj , Oashi Taiji , Sarikas Antonio , Gazdoiu Stefan , Osman Roman , Pan Zhen-Qiang
Published: August 2008

SCF (Skp1·CUL1·F-box protein·ROC1) E3 ubiquitin ligase and Cdc34 E2-conjugating enzyme catalyze polyubiquitination in a precisely regulated fashion. Here, we describe biochemical evidence suggesting an autoinhibitory role played by the human CUL1 ECTD (extreme C-terminal domain; spanning the C-terminal 50 amino acids), a region that is predicted to contact the ROC1 RING finger protein by structural studies. We showed that ECTD did not contribute to CUL1's stable association with ROC1. Remarkably, deletion of ECTD, or missense mutations designed to disrupt the predicted ECTD·ROC1 interaction, markedly increased the ability of SCF
βTrCP2
to promote IκBα polyubiquitination and polyubiquitin chain assembly by Cdc34
in vitro
. Thus, disruption of ECTD yields
in vitro
effects that parallel SCF activation by Nedd8 conjugation to CUL1. We propose that SCF may be subject to autoinhibitory regulation, in which Nedd8 conjugation acts as a molecular switch to drive the E3 into an active state by diminishing the inhibitory ECTD·ROC1 interaction.
A ketoreductase domain in the PksJ protein of the bacillaene assembly line carries out both α- and β-ketone reduction during chain growth
Authors: Calderone Christopher T. , Bumpus Stefanie B. , Kelleher Neil L. , Walsh Christopher T. , Magarvey Nathan A.
Published: August 2008

The polyketide signaling metabolites bacillaene and dihydrobacillaene are biosynthesized in
Bacillus subtilis
on an enzymatic assembly line with both nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) modules acting along with catalytic domains servicing the assembly line
in trans
. These signaling metabolites possess the unusual starter unit α-hydroxyisocaproate (α-HIC). We show here that it arises from initial activation of α-ketoisocaproate (α-KIC) by the first adenylation domain of PksJ (a hybrid PKS/NRPS) and installation on the pantetheinyl arm of the adjacent thiolation (T) domain. The α-KIC unit is elongated to α-KIC-Gly by the second NRPS module in PksJ as demonstrated by mass spectrometric analysis. The third module of PksJ uses PKS logic and contains an embedded ketoreductase (KR) domain along with two adjacent T domains. We show that this KR domain reduces canonical 3-ketobutyryl chains but also the α-keto group of α-KIC-containing intermediates on the PksJ T-domain doublet. This KR activity accounts for the α-HIC moiety found in the dihydrobacillaene/bacillaene pair and represents an example of an assembly-line dual-function α- and β-KR acting on disparate positions of a growing chain intermediate.
The role of language cues in constraining cross-language activity
Authors: Bobb Susan C. , Hoshino Noriko , Kroll Judith F.
Published: August 2008

Recent psycholinguistic studies provide compelling evidence for the claim that both languages are active when second language (L2) learners and bilinguals process information in one language alone. The parallel activation of the two languages occurs even when individuals are performing highly practiced tasks such as reading, listening, and speaking, and even when they are highly proficient in both languages. The presence of cross-language activity in the absence of random errors, particularly for those who are highly proficient in the L2, suggests that a mechanism of cognitive control is in place to guide the selection of the intended language. The focus of current research is to understand the basis of this cognitive mechanism, how it varies as a function of individual differences in cognitive resources, and what consequences it holds for cognition more generally. In this paper we consider whether L2 learners and bilinguals are able to exploit cues to language status that might allow them to focus their attention on languagerelevant attributes of processing or to effectively inhibit information related to the language not in use as a means to control language selection. The results of the present study suggest that it is possible to create a functional language cue for planning the L2 and bias language selection.
Bilingual first language acquisition at the interface between syntax and pragmatics
Authors: Müller Natascha
Published: August 2008

The present article provides an overview of some recent research in bilingual first language acquisition with special reference to Romance languages. It addresses two language contact phenomena, language mixing at the lexical level and crosslinguistic influence at the syntactic level. For both contact phenomena, there is evidence that they are unrelated to language dominance (as measured in terms of MLU). Language mixing is negatively correlated with the number of utterances per minute, a measure for language fluency. Cross-linguistic influence at the syntactic level is due to computational complexity which is caused for example by the invasive interplay of pragmatics and syntax. This kind of interplay will be discussed on the basis of the presence or absence of the null-subject property, comparing Italian and German, and by studying the presence or absence of object clitics, comparing French and German. Since cross-linguistic influence affects bilingual individuals to different degrees (sometimes referred to as individual variation), we discuss the assumption that the degree to which the influence manifests itself differs as a function of fluency (measured in words produced per minute). The more fluent the child is in the language with the computationally complex analysis, the less the effect of cross-linguistic influence. In sum, the language which exhibits influence is determined by computational complexity as defined, for example, by the invasive interplay between pragmatics and syntax. The degree of manifestation of the influence depends on fluency in the computationally complex language.
Interpreting tense in a second language
Authors: Gabriele Alison , Maekawa Junko
Published: August 2008

The question of whether adult native speakers of Chinese, a language that does not morphosyntactically represent tense, are able to acquire tense in English has been a topic of great interest in part because it allows us to examine whether there is a critical period for features that are not instantiated in the native language (Hawkins 2001; Hawkins & Liszka 2003; Lardiere 1998a, 2003).While most previous studies have focused on production data, the present study examines the semantics of tense, investigating whether or not learners’ interpretations are sensitive to temporal distinctions. Native speakers of Mandarin are compared with native speakers of Japanese and Korean, languages which both morphosyntactically encode tense. Results of an interpretation task targeting the present progressive and past progressive in English show that by advanced levels of proficiency the three groups of learners performsimilarly. The results provide evidence that tense is fully acquirable in L2 acquisition regardless of the properties of the native language.
Anaphora resolution in near-native Italian grammars: Evidence from native speakers of Croatian
Authors: Kraš Tihana
Published: August 2008

This paper reports the results of an experimental study on the resolution of intra-sentential anaphora in Italian, by native Italian speakers and near-native Italian speakers whose L1 is Croatian. In a picture-selection task, the two groups of speakers had to identify the antecedents of third person null and overt subject pronouns in ambiguous forward and backward anaphora sentences and their unambiguous counterparts. In all contexts under investigation, near-natives expressed native-like antecedent preferences, indicating that they have acquired not only the syntactic, but also the discourse-pragmatic constraints on the realisation of pronominal subjects in Italian. Given that Croatian and Italian do not differ with respect to the licensing and distribution of pronominal forms, the results provide additional evidence for an account attributing the well-attested tendency of bilingual speakers of a null subject language and a non-null subject language to overuse and misinterpret overt subjects in the null subject language to crosslinguistic influence.
Interface vulnerability and knowledge of the subjunctive/indicative distinction with negated epistemic predicates in L2 Spanish
Authors: Iverson Michael , Kempchinsky Paula , Rothman Jason
Published: August 2008

Much recent research in SLA is guided by the hypothesis of L2 interface vulnerability (see Sorace 2005). This study contributes to this general project by examining the acquisition of two classes of subjunctive complement clauses in L2 Spanish: subjunctive complements of volitional predicates (purely syntactic) and subjunctive vs. indicative complements with negated epistemic matrix predicates, where the mood distinction is discourse dependent (thus involving the syntax–discourse interface). We provide an analysis of the volitional subjunctive in English and Spanish, suggesting that English learners of L2 Spanish need to access the functional projection Mood P and an uninterpretable modal feature on the Force head available to them from their formal English register grammar, and simultaneously must unacquire the structure of English for-to clauses. For negated epistemic predicates, our analysis maintains that they need to revalue the modal feature on the Force head from uninterpretable to interpretable, within the L2 grammar.With others (e.g. Borgonovo & Prévost 2003; Borgonovo, Bruhn de Garavito & Prévost 2005) and in line with Sorace’s (2000, 2003, 2005) notion of interface vulnerability, we maintain that the latter case is more difficult for L2 learners, which is borne out in the data we present. However, the data also show that the indicative/subjunctive distinction with negated epistemics can be acquired by advanced stages of acquisition, questioning the notion of obligatory residual optionality for all properties which require the integration of syntactic and discourse information.
'What is happened' in L2 English does not happen in L2 Chinese
Authors: Shan Chuan-Kuo , Yuan Boping
Published: August 2008

In the literature, L2 learners of English are reported to have problems accepting grammatical unaccusative sentences like the cup broke yesterday although they accept the passivized form like the cup was broken yesterday (e.g. Yip 1995; Ju 2000). They also produce ungrammatical sentences like “If the World War III is happened, . . .”. It has been suggested that these phenomena are universal in the development of L2 English because they occur in the English of L2 learners with different L1s (cf. Ju 2000). In this paper, we present an empirical study investigating whether these non-target phenomena also occur in L2 Chinese. It is found that English speakers of Chinese at different proficiency levels fully accept the NP-V unaccusative construction. Optionality is observed in English speakers’ non-target passivized unaccusative verbs of change of state, which are argued to be due to L1 transfer when English speakers incorrectly treat Chinese change-of-state verbs as causative. Overall, our results suggest that the overpassivization phenomenon should not be considered universal in the L2 acquisition of unaccusativity despite their prevalence in L2 English.
The development of finiteness from a lexical to a functional category
Authors: Jordens Peter
Published: August 2008

Finiteness in adult Dutch is expressed by use of formal means of morpho-syntax, i.e. with both inflectional morphology and word order (verb-second). These formal means are linked to a projection of the functional category FIN as in:

FIN

SpecFIN FIN

FIN VP

SpecVP VP

At the initial stage of acquisition, there is no productive use of functional elements nor do learner languages have verb-second. This is due to the fact that initially learner languages are systems in which the functional category FIN is absent. Properties of validation and anchoring are expressed by lexical means: Expression of illocutionary force occurs with modal predicates, contextual anchoring is expressed with deictic elements. Instantiation of the functional projection FIN is caused by the acquisition of the auxiliary verb heb/heeft (have/has). As a functional category, AUX provides a position for functional elements to express modal or – in the default case – non-modal illocutionary force. With the instantiation of AUX, the initial, i.e. specifier position serves as a position for elements with topic function, i.e. for elements used to establish contextual anchoring of the utterance. The acquisition of AUX is the driving force in the development from the lexical to the functional stage. However, the acquisition of AUX does not come as a deus ex machina. Structures with AUX are learned for reasons of information processing. Utterances with an auxiliary are typically used as a topicalisation device. Due to the fact that structures with AUX are learned as a topicalisation device, it seems possible (1) to provide a functional explanation for why auxiliaries, inversion and subject pronouns are learned simultaneously and (2) to account for the fact that the acquisition process occurs similarly in both L1- and L2-learner languages.
AMIN domains have a predicted role in localization of diverse periplasmic protein complexes
Authors: de Souza Robson Francisco , Anantharaman Vivek , de Souza Sandro José , Aravind L. , Gueiros-Filho Frederico J.
Published: August 2008

We describe AMIN (Amidase N-terminal domain), a novel protein domain found specifically in bacterial periplasmic proteins. AMIN domains are widely distributed among peptidoglycan hydrolases and transporter protein families. Based on experimental data, contextual information and phyletic profiles, we suggest that AMIN domains mediate the targeting of periplasmic or extracellular proteins to specific regions of the bacterial envelope.

Contact:  fgueiros@iq.usp.br

Supplementary information: Supplementary data are available at Bioinformatics online.
Optimal design of thermally stable proteins
Authors: Bannen Ryan M. , Suresh Vanitha , Phillips George N. , Wright Stephen J. , Mitchell Julie C.
Published: August 2008

Motivation: For many biotechnological purposes, it is desirable to redesign proteins to be more structurally and functionally stable at higher temperatures. For example, chemical reactions are intrinsically faster at higher temperatures, so using enzymes that are stable at higher temperatures would lead to more efficient industrial processes. We describe an innovative and computationally efficient method called Improved Configurational Entropy (ICE), which can be used to redesign a protein to be more thermally stable (i.e. stable at high temperatures). This can be accomplished by systematically modifying the amino acid sequence via local structural entropy (LSE) minimization. The minimization problem is modeled as a shortest path problem in an acyclic graph with nonnegative weights and is solved efficiently using Dijkstra's method.

Contact:  mitchell@biochem.wisc.edu
Improving position-specific predictions of protein functional sites using phylogenetic motifs
Authors: Dukka Bahadur K. C. , Livesay Dennis R.
Published: August 2008

Motivation: Accurate computational prediction of protein functional sites is critical to maximizing the utility of recent high-throughput sequencing efforts. Among the available approaches, position-specific conservation scores remain among the most popular due to their accuracy and ease of computation. Unfortunately, high false positive rates remain a limiting factor. Using phylogenetic motifs (PMs), we have developed two combined (conservation + PMs) prediction schemes that significantly improve prediction accuracy.

Results: Our first approach, called position-specific MINER (psMINER), rank orders alignment columns by conservation. Subsequently, positions that are also not identified as PMs are excluded from the prediction set. This approach improves prediction accuracy, in a statistically significant way, compared to the underlying conservation scores. Increased accuracy is a general result, meaning improvement is observed over several different conservation scores that span a continuum of complexity. In addition, a hybrid MINER (hMINER) that quantitatively considers both scoring regimes provides further improvement. More importantly, it provides critical insight into the relative importance of phylogeny versus alignment conservation. Both methods outperform other common prediction algorithms that also utilize phylogenetic concepts. Finally, we demonstrate that the presented results are critically sensitive to functional site definition, thus highlighting the need for more complete benchmarks within the prediction community.

Availability: Our benchmark datasets are available for download at http://www.cs.uncc.edu/~drlivesa/dataset.html.

Contact:  drlivesa@uncc.edu

Supplementary information:  Supplementary data is available at Bioinformatics online.
Penalties and rewards for over- and underages of catch allocations
Authors: Powers Joseph E. , Brooks Elizabeth N.
Published: August 2008

Powers, J. E., and Brooks, E. N. 2008. Penalties and rewards for over- and underages of catch allocations. – ICES Journal of Marine Science, 65: 1541–1551. Many fisheries are managed using a total allowable catch (TAC) that is subsequently sub-allocated to different fisheries sectors. These allocations are then monitored separately to ensure the adherence of each fishery to its particular allocation quota and to the overall TAC. In some management arenas, there are systems of “payback” where over- and underages are punished or rewarded using particular decision rules. Differences between fishing gear, the sizes and ages of fish being targeted by those gears, and the spatio-temporal distribution of the fishers using those gears can lead to different precision, accuracy, and cost of monitoring the allocation, affecting the probability that an overall management objective is reached. Weaknesses in monitoring may be exploited by user groups in their competition for larger catches and, subsequently, bigger allocations, so differential monitoring precision and accuracy can lead to both short- and long-term reallocations, i.e. a new set of winners and losers. Simulations in a management strategy evaluation framework were used to demonstrate the implications of alternative decision rules regarding payback on conservation and sustainability objectives and rebuilding time frames. The efficacy of the rules under alternative monitoring systems was also examined. Decision rules allowing payback prolong rebuilding (compared with perfect implementation or more precautionary TACs), especially if monitoring is biased (catches misreported) or imprecise. When precision of reported catches was increased and/or bias decreased, better yields and stock abundance resulted. When overages were penalized and underages not rewarded, recovery was achieved earlier. Conversely, policies in which transgressions were ignored and underages rewarded did not perform well. Underreporting by one nation may result in stocks that are well below the stock size conservation standards, yet produce substantial gains in yield for that nation, unless other nations retaliate by underreporting.
DNA base flipping by both members of the PspGI restriction-modification system
Authors: Carpenter Michael A. , Bhagwat Ashok S.
Published: August 2008

The PspGI restriction–modification system recognizes the sequence CCWGG. R.PspGI cuts DNA before the first C in the cognate sequence and M.PspGI is thought to methylate N4 of one of the cytosines in the sequence. M.PspGI enhances fluorescence of 2-aminopurine in DNA if it replaces the second C in the sequence, while R.PspGI enhances fluorescence when the fluorophore replaces ade-nine in the central base pair. This strongly suggests that the methyltransferase flips the second C in the recognition sequence, while the endonuclease flips both bases in the central base pair out of the duplex. M.PspGI is the first N4-cytosine MTase for which biochemical evidence for base flipping has been presented. It is also the first type IIP methyltransferase whose catalytic activity is strongly stimulated by divalent metal ions. However, divalent metal ions are not required for its base-flipping activity. In contrast, these ions are required for both base flipping and catalysis by the endonuclease. The two enzymes have similar temperature profiles for base flipping and optimal flipping occurs at temperatures substantially below the growth temperature of the source organism for PspGI and for the catalytic activity of endonuclease. We discuss the implications of these results for DNA binding by these enzymes and their evolutionary origin.
Nucleosome positioning in human HOX gene clusters
Authors: Kharchenko Peter V. , Woo Caroline J. , Tolstorukov Michael Y. , Kingston Robert E. , Park Peter J.
Published: August 2008

The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and is thought to influence gene regulation through modulation of DNA accessibility. However, properties of nucleosome organization remain poorly understood, particularly in mammalian genomes. Toward this goal we used tiled microarrays to identify stable nucleosome positions along the HOX gene clusters in human cell lines. We show that nucleosome positions exhibit sequence properties and long-range organization that are different from those characterized in other organisms. Despite overall variability of internucleosome distances, specific loci contain regular nucleosomal arrays with 195-bp periodicity. Moreover, such arrays tend to occur preferentially toward the 3′ ends of genes. Through comparison of different cell lines, we find that active transcription is correlated with increased positioning of nucleosomes, suggesting an unexpected role for transcription in the establishment of well-positioned nucleosomes.
Abnormal Chloroplast Development and Growth Inhibition in Rice ThioredoxinmKnock-Down Plants
Authors: Chi Yong Hun , Moon Jeong Chan , Park Jin Ho , Kim Ho-Seung , Zulfugarov Ismayil S. , Fanata Wahyu Indra , Jang Ho Hee , Lee Jung Ro , Lee Young Mee , Kim Sun Tae , Chung Yong-Yoon , Lim Chae Oh , Kim Jae-Yean , Yun Dae-Jin , Lee Choon-Hwan , Lee Kyun Oh , Lee Sang Yeol
Published: August 2008

Plant cells contain several thioredoxin isoforms that are characterized by subcellular localization and substrate specificity. Here, we describe the functional characterization of a rice (Oryza sativa) thioredoxin m isoform (Ostrxm) using a reverse genetics technique. Ostrxm showed green tissue-specific and light-responsive mRNA expression. Ostrxm was localized in chloroplasts of rice mesophyll cells, and the recombinant protein showed dithiothreitol-dependent insulin β-chain reduction activity in vitro. RNA interference (RNAi) of Ostrxm resulted in rice plants with developmental defects, including semidwarfism, pale-green leaves, abnormal chloroplast structure, and reduced carotenoid and chlorophyll content. Ostrxm RNAi plants showed remarkably decreased F  v/F  m values under high irradiance conditions (1,000 μmol m−2 s−1) with delayed recovery. Two-dimensional electrophoresis and matrix-assisted laser-desorption/ionization time-of-flight analysis showed that the levels of several chloroplast proteins critical for photosynthesis and biogenesis were significantly decreased in Ostrxm RNAi plants. Furthermore, 2-Cys peroxiredoxin, a known target of thioredoxin, was present in oxidized forms, and hydrogen peroxide levels were increased in Ostrxm RNAi plants. The pleiotropic effects of Ostrxm RNAi suggest that Ostrxm plays an important role in the redox regulation of chloroplast target proteins involved in diverse physiological functions.
Independently Silencing Two Photosynthetic Proteins inNicotiana attenuataHas Different Effects on Herbivore Resistance
Authors: Mitra Sirsha , Baldwin Ian T.
Published: August 2008

Insect attack frequently down-regulates photosynthetic proteins. To understand how this influences the plant-insect interaction, we transformed Nicotiana attenuata to independently silence ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCase) activase (RCA) and RuBPCase and selected lines whose photosynthetic capacity was similarly reduced. Decreases in plant growth mirrored the decreases in photosynthesis, but the effects on herbivore performance differed. Both generalist (Spodoptera littoralis) and specialist (Manduca sexta) larvae grew larger on RCA-silenced plants, which was consistent with decreased levels of trypsin protease inhibitors and diterpene glycosides and increased levels of RuBPCase, the larvae's main dietary protein. RCA-silenced plants were impaired in their attack-elicited jasmonate (JA)-isoleucine (Ile)/leucine levels, but RuBPCase-silenced plants were not, a deficiency that could not be restored by supplementation with Ile or attributed to lower transcript levels of JAR4/6, the key enzyme for JA-Ile conjugation. From these results, we infer that JA-Ile/leucine signaling and the herbivore resistance traits elicited by JA-Ile are influenced by adenylate charge, or more generally, carbon availability in RCA- but not RuBPCase-silenced plants. Growth of generalist larvae on RuBPCase-silenced plants did not differ from growth on empty vector controls, but the specialist larvae grew faster on RuBPCase-silenced plants, which suggests that the specialist can better tolerate the protein deficiency resulting from RuBPCase silencing than the generalist can. We conclude that the plant-herbivore interaction is more influenced by the particular mechanisms that reduce photosynthetic capacity after herbivore attack than by the magnitude of the decrease, which highlights the value of understanding defense mechanisms in evaluating growth-defense tradeoffs.
RACK1 Functions in Rice Innate Immunity by Interacting with the Rac1 Immune Complex
Authors: Nakashima Ayako , Chen Letian , Thao Nguyen Phuong , Fujiwara Masayuki , Wong Hann Ling , Kuwano Masayoshi , Umemura Kenji , Shirasu Ken , Kawasaki Tsutomu , Shimamoto Ko
Published: August 2008

A small GTPase, Rac1, plays a key role in rice (Oryza sativa) innate immunity as part of a complex of regulatory proteins. Here, we used affinity column chromatography to identify rice RACK1 (for Receptor for Activated C-Kinase 1) as an interactor with Rac1. RACK1 functions in various mammalian signaling pathways and is involved in hormone signaling and development in plants. Rice contains two RACK1 genes, RACK1A and RACK1B, and the RACK1A protein interacts with the GTP form of Rac1. Rac1 positively regulates RACK1A at both the transcriptional and posttranscriptional levels. RACK1A transcription was also induced by a fungal elicitor and by abscisic acid, jasmonate, and auxin. Analysis of transgenic rice plants and cell cultures indicates that RACK1A plays a role in the production of reactive oxygen species (ROS) and in resistance against rice blast infection. Overexpression of RACK1A enhances ROS production in rice seedlings. RACK1A was shown to interact with the N terminus of NADPH oxidase, RAR1, and SGT1, key regulators of plant disease resistance. These results suggest that RACK1A functions in rice innate immunity by interacting with multiple proteins in the Rac1 immune complex.
Type B Response Regulators of Arabidopsis Play Key Roles in Cytokinin Signaling and Plant Development
Authors: Argyros Rebecca D. , Mathews Dennis E. , Chiang Yi-Hsuan , Palmer Christine M. , Thibault Derek M. , Etheridge Naomi , Argyros D. Aaron , Mason Michael G. , Kieber Joseph J. , Schaller G. Eric
Published: August 2008

The type B Arabidopsis Response Regulators (ARRs) of Arabidopsis thaliana are transcription factors that act as positive regulators in the two-component cytokinin signaling pathway. We employed a mutant-based approach to perform a detailed characterization of the roles of ARR1, ARR10, and ARR12 in plant growth and development. The most pronounced phenotype was found in the arr1-3 arr10-5 arr12-1 triple loss-of-function mutant, which showed almost complete insensitivity to high levels of exogenously applied cytokinins. The triple mutant exhibited reduced stature due to decreased cell division in the shoot, enhanced seed size, increased sensitivity to light, altered chlorophyll and anthocyanin concentrations, and an aborted primary root with protoxylem but no metaxylem. Microarray analysis revealed that expression of the majority of cytokinin-regulated genes requires the function of ARR1, ARR10, and ARR12. Characterization of double mutants revealed differing contributions of the type B ARRs to mutant phenotypes. Our results support a model in which cytokinin regulates a wide array of downstream responses through the action of a multistep phosphorelay that culminates in transcriptional regulation by ARR1, ARR10, and ARR12.
Effective adoption of agri‐food assurance systems
Authors: Soderlund Russell , Williams Richard , Mulligan Cathy
Published: August 2008

Purpose

The purpose of this article is to identify the drivers for, and barriers to, the adoption of assurance systems in a range of agri‐food value chains that will allow the design of better, more appropriate‐for‐the‐task assurance systems that are more likely to be fully utilised by value chain members.

Design/methodology/approach

Semi‐structured interviews were used to collect a snapshot of the knowledge, attitudes, skills and aspirations (KASA) of value‐chain members with regard to assurance systems in fruit (cherries), seafood (mussels) and red meat (lamb). Responses were grouped by KASA characteristic for qualitative analysis. The nature of the dairy industry necessitated the use of a desktop review of the food‐safety assurance system.

Findings

The actual drivers for, and barriers to, adoption varied with the industry studied but included the requirements of domestic and export market customers, realistic appreciation of risk, mandatory schemes, the influence of other value chain members, financial incentives and external influences. The major barrier to the adoption of assurance systems was the perception that the costs of such an assurance system outweigh its benefits.

Research limitations/implications

This study was purely qualitative and covered only one value chain within each of three industries with a desktop review in a fourth industry.

Practical implications

A suite of drivers that includes financial incentives results in more effective adoption of assurance systems than a single driver such as market access.

Originality/value

The observations could lead to a series of design principles for the development and deployment of agri‐food assurance systems.
Food safety practices in milk collection centers in Turkey: a case study
Authors: Demirbaş Nevin , Gölge Evren , Tosun Duygu , Çukur Figen
Published: August 2008

Purpose

The aim of this study was to reveal the role and importance of the milk collection centers in İzmir in assuring food safety in the Turkish dairy sector.

Design/methodology/approach

A five‐point Likert scale was applied to collect data on the food safety practices and the problems confronted in MCCs. The difference between the groups in the managers' and MCCs' specifications and the food safety applications in the MCCs were determined by one‐way ANOVA for continuous variables. For the continuous variables, a normal distribution test was applied by Jarque‐Bera test. For variables displaying normal distribution, analysis of variance (one‐way ANOVA) was performed. For the variables not displaying normal distribution, Kruskall‐Wallis test. In the evaluation of other data descriptive statistics were applied.

Findings

Because the milk in the MCCs is generally obtained from small‐scale family farms, it is not of the desired quality from a food safety and food quality perspective. The quality control analysis of raw milk cannot be carried out because of the lack of qualified specialists and equipment inadequacies. The most general test applied on milk delivery is based on the monitoring of the sensory properties of the milk.

Research limitations/implications

All MCCs were covered in the sample size of the research and the questionnaires were applied to all 43 MCC managers in İzmir.

Practical implications

An effective organizational and educational structure must be established to monitor food safety and related practices in MCCs.

Originality/value

The paper adds to the body of knowledge on procecessors and their attitudes to food safety and suggests implementation of various practices which could improve results.
Consumer perspectives: take‐out packaging and food safety
Authors: Boyce Janice , Broz Charles C. , Binkley Margaret
Published: August 2008

Purpose

A consumer focus group was conducted in West Texas, to discuss consumer opinion about desired features in take‐out containers or packaging, and perceptions related to food safety practices.

Findings

The results of this qualitative case study indicated that the majority of take‐out food was purchased for personal consumption, and that location, convenience and time are the primary factors influencing the decision for purchase. The main features considered desirable in take‐out containers were these: the ability to insulate food, to contain product without spillage, and to keep individual foods separate within the same package.

Practical implications

As the desirability for take‐out food continues to increase, risks emerge surrounding the lack of handling instructions on most take‐out packaging, and the scarcity of consumer food safety knowledge. Though most participants in this study claimed to return home quickly with take‐out food after purchase, and consume the food as soon as possible, a good number admitted to not being as knowledgeable about food safety and handling as they would like.

Research limitations/implications

Though data were collected from a diverse group of panelists, the small scope of this research could not be said to represent the USA as a whole. Future studies would need to include multiple focus group studies in metropolitan regions across the nation.

Originality/value

The paper adds to the body of knowledge on take‐out food and customer attitudes to food safety.
Marketing aspects of quality assurance systems
Authors: Achilleas Kontogeorgos , Anastasios Semos
Published: August 2008

Purpose

The purpose of this paper is to describe the effect of quality assurance systems on business performance and subsequently, how a quality assurance system can be utilized as a determinant factor of a firm's marketing strategy, especially for the organic food sector.

Design/methodology/approach

Based on literature and the quality theory, the following subjects are examined: the types of goods according to their quality attributes, the benefits of participating in a quality award procedure, how a quality assurance system affect on firms' performance, and finally, the factors that determine consumers' willingness to pay a price premium for organic products.

Findings

The findings showed that, better quality conformance is associated with sales growth and better sales margins. Moreover, the most important benefit of a quality certification is its ability to increase market share and provide access to new market. In addition, the key to define quality is consumers and a company's internal definition of quality must reflect consumers' requirements. Finally, factors such as socio‐demographic characteristics, the perceived quality and risks have been found to be important determinants of consumers' willingness to pay a price premium to buy organic food products.

Originality/value

This study presents an outline of how a quality assurance system can be used to provide not only consistent product quality but also different elements that can be used to determine a firm's marketing strategy. The findings can help all the involved bodies to avoid the impediments and develop an appropriate marketing strategy for the effective promotion of certified organic food products.