bluuebunny/crossref_metadata_2025 huggingface dataset:
Using simulated escape events to assess the annual numbers and
destinies of escaped farmed Atlantic salmon of different life stages from farm
sites in Norway
Authors: Skilbrei Ove T. , Heino Mikko , Svåsand Terje
Published: August 2014

To improve assessments of the environmental risks of aquaculture, a series of simulated escapes of farmed Atlantic salmon (Salmo salar L.) from seawater netpens were performed. Individually tagged post-smolts and adult Atlantic salmon were released from various locations at different times of the year. Post-smolts that escaped during their first summer were capable of rapid migration towards the open sea. A small fraction returned to spawn and were recaptured after 1–3 years at sea (0.4%, range 0.0–1.1%). A total of 13% of the post-smolts that escaped during autumn were reported in nearby fisheries during subsequent months, partly because they had grown large enough to be caught in the gillnets used, but more importantly because migratory behaviour diminished towards the end of the year. The mean recapture rate of adult salmon was high after releases in fjords (7–33%), lower after coastal releases (4–7%), and zero on the outer coast. Most of these recaptures were immature fish recaptured in sea relatively close to the release site during their first months post-release. Recaptures of adult escapees after 1–2 years in the wild were very rare (0.09%), probably because of their low survival. A Monte-Carlo method was developed to estimate the annual numbers of escapees from Norwegian fish farms based on reported catches of escaped farmed salmon in the sea and in rivers and the recapture probabilities reported here. The model provides a tool to estimate numbers of escapees independently from the reported numbers. Importantly, our analysis suggests that the total numbers of post-smolt and adult escapees have been two- to fourfold as high as the numbers reported to the authorities by fish farmers, depending on whether the incomplete sea fishery statistics are compensated for.
ZFP36L1 and ZFP36L2 control LDLR mRNA stability via the ERK–RSK pathway
Authors: Adachi Shungo , Homoto Masae , Tanaka Rikou , Hioki Yusaku , Murakami Hiroshi , Suga Hiroaki , Matsumoto Masaki , Nakayama Keiichi I. , Hatta Tomohisa , Iemura Shun-ichiro , Natsume Tohru
Published: August 2014

Low-density lipoprotein receptor (LDLR) mRNA is unstable, but is stabilized upon extracellular signal-regulated kinase (ERK) activation, possibly through the binding of certain proteins to the LDLR mRNA 3′-untranslated region (UTR), although the detailed mechanism underlying this stability control is unclear. Here, using a proteomic approach, we show that proteins ZFP36L1 and ZFP36L2 specifically bind to the 3′-UTR of LDLR mRNA and recruit the CCR4-NOT-deadenylase complex, resulting in mRNA destabilization. We also show that the C-terminal regions of ZFP36L1 and ZFP36L2 are directly phosphorylated by p90 ribosomal S6 kinase, a kinase downstream of ERK, resulting in dissociation of the CCR4-NOT-deadenylase complex and stabilization of LDLR mRNA. We further demonstrate that targeted disruption of the interaction between LDLR mRNA and ZFP36L1 and ZFP36L2 using antisense oligonucleotides results in upregulation of LDLR mRNA and protein. These results indicate that ZFP36L1 and ZFP36L2 regulate LDLR protein levels downstream of ERK. Our results also show the usefulness of our method for identifying critical regulators of specific RNAs and the potency of antisense oligonucleotide-based therapeutics.
ATP insertion opposite 8-oxo-deoxyguanosine by Pol4 mediates error-free tolerance in Schizosaccharomyces pombe
Authors: Sastre-Moreno Guillermo , Sánchez Arancha , Esteban Verónica , Blanco Luis
Published: August 2014

7,8-Dihydro-8-oxo-deoxyguanosine (8oxodG) is a highly premutagenic DNA lesion due to its ability to mispair with adenine. Schizosaccharomyces pombe lacks homologs for relevant enzymes that repair 8oxodG, which suggests that this lesion could be persistent and must be tolerated. Here we show that SpPol4, the unique PolX in fission yeast, incorporates ATP opposite 8oxodG almost exclusively when all nucleotides (ribos and deoxys) are provided at physiological concentrations. Remarkably, this SpPol4-specific reaction could also occur during the NHEJ of DSBs. In cell extracts, misincorporation of ATP opposite 8oxodG was shown to be SpPol4-specific, although RNase H2 efficiently recognized the 8oxodG:AMP mispair to remove AMP and trigger error-free incorporation of dCTP. These data are the first evidence that ribonucleotides can be used safely for 8oxodG tolerance, suggesting that insertion of the highly abundant ATP substrate could be beneficial to promote efficient and error-free repair of 8oxodG-associated DSBs. Moreover, we demonstrate that purified SpPol4 uses 8oxo-dGTP and 8oxo-GTP as substrates for DNA polymerization, although with poor efficiency compared to the incorporation of undamaged nucleotides opposite either 8oxodG or undamaged templates. This suggests that SpPol4 is specialized in tolerating 8oxodG as a DNA template, without contributing significantly to the accumulation of this lesion in the DNA.
Drosophila COP9 signalosome subunit 7 interacts with multiple genomic loci to regulate development
Authors: Singer Ruth , Atar Shimshi , Atias Osnat , Oron Efrat , Segal Daniel , Hirsch Joel A. , Tuller Tamir , Orian Amir , Chamovitz Daniel A.
Published: August 2014

The COP9 signalosome protein complex has a central role in the regulation of development of multicellular organisms. While the function of this complex in ubiquitin-mediated protein degradation is well established, results over the past few years have hinted that the COP9 signalosome may function more broadly in the regulation of gene expression. Here, using DamID technology, we show that COP9 signalosome subunit 7 functionally associates with a large number of genomic loci in the Drosophila genome, and show that the expression of many genes within these loci is COP9 signalosome-dependent. This association is likely direct as we show CSN7 binds DNA in vitro. The genes targeted by CSN7 are preferentially enriched for transcriptionally active regions of the genome, and are involved in the regulation of distinct gene ontology groupings including imaginal disc development and cell-cycle control. In accord, loss of CSN7 function leads to cell-cycle delay and altered wing development. These results indicate that CSN7, and by extension the entire COP9 signalosome, functions directly in transcriptional control. While the COP9 signalosome protein complex has long been known to regulate protein degradation, here we expand the role of this complex by showing that subunit 7 binds DNA in vitro and functions directly in vivo in transcriptional control of developmentally important pathways that are relevant for human health.
Number Representations and their Relation with Mathematical Ability
Authors: Gebuis Titia , Reynvoet Bert
Published: August 2014

In this chapter we review research on the processes that underlie the development of mathematical abilities. It is proposed that numerical deficiencies might arise from domain specific problems. The approximate number system that supports reasoning with non-symbolic numbers, on the one hand, and the symbolic number system on the other hand were put forth as possible candidates. To gain insight into the two different systems, we will describe the development of non-symbolic and symbolic number processing and introduce the two main theories about numerical deficiencies: the approximate number system and the access deficit hypothesis. The paradigms used to study both accounts differ in several ways and are of importance for research on the relation between non-symbolic and symbolic number and mathematical abilities. Then, we will review how the studies investigating both accounts relate to two different sets of developmental models that describe the neural representation of number.
Mapping the Brain for Math
Authors: Salillas Elena , Semenza Carlo
Published: August 2014

Brain stimulation techniques allow for the search of crucial areas for a given function. Not always convergent with neuroimaging, TMS studies have targeted parietal areas critical for quantity representation, spatio-numerical links, numerical and non-numerical quantity, finger gnosis and calculation. TMS data indicate the intraparietal sulcus and surrounding areas in the left and right hemisphere as crucial for quantity processing, although left hemisphere might be dominant. Bilateral parietal loci are essential for calculation and bilateral parietal areas are behind the spatio-numerical link, which extends to frontal and posterior parietal sites. DCE studies to date have focused on the dominant hemisphere, have used calculation tasks and have found both dissociation and overlap between operations. An integrative view of positive findings and a focus on convergence and possible improvement is proposed. Although regularities are found between these techniques, more research is needed before arriving at conclusions that will have basic and clinical importance.
The Neuroscience of Singing
Authors: Kleber Boris A. , Zarate Jean Mary
Published: August 2014

To produce vocalizations including speech and song, the control of all muscles along the vocal tract (e.g. for respiration, vocal fold motion, resonance changes, and articulation) requires the concerted effort of a vast network of brain regions. However, singers are usually unaware of the neural networks that govern and coordinate all of these muscle groups, or what happens in these networks when auditory or somatosensory feedback notifies the singer of vocal errors, or if feedback is compromised even temporarily. In this chapter, the authors attempt to define the basic neural networks involved in singing, discuss how these networks may change due to extensive vocal training and practice, and present recent findings that illustrate how the networks respond to alterations to auditory and kinesthetic feedback.
In Praise of Imperfect Commitment
Authors: Welch Sharon D.
Published: August 2014

There are moments in history where there are major breakthroughs in the power of social movements. Large numbers of people recognize the depth of injustice, see possibilities of beauty and integrity heretofore unknown, and find new forms of coming together to bring about change. We are living in such a moment. In this chapter I explore the work of historians, social scientists, economists, and political activists who are helping us understand how to be creative, constructive, and effective agents of social justice. At the core of this effective work for social justice is the embrace of a fallibility based world view and an ethic of risk. This embrace constitutes the emergence of a new honor code in which the measure of our success is not the perfection of our efforts but our honesty, humility, accountably, resilience, and audacity in the face of unintended consequences and ongoing challenges.
Crime and Punishment in Emerging Adulthood
Authors: Craig Jessica , Piquero Alex R.
Published: August 2014

Emerging adulthood is a time of transition and identity development, largely between late adolescence and into early adulthood. During this period, individuals are navigating their new roles as adulthood ensues and, for some, antisocial behavior is part of this time period. This chapter highlights some of the main findings regarding the age–crime relationship, discusses some of the most central theories for understanding this relationship, and reviews the various punishment and rehabilitation strategies that have been applied to adolescent (and, very recently, emerging adulthood) offending. The authors identify gaps in the knowledge base, and possible avenues for both theoretical and empirical research are suggested.
Utilizing a Preplant Soil Test for Predicting and Estimating Root Rot Severity in Sugar Beet in the Central High Plains of the United States
Authors: Harveson R. M. , Nielsen K. A. , Eskridge K. M.
Published: August 2014

Aphanomyces cochlioides and Rhizoctonia solani are important soilborne pathogens causing root diseases that are primary constraints to sugar beet production in Nebraska, Colorado, and Wyoming. These types of diseases are difficult to control because they are often not noticed until substantial damage has already occurred. Efforts to manage them would be more effective if techniques were available that were more predictive than reactive. Therefore, a preplant soil test was developed to estimate the relative pathogen populations in the soil and to predict potential root disease problems later in the growing season. Preplant soil samples collected from fields to be sown with sugar beet were planted with a susceptible cultivar and tests were conducted for 1 month in the greenhouse. A preplant disease index was developed based on the time period during the test that seedlings became infected and was calculated on a 0-to-100 scale. Disease index values were compared with yields obtained from the same fields after harvest. Analysis of data collected for 5 years (2003 to 2007) with analysis of covariance revealed a strong relationship between the preplant disease index values and recoverable sucrose and root yields but not sucrose concentration. Results indicated that, for each unit increase in the preplant disease index, root yield decreased by 0.27 metric tons (270 kg) per hectare (P < 0.05, R2 = 0.44) and recoverable sucrose decreased by 49 kg/ha (P < 0.05, R2 = 0.45). We concluded that this preplant soil test can accurately predict root disease potential due to R. solani and A. cochlioides, and has the potential to help producers make effective management decisions in production fields using the index procedure. This soil assay has additionally provided new information on the biology, incidence, and distribution of root pathogens in production fields throughout the Central High Plains.
Distribution of Potato spindle tuber viroid in Reproductive Organs of Petunia During Its Developmental Stages
Authors: Matsushita Yosuke , Tsuda Shinya
Published: August 2014

Embryo infection is important for efficient seed transmission of viroids. To identify the major pattern of seed transmission of viroids, we used in situ hybridization to histochemically analyze the distribution of Potato spindle tuber viroid (PSTVd) in each developmental stage of petunia (flowering to mature seed stages). In floral organs, PSTVd was present in the reproductive tissues of infected female × infected male and infected female × healthy male but not of healthy female × infected male before embryogenesis. After pollination, PSTVd was detected in the developed embryo and endosperm in all three crosses. These findings indicate that PSTVd is indirectly delivered to the embryo through ovule or pollen during the development of reproductive tissues before embryogenesis but not directly through maternal tissues as cell-to-cell movement during embryogenesis.
Impact of the Anesthetic Conserving Device on Respiratory Parameters and Work of Breathing in Critically Ill Patients under Light Sedation with Sevoflurane
Authors: Chabanne Russell , Perbet Sebastien , Futier Emmanuel , Said Nordine Ait Ben , Jaber Samir , Bazin Jean-Etienne , Pereira Bruno , Constantin Jean-Michel
Published: August 2014

Background:

Sevoflurane sedation in the intensive care unit is possible with a special heat and moisture exchanger called the Anesthetic Conserving Device (ACD) (AnaConDa®; Sedana Medical AB, Uppsala, Sweden). The ACD, however, may corrupt ventilatory mechanics when used during the weaning process of intensive care unit patients. The authors compared the ventilatory effects of light-sedation with sevoflurane administered with the ACD and those of classic management, consisting of a heated humidifier and intravenous sedation, in intensive care unit patients receiving pressure-support ventilation.

Methods:

Fifteen intensive care unit patients without chronic pulmonary disease were included. A target Richmond Agitation Sedation Scale level of −1/−2 was obtained with intravenous remifentanil (baseline 1-condition). Two successive interventions were tested: replacement of the heated humidifier by the ACD without sedation change (ACD-condition) and sevoflurane with the ACD with an identical target level (ACD-sevoflurane-condition). Patients finally returned to baseline (baseline 2-condition). Work of breathing, ventilatory patterns, blood gases, and tolerance were recorded. A steady state of 30 min was achieved for each experimental condition.

Results:

ACD alone worsened ventilatory parameters, with significant increases in work of breathing (from 1.7 ± 1.1 to 2.3 ± 1.2 J/l), minute ventilation, P0,1, intrinsic positive end-expiratory pressure (from 1.3 ± 2.6 to 4.7 ± 4.2 cm H2O), inspiratory pressure swings, and decreased patient comfort. Sevoflurane normalized work of breathing (from 2.3 ± 1.2 to 1.8 ± 1 J/l), intrinsic positive end-expiratory pressure (from 4.7 ± 4.2 to 1.8 ± 2 cm H2O), inspiratory pressure swings, other ventilatory parameters, and patient tolerance.

Conclusions:

ACD increases work of breathing and worsens ventilatory parameters. Sevoflurane use via the ACD (for a light-sedation target) normalizes respiratory parameters. In this patient’s population, light-sedation with sevoflurane and the ACD may be possible during the weaning process.
Lunar and terrestrial planet formation in the Grand Tack scenario
Authors: Jacobson S. A. , Morbidelli A.
Published: August 2014

We present conclusions from a large number ofN-body simulations of the giant impact phase of terrestrial planet formation. We focus on new results obtained from the recently proposed Grand Tack model, which couples the gas-driven migration of giant planets to the accretion of the terrestrial planets. The giant impact phase follows the oligarchic growth phase, which builds a bi-modal mass distribution within the disc of embryos and planetesimals. By varying the ratio of the total mass in the embryo population to the total mass in the planetesimal population and the mass of the individual embryos, we explore how different disc conditions control the final planets. The total mass ratio of embryos to planetesimals controls the timing of the last giant (Moon-forming) impact and its violence. The initial embryo mass sets the size of the lunar impactor and the growth rate of Mars. After comparing our simulated outcomes with the actual orbits of the terrestrial planets (angular momentum deficit, mass concentration) and taking into account independent geochemical constraints on the mass accreted by the Earth after the Moon-forming event and on the time scale for the growth of Mars, we conclude that the protoplanetary disc at the beginning of the giant impact phase must have had most of its mass in Mars-sized embryos and only a small fraction of the total disc mass in the planetesimal population. From this, we infer that the Moon-forming event occurred between approximately 60 and approximately 130 Myr after the formation of the first solids and was caused most likely by an object with a mass similar to that of Mars.
Pedobacter xixiisoli sp. nov., isolated from bank soil
Authors: Zeng Yanhua , Feng Hao , Huang Yili
Published: August 2014

A Gram-stain-negative, rod-shaped, yellow, non-motile, aerobic bacterium (strain S27T) was isolated from bank soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on its 16S rRNA gene sequence, revealed that strain S27T could represent a novel species of the genus

Pedobacter

showing highest similarity to

Pedobacter koreensis

WPCB189T (95.45 %), followed by ‘Pedobacter zeaxanthinifaciens’ TDMA-5 (95.22 %). The temperature, pH and NaCl concentration ranges for growth were 6–37 °C (optimum 28 °C), pH 5.0–9.0 (optimum pH 7.5) and 0–3 % (w/v) [optimum 0.5 % (w/v)], respectively. The DNA G+C content was 36.1 mol%, MK-7 was the only respiratory quinone, and iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH) were the major fatty acids. These data all support the affiliation of strain S27T to the genus

Pedobacter

. The polar lipids of strain S27T comprised phosphatidylethanolamine, one unidentified aminophospholipid, four unidentified aminolipids and three unidentified lipids. However, strain S27T could be distinguished from other members of the genus

Pedobacter

due to its physiological and biochemical characteristics. Therefore, strain S27T represents a novel species of the genus

Pedobacter

, for which the name Pedobacter xixiisoli sp. nov. is proposed; the type strain is S27T ( = CGMCC 1.12803T = NBRC 110388T).
Desertibacter xinjiangensis sp. nov., isolated from the soil of a Euphrates poplar forest, and emended description of the genus Desertibacter
Authors: Jiang Fan , Xue Xiuqing , Qiu Xia , Zhang Kundi , Chang Xulu , Da Xuyang , Tang Yali , Fang Chengxiang , Guo Youhao , Peng Fang
Published: August 2014

A pale pink and strictly aerobic bacterium, designated strain M71T, was isolated from the soil of a Euphrates poplar forest in Xingjiang, PR China. Cells of the strain were Gram-reaction-negative, rod-shaped and motile by means of a single polar flagellum. Growth occurred at 10–37 °C (optimum 30 °C), at pH 6.0–9.0 (optimum pH 7.0–8.0) and with 0–2.0 % NaCl (w/v, optimum 0 %). Phylogenetic analysis, based on 16S rRNA gene sequences, indicated that strain M71T belongs to the genus

Desertibacter

in the family

Rhodospirillaceae

. The 16S rRNA gene sequence of this strain showed 96.2 % sequence similarity with the type strain of

Desertibacter roseus

2262T. The respiratory quinone was Q-10 and the predominant cellular fatty acids were C18 : 1ω7c (53.2 %), C16 : 1ω5c (11.0 %), summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 10.2 %) and C16 : 0 (8.5 %). The DNA G+C content was 71.2 mol% (HPLC). The strain contained phosphatidylcholine and phosphatidylethanolamine as the predominant polar lipids. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain M71T is considered to represent a novel species of the genus

Desertibacter

, for which the name Desertibacter
xinjiangensis sp. nov. is proposed. The type strain is M71T ( = CCTCC AB 209291T = CIP 110127T).
Metschnikowia drakensbergensis sp. nov. and Metschnikowia caudata sp. nov., endemic yeasts associated with Protea flowers in South Africa
Authors: de Vega Clara , Guzmán Beatriz , Steenhuisen Sandy-Lynn , Johnson Steven D. , Herrera Carlos M. , Lachance Marc-André
Published: August 2014

In a taxonomic study of yeasts recovered from nectar of flowers and associated insects in South Africa, 11 strains were found to represent two novel species. Morphological and physiological characteristics and sequence analyses of the large-subunit rRNA gene D1/D2 region, as well as the actin, RNA polymerase II and elongation factor 2 genes, showed that the two novel species belonged to the genus Metschnikowia. Metschnikowia drakensbergensis sp. nov. (type strain EBD-CdVSA09-2T = CBS 13649T = NRRL Y-63721T; MycoBank no. MB809688; allotype EBD-CdVSA10-2A = CBS13650A = NRRL Y-63720A) was recovered from nectar of Protea roupelliae and the beetle Heterochelus sp. This species belongs to the large-spored Metschnikowia clade and is closely related to Metschnikowia proteae, with which mating reactions and single-spored asci were observed. Metschnikowia caudata sp. nov. (type strain EBD-CdVSA08-1T = CBS 13651T = NRRL Y-63722T; MycoBank no. MB809689; allotype EBD-CdVSA57-2A = CBS 13729A = NRRL Y-63723A) was isolated from nectar of Protea dracomontana, P. roupelliae and P. subvestita and a honeybee, and is a sister species to Candida hainanensis and Metschnikowia lopburiensis. Analyses of the four sequences demonstrated the existence of three separate phylotypes. Intraspecies matings led to the production of mature asci of unprecedented morphology, with a long, flexuous tail. A single ascospore was produced in all compatible crosses, regardless of sequence phylotype. The two species appear to be endemic to South Africa. The ecology and habitat specificity of these novel species are discussed in terms of host plant and insect host species.
Mycobacterium abscessus infection in cystic fibrosis: molecular typing and clinical outcomes
Authors: Harris Kathryn A. , Kenna Dervla T. D.
Published: August 2014

Mycobacterium abscessus is a significant pathogen in the cystic fibrosis patient population. PCR amplification and sequencing can provide accurate subspecies identification, and can predict macrolide susceptibility, which is becoming increasingly important for patient management. Molecular techniques for further typing of isolates provide tools for the ongoing investigations into the clinical impact of particular M. abscessus strains. Whole-genome sequencing is likely to be the only technique that provides sufficient resolution for investigating transmission events between patients.
Clonal diversity of Acinetobacter baumannii from diabetic patients in Saudi Arabian hospitals
Authors: Alsultan Abdulrahman A. , Aboulmagd Elsayed , Evans Benjamin A. , Amyes Sebastian G. B.
Published: August 2014

Carbapenem-resistantAcinetobacter baumannii(CR-AB) represents a major health-care problem, causing high rates of morbidity and mortality. This study investigated the clonality of CR-AB isolated from diabetic patients from different regions in Saudi Arabia, as well as the relatedness of the β-lactamase genes. A total of 64 non-repetitive CR-AB clinical isolates were collected from 16 different regions in Saudi Arabia from intensive care patients. Isolates were identified phenotypically by the Vitek 2 compact system and genotypically by amplification of theblaOXA-51-likegene. The target sequences were amplified by PCR and the clonal diversity of the isolates was explored by PFGE. Resistance studies revealed that the prevalence of imipenem and meropenem resistance was 92 % and 96 %, respectively, while the vast majority of the isolates were susceptible to tigecycline and colistin. In addition,blaVIMandblaOXA-23were the most prevalent genes in the isolates under investigation, while ISAba1was the most dominant insertion sequence. PFGE results showed 13 clusters; clone H was dominant, comprising 20 isolates from four hospitals, followed by clones C and F, comprising 11 isolates each from three and six hospitals, respectively. Moreover, the current study signified the clonal diversity of CR-AB in Saudi Arabia and showed the ability of some clones to infect patients in many different cities.
NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases
Authors: Costa Marta , Manton James D. , Ostrovsky Aaron D. , Prohaska Steffen , Jefferis Gregory S. X. E.
Published: August 2014

Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches.

We validated NBLAST on a published dataset of 16,129 singleDrosophilaneurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) withouta prioriinformation. Cluster analysis of extensively studied neuronal classes identified new types and un-reported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish.
Seasonality dynamics of avian influenza occurrences in Central and West Africa
Authors: Fuller T. L. , Ducatez M. F. , Njabo K. Y. , Couacy-Hymann E. , Chasar T. , Aplogan G. L. , Lao S. , Awoume F. , Téhou A. , Langeois Q. , Krauss S. , Smith T. B.
Published: August 2014

Understanding seasonal cycles of viruses originating in wildlife can provide insight into their likelihood of persistence in animal populations and inform policies to limit spillover to human populations. Avian influenza virus (AIV) is an important zoonotic agent causing seasonal occurrence of avian influenza (AI) in wild birds in temperate areas. Although the seasonality of AIV transmission in tropical birds is largely unknown, peaks of influenza activity in human populations in the tropics coincide with the rainy season. To assess the seasonality of AI in tropical birds, from 2010-14, we sampled 40,099 birds at 32 sites in Central Africa (Cameroon, Central African Republic, Congo-Brazzaville, and Gabon) and West Africa (Benin, Côte d’Ivoire, and Togo). Although AIV was not isolated by egg culture, in Central Africa, detection rates by real-time RT-PCR were 3.57% for passerine songbirds and 8.74% for Anatid ducks. RT-PCR positivity in resident birds increased when Palearctic migrants arrived in Central Africa. At sampling sites with two annual wet seasons, the positive rate in wild birds was greatest during the big rainy season in September – October. This study provides the first evidence that AI is present in Central African birds and identifies environmental factors associated with cases.
Mapping migration in a songbird using high-resolution genetic markers
Authors: Ruegg Kristen , Anderson Eric C. , Paxton Kristina L. , Apkenas Vanessa , Lao Sirena , Siegel Rodney B. , DeSante David F. , Moore Frank , Smith Thomas B.
Published: August 2014

Neotropical migratory birds are declining across the Western Hemisphere, but conservation efforts have been hampered by the inability to assess where migrants are most limited – the breeding grounds, migratory stopover sites, or wintering areas. A major challenge has been the lack of an efficient, reliable, and broadly applicable method for connecting populations across the annual cycle. Here we show how high-resolution genetic markers can be used to identify populations of a migratory bird, the Wilson’s warbler (Cardellina pusilla), at fine enough spatial scales to facilitate assessing regional drivers of demographic trends. By screening 1626 samples using 96 single nucleotide polymorphisms (SNPs) selected from a large pool of candidates (∼450,000), we identify novel region-specific migratory routes and timetables of migration along the Pacific Flyway. Our results illustrate that high-resolution genetic markers are more reliable, accurate, and amenable to high throughput screening than previously described tracking techniques, making them broadly applicable to large-scale monitoring and conservation of migratory organisms.
Induced sensitivity of Bacillus subtilis colony morphology to mechanical media compression
Authors: Polka Jessica K. , Silver Pamela A.
Published: August 2014

Bacteria from several taxa, including Kurthia zopfii, Myxococcus xanthus, and Bacillus mycoides, have been reported to align growth of their colonies to small features on the surface of solid media, including anisotropies created by compression. While the function of this phenomenon is unclear, it may help organisms navigate on solid phases, such as soil. The origin of this behavior is also unknown: it may be biological (that is, dependent on components that sense the environment and regulate growth accordingly) or merely physical. Here we show that B. subtilis, an organism that typically does not respond to media compression, can be induced to do so with two simple and synergistic perturbations: a mutation that maintains cells in the swarming (chained) state, and the addition of EDTA to the growth media, which further increases chain length. EDTA apparently increases cell length by inducing defects in cell separation, as the treatment has only marginal effects on the length of individual cells. These results lead us to three conclusions. First, the wealth of genetic tools available to B. subtilis will provide a new, tractable chassis for engineering compression sensitive organisms. Second, the sensitivity of colony morphology to media compression in Bacillus is a physical rather than biological phenomenon dependent on a simple physical property of rod-shaped cells. And third, colony morphology under compression holds promise as a rapid, simple, and low-cost way to screen for changes in the length of rod-shaped cells or chains thereof.
Predicting genome sizes and restriction enzyme recognition-sequence probabilities across the eukaryotic tree of life
Authors: Herrera Santiago , Reyes-Herrera Paula H. , Shank Timothy M.
Published: August 2014

High-throughput sequencing of reduced representation libraries obtained through digestion with restriction enzymes ? generically known as restriction-site associated DNA sequencing (RAD-seq) ? is a common strategy to generate genome-wide genotypic and sequence data from eukaryotes. A critical design element of any RAD-seq study is a knowledge of the approximate number of genetic markers that can be obtained for a taxon using different restriction enzymes, as this number determines the scope of a project, and ultimately defines its success. This number can only be directly determined if a reference genome sequence is available, or it can be estimated if the genome size and restriction recognition sequence probabilities are known. However, both scenarios are uncommon for non-model species. Here, we performed systematic in silico surveys of recognition sequences, for diverse and commonly used type II restriction enzymes across the eukaryotic tree of life. Our observations reveal that recognition-sequence frequencies for a given restriction enzyme are strikingly variable among broad eukaryotic taxonomic groups, being largely determined by phylogenetic relatedness. We demonstrate that genome sizes can be predicted from cleavage frequency data obtained with restriction enzymes targeting ?neutral? elements. Models based on genomic compositions are also effective tools to accurately calculate probabilities of recognition sequences across taxa, and can be applied to species for which reduced-representation data is available (including transcriptomes and ?neutral? RAD-seq datasets). The analytical pipeline developed in this study, PredRAD (https://github.com/phrh/PredRAD), and the resulting databases constitute valuable resources that will help guide the design of any study using RAD-seq or related methods.
Efficient Bayesian mixed model analysis increases association power in large cohorts
Authors: Loh Po-Ru , Tucker George , Bulik-Sullivan Brendan K , Vilhjálmsson Bjarni J , Finucane Hilary K , Chasman Daniel I , Ridker Paul M , Neale Benjamin M , Berger Bonnie , Patterson Nick , Price Alkes L
Published: August 2014

Linear mixed models are a powerful statistical tool for identifying genetic associations and avoiding confounding. However, existing methods are computationally intractable in large cohorts, and may not optimize power. All existing methods require time cost O(MN2) (where N = #samples and M = #SNPs) and implicitly assume an infinitesimal genetic architecture in which effect sizes are normally distributed, which can limit power. Here, we present a far more efficient mixed model association method, BOLT-LMM, which requires only a small number of O(MN) iterations and increases power by modeling more realistic, non-infinitesimal genetic architectures via a Bayesian mixture prior on marker effect sizes. We applied BOLT-LMM to nine quantitative traits in 23,294 samples from the Women’s Genome Health Study (WGHS) and observed significant increases in power, consistent with simulations. Theory and simulations show that the boost in power increases with cohort size, making BOLT-LMM appealing for GWAS in large cohorts.
Expanding xylose metabolism in yeast for plant cell wall conversion to biofuels
Authors: Li Xin , Yu Vivian Yaci , Lin Yuping , Chomvong Kulika , Estrela Raíssa , Liang Julie M. , Znameroski Elizabeth A. , Feehan Joanna , Kim Soo Rin , Jin Yong-Su , Glass N. Louise , Cate Jamie H. D.
Published: August 2014

Sustainable biofuel production from renewable biomass will require the efficient and complete use of all abundant sugars in the plant cell wall. Using the cellulolytic fungusNeurospora crassaas a model, we identified a xylodextrin transport and consumption pathway required for its growth on hemicellulose. Successful reconstitution of this xylodextrin utilization pathway inSaccharomyces cerevisiaerevealed that fungal xylose reductases act as xylodextrin reductases, and together with two hydrolases, generate intracellular xylose and xylitol. Xylodextrin consumption using xylodextrin reductases and tandem intracellular hydrolases greatly expands the capacity of yeasts to use plant cell wall-derived sugars, and should be adaptable to increase the efficiency of both first-generation and next-generation biofuel production.
Metabolism-Based Herbicide Resistance and Cross-Resistance in Crop Weeds: A Threat to Herbicide Sustainability and Global Crop Production
Authors: Yu Qin , Powles Stephen
Published: August 2014

Weedy plant species that have evolved resistance to herbicides due to enhanced metabolic capacity to detoxify herbicides (metabolic resistance) are a major issue. Metabolic herbicide resistance in weedy plant species first became evident in the 1980s in Australia (in Lolium rigidum) and the United Kingdom (in Alopecurus myosuroides) and is now increasingly recognized in several crop-weed species as a looming threat to herbicide sustainability and thus world crop production. Metabolic resistance often confers resistance to herbicides of different chemical groups and sites of action and can extend to new herbicide(s). Cytochrome P450 monooxygenase, glycosyl transferase, and glutathione S-transferase are often implicated in herbicide metabolic resistance. However, precise biochemical and molecular genetic elucidation of metabolic resistance had been stalled until recently. Complex cytochrome P450 superfamilies, high genetic diversity in metabolic resistant weedy plant species (especially cross-pollinated species), and the complexity of genetic control of metabolic resistance have all been barriers to advances in understanding metabolic herbicide resistance. However, next-generation sequencing technologies and transcriptome-wide gene expression profiling are now revealing the genes endowing metabolic herbicide resistance in plants. This Update presents an historical review to current understanding of metabolic herbicide resistance evolution in weedy plant species.
Unraveling the Mechanism Underlying the Glycosylation and Methylation of Anthocyanins in Peach
Authors: Cheng Jun , Wei Guochao , Zhou Hui , Gu Chao , Vimolmangkang Sornkanok , Liao Liao , Han Yuepeng
Published: August 2014

Modification of anthocyanin plays an important role in increasing its stability in plants. Here, six anthocyanins were identified in peach (Prunus persica), and their structural diversity is attributed to glycosylation and methylation. Interestingly, peach is quite similar to the wild species Prunus ferganensis but differs from both Prunus davidiana and Prunus kansueasis in terms of anthocyanin composition in flowers. This indicates that peach is probably domesticated from P. ferganensis. Subsequently, genes responsible for both methylation and glycosylation of anthocyanins were identified, and their spatiotemporal expression results in different patterns of anthocyanin accumulation in flowers, leaves, and fruits. Two tandem-duplicated genes encoding flavonoid 3-O-glycosyltransferase (F3GT) in peach, PpUGT78A1 and PpUGT78A2, showed different activity toward anthocyanin, providing an example of divergent evolution of F3GT genes in plants. Two genes encoding anthocyanin O-methyltransferase (AOMT), PpAOMT1 and PpAOMT2, are expressed in leaves and flowers, but only PpAOMT2 is responsible for the O-methylation of anthocyanins at the 3′ position in peach. In addition, our study reveals a novel branch of UGT78 genes in plants that lack the highly conserved intron 2 of the UGT gene family, with a great variation of the amino acid residue at position 22 of the plant secondary product glycosyltransferase box. Our results not only provide insights into the mechanisms underlying anthocyanin glycosylation and methylation in peach but will also aid in future attempts to manipulate flavonoid biosynthesis in peach as well as in other plants.
Comparative Transcriptome Atlases Reveal Altered Gene Expression Modules between Two Cleomaceae C3 and C4 Plant Species
Authors: Külahoglu Canan , Denton Alisandra K. , Sommer Manuel , Maß Janina , Schliesky Simon , Wrobel Thomas J. , Berckmans Barbara , Gongora-Castillo Elsa , Buell C. Robin , Simon Rüdiger , De Veylder Lieven , Bräutigam Andrea , Weber Andreas P.M.
Published: August 2014

C4 photosynthesis outperforms the ancestral C3 state in a wide range of natural and agro-ecosystems by affording higher water-use and nitrogen-use efficiencies. It therefore represents a prime target for engineering novel, high-yielding crops by introducing the trait into C3 backgrounds. However, the genetic architecture of C4 photosynthesis remains largely unknown. To define the divergence in gene expression modules between C3 and C4 photosynthesis during leaf ontogeny, we generated comprehensive transcriptome atlases of two Cleomaceae species, Gynandropsis gynandra (C4) and Tarenaya hassleriana (C3), by RNA sequencing. Overall, the gene expression profiles appear remarkably similar between the C3 and C4 species. We found that known C4 genes were recruited to photosynthesis from different expression domains in C3, including typical housekeeping gene expression patterns in various tissues as well as individual heterotrophic tissues. Furthermore, we identified a structure-related module recruited from the C3 root. Comparison of gene expression patterns with anatomy during leaf ontogeny provided insight into genetic features of Kranz anatomy. Altered expression of developmental factors and cell cycle genes is associated with a higher degree of endoreduplication in enlarged C4 bundle sheath cells. A delay in mesophyll differentiation apparent both in the leaf anatomy and the transcriptome allows for extended vein formation in the C4 leaf.
TheArabidopsis14-3-3 Protein RARE COLD INDUCIBLE 1A Links Low-Temperature Response and Ethylene Biosynthesis to Regulate Freezing Tolerance and Cold Acclimation
Authors: Catalá Rafael , López-Cobollo Rosa , Mar Castellano M. , Angosto Trinidad , Alonso José M. , Ecker Joseph R. , Salinas Julio
Published: August 2014

In plants, the expression of 14-3-3 genes reacts to various adverse environmental conditions, including cold, high salt, and drought. Although these results suggest that 14-3-3 proteins have the potential to regulate plant responses to abiotic stresses, their role in such responses remains poorly understood. Previously, we showed that the RARE COLD INDUCIBLE 1A (RCI1A) gene encodes the 14-3-3 psi isoform. Here, we present genetic and molecular evidence implicating RCI1A in the response to low temperature. Our results demonstrate that RCI1A functions as a negative regulator of constitutive freezing tolerance and cold acclimation in Arabidopsis thaliana by controlling cold-induced gene expression. Interestingly, this control is partially performed through an ethylene (ET)-dependent pathway involving physical interaction with different ACC SYNTHASE (ACS) isoforms and a decreased ACS stability. We show that, consequently, RCI1A restrains ET biosynthesis, contributing to establish adequate levels of this hormone in Arabidopsis under both standard and low-temperature conditions. We further show that these levels are required to promote proper cold-induced gene expression and freezing tolerance before and after cold acclimation. All these data indicate that RCI1A connects the low-temperature response with ET biosynthesis to modulate constitutive freezing tolerance and cold acclimation in Arabidopsis.
Identification of a Sphingolipid α-Glucuronosyltransferase That Is Essential for Pollen Function inArabidopsis
Authors: Rennie Emilie A. , Ebert Berit , Miles Godfrey P. , Cahoon Rebecca E. , Christiansen Katy M. , Stonebloom Solomon , Khatab Hoda , Twell David , Petzold Christopher J. , Adams Paul D. , Dupree Paul , Heazlewood Joshua L. , Cahoon Edgar B. , Scheller Henrik Vibe
Published: August 2014

Glycosyl inositol phosphorylceramide (GIPC) sphingolipids are a major class of lipids in fungi, protozoans, and plants. GIPCs are abundant in the plasma membrane in plants, comprising around a quarter of the total lipids in these membranes. Plant GIPCs contain unique glycan decorations that include a conserved glucuronic acid (GlcA) residue and various additional sugars; however, no proteins responsible for glycosylating GIPCs have been identified to date. Here, we show that the Arabidopsis thaliana protein INOSITOL PHOSPHORYLCERAMIDE GLUCURONOSYLTRANSFERASE1 (IPUT1) transfers GlcA from UDP-GlcA to GIPCs. To demonstrate IPUT1 activity, we introduced the IPUT1 gene together with genes for a UDP-glucose dehydrogenase from Arabidopsis and a human UDP-GlcA transporter into a yeast mutant deficient in the endogenous inositol phosphorylceramide (IPC) mannosyltransferase. In this engineered yeast strain, IPUT1 transferred GlcA to IPC. Overexpression or silencing of IPUT1 in Nicotiana benthamiana resulted in an increase or a decrease, respectively, in IPC glucuronosyltransferase activity in vitro. Plants in which IPUT1 was silenced accumulated IPC, the immediate precursor, as well as ceramides and glucosylceramides. Plants overexpressing IPUT1 showed an increased content of GIPCs. Mutations in IPUT1 are not transmitted through pollen, indicating that these sphingolipids are essential in plants.
Protection of Wistar‐Furth rats against postischaemic acute renal injury: Role for nitric oxide and thromboxane?
Authors: Voisin Viginie , Declèves Anne‐Emilie , Hubert Virginie , Colombaro Vanessa , Giordano Laetitia , Habsch Isabelle , Bouby Nadine , Nonclercq Denis , Caron Nathalie
Published: August 2014

The Wistar‐Furth (WF) rat strain is usually used in models of full major histocompatibility complex‐mismatched kidney transplantation. Because these rats have been demonstrated to be resistant to several models of chronic kidney disease, the aim of the present study was to investigate their potential resistance to renal ischaemia–reperfusion (I/R) injury compared with another strain, namely Wistar‐Hanover (WH) rats. Anaesthetized male WH and WF rats were submitted to I/R by occlusion of the left renal artery and contralateral nephrectomy. Urine, blood and tissue samples were collected at different time points after I/R to evaluate renal function, inflammation and tubular injury, along with determination of nitric oxide synthase (NOS) expression and thromboxane A2 (TxA2) production. Post‐ischaemic renal function was better preserved in WF than WH rats, as evidenced by reduced levels of creatininaemia, urinary neutrophil gelatinase‐associated lipocalin excretion and proteinuria. In addition, WF rats had less intrarenal inflammation than WH rats after I/R injury. These observations were associated with maintenance of neuronal NOS expression, along with lower induction of inducible NOS expression in WF versus WH rats. Moreover, WF rats excreted a significantly lower amount of TxB2. The results indicate that WF rats are more resistant to an I/R injury than WH rats in terms of renal function and inflammation. These observations are associated with differential regulation of intrarenal NOS expression, as well as a reduction in thromboxane production, which could contribute to a better outcome for the postischaemic kidney in WF rats.