Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Nucleotide binding site-leucine rich repeat (NBS-LRR)-encoding genes comprise the largest class of plant disease resistance genes. The 149 NBS-LRR-encoding genes and the 58 related genes that do not encode LRRs represent approximately 0.8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes.</p> <p>Results</p> <p>We analyzed the expression patterns of ~170 NBS-LRR-encoding and related genes in Arabidopsis Col-0 using multiple analytical approaches: expressed sequenced tag (EST) representation, massively parallel signature sequencing (MPSS), microarray analysis, rapid amplification of cDNA ends (RACE) PCR, and gene trap lines. Most of these genes were expressed at low levels with a variety of tissue specificities. Expression was detected by at least one approach for all but 10 of these genes. The expression of some but not the majority of NBS-LRR-encoding and related genes was affected by salicylic acid (SA) treatment; the response to SA varied among different accessions. An analysis of previously published microarray data indicated that ten NBS-LRR-encoding and related genes exhibited increased expression in wild-type Landsberg <it>erecta </it>(L<it>er</it>) after flagellin treatment. Several of these ten genes also showed altered expression after SA treatment, consistent with the regulation of <it>R </it>gene expression during defense responses and overlap between the basal defense response and salicylic acid signaling pathways. Enhancer trap analysis indicated that neither jasmonic acid nor benzothiadiazole (BTH), a salicylic acid analog, induced detectable expression of the five NBS-LRR-encoding genes and one TIR-NBS-encoding gene tested; however, BTH did induce detectable expression of the other TIR-NBS-encoding gene analyzed. Evidence for alternative mRNA polyadenylation sites was observed for many of the tested genes. Evidence for alternative splicing was found for at least 12 genes, 11 of which encode TIR-NBS-LRR proteins. There was no obvious correlation between expression pattern, phylogenetic relationship or genomic location of the NBS-LRR-encoding and related genes studied.</p> <p>Conclusion</p> <p>Transcripts of many NBS-LRR-encoding and related genes were defined. Most were present at low levels and exhibited tissue-specific expression patterns. Expression data are consistent with most Arabidopsis NBS-LRR-encoding and related genes functioning in plant defense responses but do not preclude other biological roles.</p

Engaging with community researchers for exposure science: lessons learned from a pesticide biomonitoring study

A major challenge in biomonitoring studies with members of the general public is ensuring their continued involvement throughout the necessary length of the research. The paper presents evidence on the use of community researchers, recruited from local study areas, as a mechanism for ensuring effective recruitment and retention of farmer and resident participants for a pesticides biomonitoring study. The evidence presented suggests that community researchers' abilities to build and sustain trusting relationships with participants enhanced the rigour of the study as a result of their on-the-ground responsiveness and flexibility resulting in data collection beyond targets expected

Sources and distribution of organic matter in northern Patagonia fjords, Chile (~44–47° S) : a multi–tracer approach for carbon cycling assessment

Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Continental Shelf Research 31 (2011): 315-329, doi:10.1016/j.csr.2010.05.013.We investigated the provenance of organic matter in the inner fjord area of northern Patagonia, Chile (~44–47° S), by studying the elemental (organic carbon, total nitrogen), isotopic (δ13C, δ15N), and biomarker (n–alkanoic acids from vascular plant waxes) composition of surface sediments as well as local marine and terrestrial organic matter. Average end–member values of N/C, δ13C, and δ15N from organic matter were 0.127 ± 0.010, –19.8 ± 0.3‰, and 9.9 ± 0.5‰ for autochthonous (marine) sources and 0.040 ± 0.018, –29.3 ± 2.1‰, 0.2 ± 3.0‰ for allochthonous (terrestrial) sources. Using a mixing equation based on these two end–members, we calculated the relative contribution of marine and terrestrial organic carbon from the open ocean to the heads of fjords close to river outlets. The input of marine–derived organic carbon varied widely and accounted for 13 to 96% (average 61%) of the organic carbon pool of surface sediments. Integrated regional calculations for the inner fjord system of northern Patagonia, which encompasses an area of ~ 4,280 km2, suggest that carbon accumulation may account for between 2.3 and 7.8 x 104 ton C yr–1. This represents a storage capacity of marine–derived carbon between 1.8 and 6.2 x 104 tons yr–1, which corresponds to an assimilation rate of CO2 by marine photosynthesis between 0.06 and 0.23 x 106 tons yr–1. This rate suggests that the entire fjord system of Patagonia, which covers an area of ~ 240,000 km2, may represent a potentially important region for the global burial of marine organic matter and the sequestration of atmospheric CO2.J. Sepúlveda was funded by a M.S. scholarship from the Graduate School at UDEC and by Fundación Andes through the Woods Hole Oceanographic Institution (WHOI)/UDEC agreement during a research visit at WHOI. This research was funded by the Ministerio de Hacienda de Chile and the Comité Oceanográfico Nacional (CONA) through the CIMAR–7 FIORDO Program (Grant C7F 01–10 to SP), CONICYT/NSF Grant 2001–120, Fundación Andes–Chile, and the Center for Oceanographic Research in the eastern South Pacific (COPAS) and COPAS Sur– Austral (PFB–31/2007)

Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics

<p>Abstract</p> <p>Background</p> <p>Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes.</p> <p>Results</p> <p>We successfully sequenced DNA from 64 samples (out of 126) comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments < 2000 years old, but we were able to successfully amplify DNA from samples up to 4600 years old. DNA sequences matched the taxonomic identity of the macrofossil from which they were extracted 79% of the time. Exceptions suggest that DNA molecules from surrounding nearby sediments may permeate or adhere to macrofossils in sediments.</p> <p>Conclusions</p> <p>An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.</p

Lignin biomarkers as tracers of mercury sources in lakes water column

This study presents the role of specific terrigenous organic compounds as important vectors of mercury (Hg) transported from watersheds to lakes of the Canadian boreal forest. In order to differentiate the autochthonous from the allochthonous organic matter (OM), lignin derived biomarker signatures [Lambda, S/V, C/V, P/(V ? S), 3,5-Bd/V and (Ad/Al)v] were used. Since lignin is exclusively produced by terrigenous plants, this approach can give a non equivocal picture of the watershed inputs to the lakes. Moreover, it allows a characterization of the source of OM and its state of degradation. The water column of six lakes from the Canadian Shield was sampled monthly between June and September 2005. Lake total dissolved Hg concentrations and Lambda were positively correlated, meaning that Hg and ligneous inputs are linked (dissolved OM r2 = 0.62, p\0.0001; particulate OM r2 = 0.76, p\0.0001). Ratios of P/(V ? S) and 3,5-Bd/V from both dissolved OM and particulate OM of the water column suggest an inverse relationship between the progressive state of pedogenesis and maturation of the OM in soil before entering the lake, and the Hg concentrations in the water column. No relation was found between Hg levels in the lakes and the watershed flora composition—angiosperm versus gymnosperm or woody versus non-woody compounds. This study has significant implications for watershed management of ecosystems since limiting fresh terrestrial OM inputs should reduce Hg inputs to the aquatic systems. This is particularly the case for largescale land-use impacts, such as deforestation, agriculture and urbanization, associated to large quantities of soil OM being transferred to aquatic systems

Sources, sinks and subsidies : terrestrial carbon storage in mid-latitude fjords

This work was supported by the Natural Environment Research Council (Grant Number: NE/L501852/1) with additional support from the NERC Life Science Mass Spectrometry Facility (CEH_L_098_11_2015) and the NERC Geophysical Equipment Facility (NGGFSC Minor Loan 1031).Fjords are recognized as globally important sites for the burial and long-term storage of carbon (C) within sediments. The proximity of fjords to the terrestrial environment in combination with their geomorphology and hydrography results in the fjordic sediments being subsidized with organic carbon (OC) from the terrestrial environment. It has been well documented that terrestrial OC (OCterr) is an important component of coastal sediments, yet our understanding of the quantity of OCterr stored in these sediments remains poorly constrained. Utilizing Bayesian isotopic sediment fingerprinting techniques to the surface sediments of Loch Sunart, we estimate that 42.0 ± 10.1% of the OC is terrestrial in origin. Through combining these outputs with sedimentary OC stock estimates, we have calculated that the surface sediments (0–15 cm) hold 0.1 megaton (Mt) OCterr and estimate that the postglacial sediment held within the fjord contains 3.96 Mt OCterr. When these totals are compared to the quantity of OC stored in the adjacent terrestrial environment, it is clear that the fjord's catchment stores a greater amount of OCterr in the form of vegetation and soil. Though when normalized for area the results suggest that the marine sediments are a more effective long-term store of OCterr than the adjacent terrestrial environment. This striking result highlights the importance of the terrestrial environment as a source of OC to the coastal ocean and that the OCterr subsidy to the marine sediments is a significant mechanism for the long-term storage of OC in coastal marine sediments.Publisher PDFPeer reviewe

Enterovirus D68 outbreak detection through a syndromic disease epidemiology network

BACKGROUND: In 2014, enterovirus D68 (EV-D68) was responsible for an outbreak of severe respiratory illness in children, with 1,153 EV-D68 cases reported across 49 states. Despite this, there is no commercial assay for its detection in routine clinical care. BioFire® Syndromic Trends (Trend) is an epidemiological network that collects, in near real-time, deidentified. BioFire test results worldwide, including data from the BioFire® Respiratory Panel (RP). OBJECTIVES: Using the RP version 1.7 (which was not explicitly designed to differentiate EV-D68 from other picornaviruses), we formulate a model, Pathogen Extended Resolution (PER), to distinguish EV-D68 from other human rhinoviruses/enteroviruses (RV/EV) tested for in the panel. Using PER in conjunction with Trend, we survey for historical evidence of EVD68 positivity and demonstrate a method for prospective real-time outbreak monitoring within the network. STUDY DESIGN: PER incorporates real-time polymerase chain reaction metrics from the RPRV/EV assays. Six institutions in the United States and Europe contributed to the model creation, providing data from 1,619 samples spanning two years, confirmed by EV-D68 gold-standard molecular methods. We estimate outbreak periods by applying PER to over 600,000 historical Trend RP tests since 2014. Additionally, we used PER as a prospective monitoring tool during the 2018 outbreak. RESULTS: The final PER algorithm demonstrated an overall sensitivity and specificity of 87.1% and 86.1%, respectively, among the gold-standard dataset. During the 2018 outbreak monitoring period, PER alerted the research network of EV-D68 emergence in July. One of the first sites to experience a significant increase, Nationwide Children's Hospital, confirmed the outbreak and implemented EV-D68 testing at the institution in response. Applying PER to the historical Trend dataset to determine rates among RP tests, we find three potential outbreaks with predicted regional EV-D68 rates as high as 37% in 2014, 16% in 2016, and 29% in 2018. CONCLUSIONS: Using PER within the Trend network was shown to both accurately predict outbreaks of EV-D68 and to provide timely notifications of its circulation to participating clinical laboratories

Social Contact Networks and Disease Eradicability under Voluntary Vaccination

Certain theories suggest that it should be difficult or impossible to eradicate a vaccine-preventable disease under voluntary vaccination: Herd immunity implies that the individual incentive to vaccinate disappears at high coverage levels. Historically, there have been examples of declining coverage for vaccines, such as MMR vaccine and whole-cell pertussis vaccine, that are consistent with this theory. On the other hand, smallpox was globally eradicated by 1980 despite voluntary vaccination policies in many jurisdictions. Previous modeling studies of the interplay between disease dynamics and individual vaccinating behavior have assumed that infection is transmitted in a homogeneously mixing population. By comparison, here we simulate transmission of a vaccine-preventable SEIR infection through a random, static contact network. Individuals choose whether to vaccinate based on infection risks from neighbors, and based on vaccine risks. When neighborhood size is small, rational vaccinating behavior results in rapid containment of the infection through voluntary ring vaccination. As neighborhood size increases (while the average force of infection is held constant), a threshold is reached beyond which the infection can break through partially vaccinated rings, percolating through the whole population and resulting in considerable epidemic final sizes and a large number vaccinated. The former outcome represents convergence between individually and socially optimal outcomes, whereas the latter represents their divergence, as observed in most models of individual vaccinating behavior that assume homogeneous mixing. Similar effects are observed in an extended model using smallpox-specific natural history and transmissibility assumptions. This work illustrates the significant qualitative differences between behavior–infection dynamics in discrete contact-structured populations versus continuous unstructured populations. This work also shows how disease eradicability in populations where voluntary vaccination is the primary control mechanism may depend partly on whether the disease is transmissible only to a few close social contacts or to a larger subset of the population

Salinity of the Eocene Arctic Ocean from oxygen isotope analysis of fish bone carbonate

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/95320/1/palo1410.pd

Virus Adaptation by Manipulation of Host's Gene Expression

Viruses adapt to their hosts by evading defense mechanisms and taking over cellular metabolism for their own benefit. Alterations in cell metabolism as well as side-effects of antiviral responses contribute to symptoms development and virulence. Sometimes, a virus may spill over from its usual host species into a novel one, where usually will fail to successfully infect and further transmit to new host. However, in some cases, the virus transmits and persists after fixing beneficial mutations that allow for a better exploitation of the new host. This situation would represent a case for a new emerging virus. Here we report results from an evolution experiment in which a plant virus was allowed to infect and evolve on a naïve host. After 17 serial passages, the viral genome has accumulated only five changes, three of which were non-synonymous. An amino acid substitution in the viral VPg protein was responsible for the appearance of symptoms, whereas one substitution in the viral P3 protein the epistatically contributed to exacerbate severity. DNA microarray analyses show that the evolved and ancestral viruses affect the global patterns of host gene expression in radically different ways. A major difference is that genes involved in stress and pathogen response are not activated upon infection with the evolved virus, suggesting that selection has favored viral strategies to escape from host defenses