bluuebunny/crossref_metadata_2025_split huggingface dataset:
Response to flooding: submergence tolerance in rice.
Authors: Ismail A. M. , Mackill D. J. 
Published: November 2013

Abstract

This chapter discusses submergence tolerance as a response to flooding, focusing on rice as a model crop where progress was made in developing flood-tolerant varieties and where opportunities exist for further improvements through mining the enormous genetic diversity available in preserved collections worldwide. The impacts of climate change on rice in flood-prone areas are briefly described. The progress made in exploiting the genetic variation in flooding tolerance-associated traits is summarized for rice germplasm improvement to develop high yielding varieties for flood-affected areas and for areas where floods are expected to worsen with climate change. Future directions in flood tolerance research in rice to cope with climate change are also mentioned.
Effects of climate change on plant-insect interactions and prospects for resistance breeding using genetic resources.
Authors: Pritchard J. , Broekgaarden C. , Vosman B. 
Published: November 2013

Abstract

This chapter describes the components (elevated CO2, temperature and drought) of climate change and their direct and indirect effects on plant-insect interactions. The genetic resources (such as wild relatives and traditional, locally adapted landraces) important for increasing pest/disease resistance in crop plants are described. Some strategies for introduction of pest and disease resistance are presented, which include traditional and biotechnological (genetic modification) approaches.
Agricultural Prices, Selection, and the Evolution of the Food Industry
Authors: Gaigné Carl , Le Mener Léo 
Published: November 2013

AbstractWe present a model that explains the relationship between low input prices, high exit rates, and industrial concentration. We argue that falling input prices force less productive firms to exit the market, and lead to the expansion of more efficient incumbents at the expense of less productive producers. Our model helps reconcile some well‐established empirical results regarding the food processing industry. Indeed, agricultural prices fell between the early 1900s and 2006, and over the same period there was a trend towards higher concentration in the food industry, with an increase in average productivity.
The Impact of Immigration Enforcement on the U.S. Farming Sector
Authors: Kostandini Genti , Mykerezi Elton , Escalante Cesar 
Published: November 2013

AbstractWe examine the effects of local immigration enforcement efforts on U.S. agriculture in dozens of U.S. counties from 2002–2010 by using variations in the timing of adoption of 287(g) programs, which permit local police to enforce immigration law. Difference‐in‐differences models using microdata from the American Community Survey (2005–2010 waves) and county tabulations from the Census of Agriculture (1997, 2002, and 2007) yield robust evidence that county enforcement efforts have reduced immigrant presence in adopting jurisdictions. We also find evidence that wages of farm workers, patterns of farm labor use, output choices, and farm profitability may have been affected in a manner consistent with farm labor shortages.
Temporal changes in the phytoplankton community along the French coast of the eastern English Channel and the southern Bight of the North Sea
Authors: Hernández-Fariñas Tania , Soudant Dominique , Barillé Laurent , Belin Catherine , Lefebvre Alain , Bacher Cédric 
Published: November 2013

Abstract
Long-term trends in the phytoplankton community along the French coast of the English Channel and southern Bight of the North Sea were studied and related to physico-chemical factors and large-climatic indices. Phytoplankton and hydrological data were acquired through three transects. Sampling took place between 1992 and 2011 as part of the French Phytoplankton Monitoring Network (REPHY) and the Regional Nutrients Monitoring Network (SRN). Trends in time-series were identified with dynamic linear models tailored to environmental monitoring data characteristics (e.g. irregular sampling frequency, missing data). Temporal and spatial patterns in the phytoplankton community were explained with a partial triadic analysis. Relationships between the phytoplankton community composition, environmental factors, and climatic indices were assessed using a redundancy analysis (RDA). The analyses revealed long-term changes in the community composition, characterized by a temporal structure that remained common to all transects. The abundance of some groups of taxa such as the one composed by Gymnodinium and Gyrodinium, as well as the group of Pseudo-nitzschia increased during the study period, whereas the abundance of other taxa as for example Guinardia and the group of Coscinodiscus and Stellarima globally decreased. More generally, the proportion of dinoflagellates relative to diatoms increased. Trends in environmental variables were also observed in most sites and related to decreases in nutrient concentrations and an increasing trend in salinity. The RDA indicated that the Atlantic Multidecadal Oscillation index and salinity were the main factors defining the temporal structure of the phytoplankton community. This suggests that variations observed in the phytoplankton community are linked to hydro-climatic changes in the coastal environment.
TRF1 and TRF2 use different mechanisms to find telomeric DNA but share a novel mechanism to search for protein partners at telomeres
Authors: Lin Jiangguo , Countryman Preston , Buncher Noah , Kaur Parminder , E Longjiang , Zhang Yiyun , Gibson Greg , You Changjiang , Watkins Simon C. , Piehler Jacob , Opresko Patricia L. , Kad Neil M. , Wang Hong 
Published: November 2013

AbstractHuman telomeres are maintained by the shelterin protein complex in which TRF1 and TRF2 bind directly to duplex telomeric DNA. How these proteins find telomeric sequences among a genome of billions of base pairs and how they find protein partners to form the shelterin complex remains uncertain. Using single-molecule fluorescence imaging of quantum dot-labeled TRF1 and TRF2, we study how these proteins locate TTAGGG repeats on DNA tightropes. By virtue of its basic domain TRF2 performs an extensive 1D search on nontelomeric DNA, whereas TRF1’s 1D search is limited. Unlike the stable and static associations observed for other proteins at specific binding sites, TRF proteins possess reduced binding stability marked by transient binding (∼9–17 s) and slow 1D diffusion on specific telomeric regions. These slow diffusion constants yield activation energy barriers to sliding ∼2.8–3.6 κBT greater than those for nontelomeric DNA. We propose that the TRF proteins use 1D sliding to find protein partners and assemble the shelterin complex, which in turn stabilizes the interaction with specific telomeric DNA. This ‘tag-team proofreading’ represents a more general mechanism to ensure a specific set of proteins interact with each other on long repetitive specific DNA sequences without requiring external energy sources.
Back to translation: removal of aIF2 from the 5′-end of mRNAs by translation recovery factor in the crenarchaeon Sulfolobus solfataricus
Authors: Märtens Birgit , Manoharadas Salim , Hasenöhrl David , Zeichen Lukas , Bläsi Udo 
Published: November 2013

Abstract
The translation initiation factor aIF2 of the crenarchaeon Sulfolobus solfataricus (Sso) recruits initiator tRNA to the ribosome and stabilizes mRNAs by binding via the γ-subunit to their 5′-triphosphate end. It has been hypothesized that the latter occurs predominantly during unfavorable growth conditions, and that aIF2 or aIF2-γ is released on relief of nutrient stress to enable in particular anew translation of leaderless mRNAs. As leaderless mRNAs are prevalent in Sso and aIF2-γ bound to the 5′-end of a leaderless RNA inhibited ribosome binding in vitro, we aimed at elucidating the mechanism underlying aIF2/aIF2-γ recycling from mRNAs. We have identified a protein termed Trf (translation recovery factor) that co-purified with trimeric aIF2 during outgrowth of cells from prolonged stationary phase. Subsequent in vitro studies revealed that Trf triggers the release of trimeric aIF2 from RNA, and that Trf directly interacts with the aIF2-γ subunit. The importance of Trf is further underscored by an impaired protein synthesis during outgrowth from stationary phase in a Sso trf deletion mutant.
Highly specific and sensitive method for measuring nucleotide excision repair kinetics of ultraviolet photoproducts in human cells
Authors: Choi Jun-Hyuk , Gaddameedhi Shobhan , Kim So-Young , Hu Jinchuan , Kemp Michael G. , Sancar Aziz 
Published: November 2013

AbstractThe nucleotide excision repair pathway removes ultraviolet (UV) photoproducts from the human genome in the form of short oligonucleotides ∼30 nt in length. Because there are limitations to many of the currently available methods for investigating UV photoproduct repair in vivo, we developed a convenient non-radioisotopic method to directly detect DNA excision repair events in human cells. The approach involves extraction of oligonucleotides from UV-irradiated cells, DNA end-labeling with biotin and streptavidin-mediated chemiluminescent detection of the excised UV photoproduct-containing oligonucleotides that are released from the genome during excision repair. Our novel approach is robust, with essentially no signal in the absence of UV or a functional excision repair system. Furthermore, our non-radioisotopic methodology allows for the sensitive detection of excision products within minutes following UV irradiation and does not require additional enrichment steps such as immunoprecipitation. Finally, this technique allows for quantitative measurements of excision repair in human cells. We suggest that the new techniques presented here will be a useful and powerful approach for studying the mechanism of human nucleotide excision repair in vivo.
Discrimination between thermodynamic models ofcis-regulation using transcription factor occupancy data
Authors: Zeigler Robert D. , Cohen Barak A. 
Published: November 2013

AbstractMany studies have identified binding preferences for transcription factors (TFs), but few have yielded predictive models of how combinations of transcription factor binding sites generate specific levels of gene expression. Synthetic promoters have emerged as powerful tools for generating quantitative data to parameterize models of combinatorial cis-regulation. We sought to improve the accuracy of such models by quantifying the occupancy of TFs on synthetic promoters in vivo and incorporating these data into statistical thermodynamic models of cis-regulation. Using chromatin immunoprecipitation-seq, we measured the occupancy of Gcn4 and Cbf1 in synthetic promoter libraries composed of binding sites for Gcn4, Cbf1, Met31/Met32 and Nrg1. We measured the occupancy of these two TFs and the expression levels of all promoters in two growth conditions. Models parameterized using only expression data predicted expression but failed to identify several interactions between TFs. In contrast, models parameterized with occupancy and expression data predicted expression data, and also revealed Gcn4 self-cooperativity and a negative interaction between Gcn4 and Nrg1. Occupancy data also allowed us to distinguish between competing regulatory mechanisms for the factor Gcn4. Our framework for combining occupancy and expression data produces predictive models that better reflect the mechanisms underlying combinatorial cis-regulation of gene expression.
Niche filtering rather than partitioning shapes the structure of temperate forest ant communities
Authors: Fowler David , Lessard Jean‐Philippe , Sanders Nathan J. 
Published: November 2013

Summary

An ever‐increasing number of studies use tools from community phylogenetics to infer the processes underlying the assembly of communities. However, very few studies simultaneously use experimental approaches to characterize the ecological niches of species and directly assess the importance of these structuring processes.

In this study, we developed an experimental approach for quantifying the use of four types of food resources and three habitat templets in temperate forest ant assemblages. We then used null models to assess whether niches overlapped more or less than expected by chance. Finally, we integrated comparative phylogenetic methods with experimental data on niche use to assess the degree of phylogenetic signal in several key components of the niche.

We found that niche filtering, rather than partitioning, was the predominant structuring force. Niche filtering resulted from conservatism in habitat niches in evolutionary time and limitations in the availability of food resources in ecological time.

Our study thus supports the idea that similarities in niches among species, rather than the differences, drive the assembly of ant communities.
Estimating the consequences of multiple threats and management strategies for semi‐aquatic turtles
Authors: Crawford Brian A. , Maerz John C. , Nibbelink Nathan P. , Buhlmann Kurt A. , Norton Terry M. 
Published: November 2013

Summary

Roads are pervasive fixtures on most landscapes but are typically among many factors contributing to wildlife population declines. Addressing road mortality as part of larger conservation efforts is challenging because it can be difficult to measure per capita mortality from roads and other concurrent threats.
We used 4 years of mark–recapture–recovery data for diamondback terrapins Malaclemys terrapin on a causeway in Georgia, USA, to directly estimate threats of adult road mortality and nest predation, contrast the consequences to population growth using stage‐based matrix models and make management recommendations to stabilize the population.
Mean estimated annual adult road mortality was 11·1% (range = 4·4–16·4%). Estimated annual nest predation was 61·9%. We estimated that the population was declining (λ < 0·98) in all scenarios where both threats were included. Variation in adult survival was the most influential (highest elasticity) contributor to population growth relative to other demographic rates; however, λ would remain below 1 with any nest predation rate exceeding our estimate even if actions to mitigate road mortality were 100% effective.
Synthesis and applications. Our study provides some of the first direct estimates of vehicle mortality rates and shows that mortality can remain sufficiently high among years to cause population declines. We also demonstrate that management actions focused on singular threats are inadequate for recovering populations. We conclude that integrated road and predator management is necessary to conserve turtle populations, and we suggest alternative strategies to compensate for some vehicle mortality and nest depredation.
Hot spots and hot moments of diamondback terrapin road‐crossing activity
Authors: Crawford Brian A. , Maerz John C. , Nibbelink Nathan P. , Buhlmann Kurt A. , Norton Terry M. , Albeke Shannon E. 
Published: November 2013

SummaryRoad mortality is a major component of human impacts on wildlife populations, and the pervasiveness of roads on the landscape presents a substantial challenge for managing those impacts. The feasibility of methods to reduce road mortality depends on the degree to which this threat is spatially or temporally concentrated, which can be based on habitat, human activities or species' ecology. Diamondback terrapinsMalaclemys terrapinare a species of conservation concern across their range, and road mortality is a major threat contributing to local population declines.We used intensive road surveys of the 8·7‐kmDowning‐MusgroveCauseway toJekyllIsland,Georgia,USA, over 2 years to determine whether road activity and mortality was diffused or concentrated spatially (hot spots) or temporally (hot moments) in order to guide efficient management.In 2009 and 2010, we documented 636 terrapin crossings that were temporally and spatially condensed. Temporally, there was a 70–80% chance of a terrapin occurring on the road within a 3‐h period around the diurnal high tide and within the first 30 days of the ˜75 day nesting season. Over the two nesting seasons, 52% of terrapin occurrences on the road occurred within the 3‐h period around high tide. Spatially, 30% of terrapins were observed crossing in three hot spots that composed less than 10% of the length of the entire causeway, and the percentage of unvegetated high marsh was negatively associated with the number of terrapins that occurred on a section of road.Synthesis and applications. Our results demonstrate that hot spots and hot moments can be identified for species at finer scales than those found by other studies and are related, strongly or weakly, to specific temporal processes or habitat features. We found patterns of road mortality, like most threats, can be diffused or concentrated; therefore, complementary management tools that focus on hot spots or moments and also address the more diffused component of road mortality will be required to reduce this threat for at‐risk wildlife.
Stability, genotypic and phenotypic diversity of Shewanella baltica in the redox transition zone of the Baltic Sea
Authors: Deng Jie , Brettar Ingrid , Luo Chengwei , Auchtung Jennifer , Konstantinidis Konstantinos T. , Rodrigues Jorge L. M. , Höfle Manfred , Tiedje James M. 
Published: November 2013

SummaryStudying how bacterial strains diverge over space and time and how divergence leads to ecotype formation is important for understanding structure and dynamics of environmental communities. Here we assess the ecological speciation and temporal dynamics of a collection of Shewanella baltica strains from the redox transition zone of the central Baltic Sea, sampled at three time points over a course of 12 years, with a subcollection containing 46 strains subjected to detailed genetic and physiological characterization. Nine clades were consistently recovered by three different genotyping approaches: gyrB gene sequencing, multilocus sequence typing (MLST) and whole genome clustering of data from comparative genomic hybridization, and indicated specialization according to nutrient availability, particle association and temporal distribution. Genomic analysis suggested higher intra‐ than inter‐clade recombination that might result from niche partitioning. Substantial heterogeneity in carbon utilization and respiratory capabilities suggested rapid diversification within the same ‘named’ species and physical habitat and showed consistency with genetic relatedness. At least two major ecotypes, represented by MLST clades A and E, were proposed based on genetic, ecological and physiological distinctiveness. This study suggests that genetic analysis in conjunction with phenotypic evaluation can provide better understanding of the ecological framework and evolutionary trajectories of microbial species.
The rulB gene of plasmid pWW0 is a hotspot for the site‐specific insertion of integron‐like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria
Authors: Rhodes Glenn , Bosma Hester , Studholme David , Arnold Dawn L. , Jackson Robert W. , Pickup Roger W. 
Published: November 2013

SummaryThe rulAB operon of Pseudomonas spp. confers fitness traits on the host and has been suggested to be a hotspot for insertion of mobile elements that carry avirulence genes. Here, for the first time, we show that rulB on plasmid pWW0 is a hotspot for the active site‐specific integration of related integron‐like elements (ILEs) found in six environmental pseudomonads (strains FH1–FH6). Integration into rulB on pWW0 occurred at position 6488 generating a 3 bp direct repeat. ILEs from FH1 and FH5 were 9403 bp in length and contained eight open reading frames (ORFs), while the ILE from FH4 was 16 233 bp in length and contained 16 ORFs. In all three ILEs, the first 5.1 kb (containing ORFs 1–4) were structurally conserved and contained three predicted site‐specific recombinases/integrases and a tetR homologue. Downstream of these resided ORFs of the ‘variable side’ with structural and sequence similarity to those encoding survival traits on the fitness enhancing plasmid pGRT1 (ILEFH1 and ILEFH5) and the NR‐II virulence region of genomic island PAGI‐5 (ILEFH4). Collectively, these ILEs share features with the previously described type III protein secretion system effector ILEs and are considered important to host survival and transfer of fitness enhancing and (a)virulence genes between bacteria.
Supporting families in genetic counselling services: a psychoeducational multifamily discussion group for at‐risk colorectal cancer families
Authors: Mendes Álvaro , Chiquelho Raquel , Santos Teresa A. , Sousa Liliana 
Published: November 2013

A non‐experimental exploratory study examining a multifamily discussion group for colorectal at‐risk individuals and their families is described. Four families attended a 90‐minute four‐session psychoeducational programme at a genetics centre of a Portuguese public hospital. A post‐programme focus group interview was performed to assess practical and psychosocial impact, and collect participants' views. Participants reported that the programme responds to the patients' and families' needs, enhancing their adaptation and coping to genetic illness. Results reinforce the need to integrate family‐centred interventions in genetic counselling services and address the holistic experience of hereditary disease. We conclude that the programme provides an integrated healthcare setting to help at‐risk individuals and their families cope with the specific biopsychosocial demands of their increased genetic susceptibility.Practitioner pointsMultifamily psychoeducational groups have a useful role in genetic counselling services.Family‐based approaches to genetic susceptibility to cancer need to be based on a family life‐cycle model incorporating the stage the cancer is diagnosed.Because of the reproductive implications of susceptibility, wider family members (and possibly adolescents) should be involved in the intervention.
Systemic sclerosis, birth order and parity
Authors: Russo Paul A. J. , Lester Susan , Roberts‐Thomson Peter J. 
Published: November 2013

AbstractAimA recent study identified increasing birth order to be a risk factor for the development of systemic sclerosis (SSc). This finding supports the theory that transplacental microchimerism may be a key pathological event in the initiation of SSc. We investigated the relationship between birth order and parity and the age of onset of SSc in South Australia.MethodA retrospective analysis of patient data in the South Australian Scleroderma Register was performed. Data were obtained from a mailed questionnaire. Control data was collected prospectively using a similar questionnaire. The relationship between birth order, family size or parity and risk of subsequent development of SSc was analyzed by mixed effects logistic regression analysis.ResultsThree hundred and eighty‐seven index probands were identified and compared with 457 controls. Controls were well matched for gender, but not for age. No statistically significant relationship was identified between SSc and birth order, parity in females, family size, age at first pregnancy in females or gender of first child in parous females.ConclusionOur data suggests that parity, age at first pregnancy and the gender of the first child are not relevant factors in our understanding of the epidemiology and pathogenesis of SSc. Birth order and family size in both genders also appears irrelevant. These results argue against microchimerism as being relevant in the pathogenesis of SSc and add further support to the theory that stochastic events may be important in the etiopathogenesis of SSc.