bluuebunny/crossref_metadata_2025_split huggingface dataset:
hnRNP A1 mediates the activation of the IRES-dependent SREBP-1a mRNA translation in response to endoplasmic reticulum stress
Authors: Damiano Fabrizio , Rochira Alessio , Tocci Romina , Alemanno Simone , Gnoni Antonio , Siculella Luisa 
Published: October 2012

A growing amount of evidence suggests the involvement of ER (endoplasmic reticulum) stress in lipid metabolism and in the development of some liver diseases such as steatosis. The transcription factor SREBP-1 (sterol-regulatory-element-binding protein 1) modulates the expression of several enzymes involved in lipid synthesis. Previously, we showed that ER stress increased the SREBP-1a protein level in HepG2 cells, by inducing a cap-independent translation of SREBP-1a mRNA, through an IRES (internal ribosome entry site), located in its leader region. In the present paper, we report that the hnRNP A1 (heterogeneous nuclear ribonucleoprotein A1) interacts with 5′-UTR (untranslated region) of SREBP-1a mRNA, as an ITAF (IRES trans-acting factor), regulating SREBP-1a expression in HepG2 cells and in primary rat hepatocytes. Overexpression of hnRNP A1 in HepG2 cells and in rat hepatocytes increased both the SREBP-1a IRES activity and SREBP-1a protein level. Knockdown of hnRNP A1 by small interfering RNA reduced either the SREBP-1a IRES activity or SREBP-1a protein level. hnRNP A1 mediates the increase of SREBP-1a protein level and SREBP-1a IRES activity in Hep G2 cells and in rat hepatocytes upon tunicamycin- and thapsigargin-induced ER stress. The induced ER stress triggered the cytosolic relocation of hnRNP A1 and caused the increase in hnRNP A1 bound to the SREBP-1a 5′-UTR. These data indicate that hnRNP A1 participates in the IRES-dependent translation of SREBP-1a mRNA through RNA–protein interaction. A different content of hnRNP A1 was found in the nuclei from high-fat-diet-fed mice liver compared with standard-diet-fed mice liver, suggesting an involvement of ER stress-mediated hnRNP A1 subcellular redistribution on the onset of metabolic disorders.
Genetic Pedigree Reconstruction Facilitates Lakewide Estimates of Age‐0 Largemouth Bass Dispersal
Authors: Hessenauer Jan‐Michael , Bremigan Mary Tate , Scribner Kim T. 
Published: October 2012

AbstractDispersal from natal areas is an important event for fishes, ultimately affecting individual adult reproductive success and population levels of recruitment and genetic diversity. However, quantification of dispersal rates and distance and the associated environmental covariates is difficult when individuals are too small to physically mark. Using genetic techniques, we studied the dispersal of largemouth bass Micropterus salmoides from their natal nests in two southern Michigan lakes. In Warner Lake, we sampled larvae from 33 nests during spring 2010 and collected 33 age‐0 fish during summer. In Lake Chemung, we collected 138 and 140 age‐0 fish during the summers of 2009 and 2010, respectively. Pedigree reconstruction techniques were used to determine (1) the dispersal distance of age‐0 largemouth bass from nests to late‐summer points of capture (Warner Lake) and (2) interindividual distances between age‐0 full‐sibling pairs (Lake Chemung). Age‐0 fish in Warner Lake dispersed an average of 301 ± 41 m (mean ± SE). In Lake Chemung, intersibling dispersion distances varied substantially among pairs, but the distribution of distances was not significantly different from that of randomly selected pairs of individuals. Together, the data showed that age‐0 largemouth bass dispersed considerable distances from their nests and that the distance and direction of dispersal by siblings appeared to be independent of nest site. Our methods can be widely used for detailed evaluation of fish dispersal and effects of physical and biotic lakescape features on dispersal and recruitment.
Empirical Standard Weight Equation for the Aegean Chub Squalius fellowesii, an Endemic Freshwater Fish Species of Western Anatolia, Turkey
Authors: Giannetto Daniela , Pompei Laura , Lorenzoni Massimo , Tarkan Ali Serhan 
Published: October 2012

Abstract
Data on length and weight of Aegean chub Squalius fellowesii, an endemic species distributed in the Aegean drainages of Anatolia, Turkey, were used to calculate a standard weight (Ws) equation by means of the empirical percentile (EmP) method. The resulting Ws equation was log10 Ws = −3.801 + 1.783·log10TL + 0.329·(log10TL)2. Over the range of application (70–220 mm TL), the EmP Ws equation was not biased by length, and the use of this equation is suggested as a way to calculate the relative weight (Wr) of Aegean chub throughout the species’ distribution area.
Received June 12, 2012; accepted July 27, 2012
Discriminating Rainbow Trout Sources Using Freshwater and Marine Otolith Growth Chemistry
Authors: Veinott Geoff , Porter Rex 
Published: October 2012

Abstract
Rainbow Trout Oncorhynchus mykiss are nonindigenous to Newfoundland. Subsequent to the development of marine cage rearing of Rainbow Trout in the Atlantic provinces in the early 1970s, Rainbow Trout have been captured in 33 rivers on the west and south coast of Newfoundland. These escapees may have negative impacts on wild populations, particularly Atlantic Salmon Salmo salar and Brook Trout Salvelinus fontinalis. In this study, the chemical fingerprints in the freshwater and marine growth sections of otoliths were used to distinguish three groups of Rainbow Trout of known origins: two hatcheries and one wild population. The results were then used to assign fish of unknown origin to the three known-origin groups and thus estimate the proportion of escapees. The three known sources produced distinct chemical fingerprints in the freshwater growth of the otoliths (cross validation test, average accuracy of over 93%); whereas, the marine growth in the otoliths produced a single chemical fingerprint for the two hatchery-origin groups distinct from the wild population. Results indicated that at least 60% of the unknown-origin fish were aquaculture escapees. Vaterite was encountered in 70–80% of the known hatchery-origin fish, 0% in the wild population, and 50% in the escapees. It appears that escapees with vaterite had a lower survival rate. The presence–absence of vaterite did not appear to be useful in distinguishing escapees from a wild population.
Dragon TIS Spotter: an Arabidopsis-derived predictor of translation initiation sites in plants
Authors: Magana-Mora Arturo , Ashoor Haitham , Jankovic Boris R. , Kamau Allan , Awara Karim , Chowdhary Rajesh , Archer John A.C. , Bajic Vladimir B. 
Published: October 2012

Abstract
Summary: In higher eukaryotes, the identification of translation initiation sites (TISs) has been focused on finding these signals in cDNA or mRNA sequences. Using Arabidopsis thaliana (A.t.) information, we developed a prediction tool for signals within genomic sequences of plants that correspond to TISs. Our tool requires only genome sequence, not expressed sequences. Its sensitivity/specificity is for A.t. (90.75%/92.2%), for Vitis vinifera (66.8%/94.4%) and for Populus trichocarpa (81.6%/94.4%), which suggests that our tool can be used in annotation of different plant genomes. We provide a list of features used in our model. Further study of these features may improve our understanding of mechanisms of the translation initiation.
Availability and implementation: Our tool is implemented as an artificial neural network. It is available as a web-based tool and, together with the source code, the list of features, and data used for model development, is accessible at http://cbrc.kaust.edu.sa/dts.
Contact: vladimir.bajic@kaust.edu.sa
Supplementary information: Supplementary data are available at Bioinformatics online.
MP-T: improving membrane protein alignment for structure prediction
Authors: Hill Jamie R. , Deane Charlotte M. 
Published: October 2012

Abstract
Motivation: Membrane proteins are clinically relevant, yet their crystal structures are rare. Models of membrane proteins are typically built from template structures with low sequence identity to the target sequence, using a sequence-structure alignment as a blueprint. This alignment is usually made with programs designed for use on soluble proteins. Biological membranes have layers of varying hydrophobicity, and membrane proteins have different amino-acid substitution preferences from their soluble counterparts. Here we include these factors into an alignment method to improve alignments and consequently improve membrane protein models.
Results: We developed Membrane Protein Threader (MP-T), a sequence-structure alignment tool for membrane proteins based on multiple sequence alignment. Alignment accuracy is tested against seven other alignment methods over 165 non-redundant alignments of membrane proteins. MP-T produces more accurate alignments than all other methods tested (δFM from +0.9 to +5.5%). Alignments generated by MP-T also lead to significantly better models than those of the best alternative alignment tool (one-fourth of models see an increase in GDT_TS of ≥4%).
Availability: All source code, alignments and models are available at http://www.stats.ox.ac.uk/proteins/resources
Contact: deane@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Phenological and phenotypic changes in Atlantic salmon populations in response to a changing climate
Authors: Todd Christopher D. , Friedland Kevin D. , MacLean Julian C. , Whyte Bryce D. , Russell Ian C. , Lonergan Michael E. , Morrissey Michael B. 
Published: October 2012

Abstract
Todd, C. D., Friedland, K. D., MacLean, J. C., Whyte, B. D., Russell, I. C., Lonergan, M. E., and Morrissey, M. B. 2012. Phenological and phenotypic changes in Atlantic salmon populations in response to a changing climate. – ICES Journal of Marine Science, 69: 1686–1698. Atlantic salmon (Salmo salar) of southern European origin migrating to the Norwegian Sea currently encounter anomalously high sea-surface temperatures, and returning adults are of low mean condition factor. For the River North Esk (Scotland), time-series changes in river age-structure of emigrant smolts and returning one- and two-sea-winter (1SW and 2SW) adults are assessed. A comparison of the river age-structure of returning adults (1977–1999) with that of their respective annual emigrant smolt cohorts shows no evidence of river age-related bias in survivorship at sea. Evidence is presented of a possible transgenerational, or maternal, influence (poor somatic condition of spawners) driving reduced quality of emigrant S2 smolts in the North Esk. This effect is concurrent with an influence of freshwater climate as indicated by the North Atlantic Oscillation Index (NAOI). The maternal influence and NAOI variation in the winter immediately prior to smolt migration jointly explain approximately 29 (S2) and 17% (S3), respectively, of the variation in the mean size of smolts over the period 1975–2010. Run-timing of 1SW adult cohorts returning to Scotland shows recent delays. Variation in river flow did influence mean return date for the River Tweed, but adult condition factor, which itself shows temporal trends likely to be associated with ocean climate change, was the primary significant explanatory variable for run-timing in the rivers North Esk and Tweed. Overall, in years of poorer adult condition, 1SW salmon stay at sea longer.
Assessment of goose barnacle (Pollicipes pollicipes Gmelin, 1789) stocks in management plans: design of a sampling program based on the harvesters' experience
Authors: Parada J. M. , Outeiral R. , Iglesias E. , Molares J. 
Published: October 2012

Abstract
Parada, J. M., Outeiral, R., Iglesias, E., and Molares, J. 2012. Assessment of goose barnacle (Pollicipes pollicipes Gmelin, 1789) stocks in management plans: design of a sampling program based on the harvesters' experience. – ICES Journal of Marine Science, 69: 1840–1849. Management plans of coastal marine resources require a wealth of information on socioeconomic topics, harvesting activities, population dynamics, and stock status. Moreover, the information provided by technical experts must take into account the needs of the managers. It must also adapt to schedules to serve a useful purpose. In many cases, the methodologies used by research teams are not directly applicable as they may be too complicated, aimed at specific objectives related to basic scientific work, or too costly to apply to long-term monitoring of extensive shellfish beds. Also, rocky coastlines exposed to heavy wave action preclude the use of sampling techniques that involve time-consuming data collection. This paper proposes a quick and simple methodology for gathering data in the field, based on the knowledge of the harvesters, to obtain stock assessments in keeping with their information needs. This methodology uses coverage percentage as an abundance index and weighting factor for the biometric information gathered from 50 specimens in each sampling. The sampling design uses the knowledge of the harvesters to define homogeneous strata. The results are in agreement with both the scientific-technical knowledge and the harvesters' knowledge of the populations being analysed.
Cusk (Brosme brosme) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act
Authors: Hare Jonathan A. , Manderson John P. , Nye Janet A. , Alexander Michael A. , Auster Peter J. , Borggaard Diane L. , Capotondi Antonietta M. , Damon-Randall Kimberly B. , Heupel Eric , Mateo Ivan , O'Brien Loretta , Richardson David E. , Stock Charles A. , Biegel Sarah T. 
Published: October 2012

AbstractHare, J.A., Manderson, J.P., Nye, J.A., Alexander, M.A., Auster, P.J., Borggaard, D.L., Capotondi, A.M., Damon-Randall, K.B., Heupel, E., Mateo, I., O'Brien, L., Richardson, D.E., Stock, C.A., and Biege, S.T. 2012. Cusk (Brosme brosme) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act. – ICES Journal of Marine Science, 69: 1753–1768. In the Northwest Atlantic Ocean cusk (Brosme brosme) has declined dramatically, primarily as a result of fishing activities. These declines have led to concern about its status, which has prompted reviews under the US Endangered Species Act and the Canadian Species at Risk Act. Changes in distribution and abundance of a number of marine fish in the Northwest Atlantic have been linked to climate variability and change, suggesting that both fishing and climate may affect the status of cusk. Our goal was to evaluate potential effects of climate change on Northwest Atlantic cusk distribution. Coupling a species niche model with the output from an ensemble of climate models, we projected cusk distribution in the future. Our results indicate cusk habitat in the region will shrink and fragment, which is a result of a spatial mismatch between high complexity seafloor habitat and suitable temperature. The importance of habitat patch connectivity for cusk is poorly understood, so the population-level consequences of climate-related habitat fragmentation are uncertain. More broadly, climate change may reduce appropriate thermal habitat and increase habitat fragmentation for other cold-water species in the region; thereby, increasing the potential for regional overexploitation and extirpation.
First Report of Laurel Oak as a Host for the Pecan Root-Knot Nematode, Meloidogyne partityla, in Florida
Authors: Brito J. A. , Han H. , Stanley J. D. , Hao M. , Dickson D. W. 
Published: October 2012

Roots of laurel oak (Quercus laurifolia Michx.), member of the family Fagaceae, were found to be heavily galled by the pecan root-knot nematode, Meloidogyne partityla, in two separate home gardens between 2010 and 2012, in Alachua Co., FL. Distinct round galls were observed on secondary and tertiary roots. Internally, root-knot nematode females were clearly visible when the roots were thinly sliced and egg masses were seen protruding from the root surfaces. The nematode species identification was performed using morphology of the male stylet, selected characters of the second-stage juveniles (J2), female perineal patterns, and esterase (EST) and malate dehydrogenase (Mdh) isozyme phenotypes. Morphology of perineal patterns of females, body, stylet, and tail length of the J2 and males all matched those of the original description of M. partityla (2). A swollen deeply grooved rectum was observed in the J2. The male stylet had a blunt tip with a prominent thickening at the junction between the cone and shaft. The stylet knobs of males and females were bipartite, each incised by a deep medium longitudinal groove (2). The isozyme phenotypes (EST = Mp3; Mdh = N1a) were consistent with those previously reported for M. partityla from Florida (1). Mitochondrial DNA (mtDNA) (3) and ribosomal internal transcriber spacer (ITS) DNA (4) of females were amplified to further confirm the nematode species identification. The mtDNA amplification using the C2F3/1108 primer set (3) and the ITS amplification using a recently available M. partityla specific primer set (4) produced fragments of approximately 530 bp and 550 bp, respectively. These were consistent with those already reported for this nematode species. This first report of a plant host for the pecan root-knot nematode outside of the family Juglandaceae indicates that the nematode may have migrated from Quercus species to pecan trees during the period when orchards were being established in Florida. To our knowledge, this is the first report of the pecan root-knot nematode infecting laurel oak. References: (1) J. A. Brito et al. Nematology 10:757, 2008. (2) Kleynhans, K. P. N. Phytophylatica 18:103, 1986. (3) T. O. Powers et al., J. Nematol. 37:226, 2005. (4) R. A. Stamler. M. S. thesis, New Mexico State University, Las Cruces, 2009.
Identification of Fusarium oxysporum f. sp. lycopersici Race 3 Infecting Tomatoes in Northeast Brazil
Authors: Barboza E. A. , Cabral C. S. , Gonçalves A. M. , Reis A. , Fonseca M. E. N. , Boiteux L. S. 
Published: October 2012

The three races of Fusarium oxysporum f. sp. lycopersici (FOL) are important tomato pathogens throughout the world, causing severe economic losses (1). In Brazil, races 1 and 2 are widespread, but the current geographic distribution of race 3 is restricted to the mild climate areas of Espírito Santo and Rio de Janeiro States in the southeast region (2,3). Here we report the spread of FOL race 3 to the warm northeast region of Brazil. Plants in commercial fields of the hybrid ‘Alambra’ (resistant to FOL races 1 and 2) were found displaying chlorosis, vascular browning, and wilt symptoms in Jaguaquara County, Bahia State, Brazil. Disease incidence ranged from 10 to 50%. The virulence profile of six isolates obtained from three distinct tomato-producing fields was investigated by root-dipping inoculation (106 conidia/ml) of 21-day-old seedlings from a set of FOL race differential accessions: ‘Ponderosa’ (susceptible to all races), ‘IPA-5’ (FOL race 1 resistance; I-1 locus); ‘Alambra’ and ‘Floradade’ (FOL races 1 and 2 resistance; I-2 gene), and Solanum pennellii ‘LA 716’ (resistant to all three races; I-3 locus). All six isolates were able to induce severe wilt symptoms in 100% of the plants from all lines but S. pennellii ‘LA 716’. FOL race 3 identity was confirmed via PCR assays employing a specific set of primers that are able to discriminate all the three FOL races as well as F. oxysporum f. sp. radicis-lycopersici isolates (1). Total DNA was extracted from pure fungal colonies growing in agar medium. The typical FOL race 3 amplicon profiles (i.e. positive for the primers uni, sp13, and sp23 and negative for the primer sprl) were observed only in the six FOL 3 isolates from Bahia as well as in five reference isolates of race 3 (previously obtained from tomato in Espírito Santo and Rio de Janeiro States), thus confirming their race identities. This recent, fast, and wide geographic expansion of the FOL race 3 in Brazil suggests that the pathogen has been introduced into new tomato producing areas via either contaminated seeds or seedlings. Because of the complexity of establishing effective chemical and cultural control strategies, these epidemics caused by FOL race 3 in distinct areas of Brazil might cause the replacement of the currently grown susceptible hybrids by resistant ones. References: (1) Y. Hirano and T. Arie. J. Gen. Plant Pathol. 72:273, 2006; (2) A. Reis et al. Fitopatol. Bras. 30:426, 2005; (3) A. Reis and L. S. Boiteux. Hort. Bras. 25:451, 2007.
First Report of Cherry necrotic rusty mottle virus on Stone Fruit Trees in China
Authors: Zhou J. F. , Wang G. P. , Qu L. N. , Deng C. L. , Wang Y. , Wang L. P. , Hong N. 
Published: October 2012

During the growing seasons of 2010 through 2012, leaf tissues from 206 stone fruit trees, including one flowering cherry, three sour cherry, six nectarine (Prunus persica L. var. nucipersica Schneider), 14 apricot, 24 plum (P. domestica L.), 41 sweet cherry, and 117 peach [P. persica (L.) Batsch] trees, grown in six provinces of China, were randomly collected and tested for the CNRMV infection by RT-PCR. Out of those sampled trees, 37 showed shot holes and vein yellowing symptoms. Total RNA was extracted from leaves using the CTAB protocol reported by Li et al. (2). The primer pair CGRMV1/CGRMV2 (1) was used to amplify a fragment of 949 bp from CNRMV genome, which includes the CP gene (804 bp). PCR products with the expected size were detected in one sweet cherry, one apricot, one peach, one plum, and two sour cherry plants. However, no correlation between PCR data and symptom expression could be found. PCR products were cloned into the vector pMD18-T (TaKaRa, Dalian, China). Three independent clones from each isolate were sequenced by Genscript Corp., Nanjing, China, and sequences were deposited in the GenBank under accession nos. JX491635, JX491636, JX491637, JX648205, and JX648206. Results of sequence analysis showed that sequences of the five CNRMV isolates shared the highest nt (99.0 to 99.6%) and aa (98.9 to 100%) similarities with a cherry isolate from Germany (GenBank Accession No. AF237816). The sequence of one isolate from a peach tree (JX648205) was divergent and shared only 84.7 to 86.1% nt and 94.4 to 95.1% aa similarities with those cp sequences. Clones intra each isolate shared more than 99% nt similarities. To confirm CNRMV infection, seedlings of peach GF 305 were graft-inoculated with bud-woods from a peach and a sweet cherry tree, which was positive to CNRMV and also two other viruses: Cherry green ring mottle virus (CGRMV) and Plum bark necrosis stem pitting-associated virus (PBNSPaV), as tested by RT-PCR. Grafted seedlings were kept in an insectproof greenhouse and observed for symptom development. In May of the following year, some newly developed leaves of inoculated seedlings showed vein yellowing, ringspot, and shot hole symptoms. Results of Protein A sandwich (PAS)-ELISA using an antiserum raised against the recombinant CP of a CNRMV isolate (unpublished) and RT-PCR confirmed CNRMV infection in inoculated trees. In addition to CNRMV, tested seedlings were also found to be infected with CGRMV and PBNSPaV by RT-PCR. To our knowledge, this is the first report on the occurrence of CNRMV on stone fruit trees in China, and also the first record of the CNRMV infection in peach and plum plants. Given the economic importance of its hosts and the visible symptoms of the viral disease, it is important to prevent the virus spread by using virus-tested propagation materials. References: (1) R. Li and R. Mock. J. Virol. Methods 129:162, 2005. (2) R. Li et al. J. Virol. Methods 154:48, 2008.