Proceedings of the National Academy of Sciences

Kelly, Erin N.; Schindler, David W.; Hodson, Peter V.; Short, Jeffrey W.; Radmanovich, Roseanna; Nielsen, Charlene C.

doi: N/Apmid: 20805486

We show that the oil sands industry releases the 13 elements considered priority pollutants (PPE) under the US Environmental Protection Agency's Clean Water Act, via air and water, to the Athabasca River and its watershed. In the 2008 snowpack, all PPE except selenium were greater near oil sands developments than at more remote sites. Bitumen upgraders and local oil sands development were sources of airborne emissions. Concentrations of mercury, nickel, and thallium in winter and all 13 PPE in summer were greater in tributaries with watersheds more disturbed by development than in less disturbed watersheds. In the Athabasca River during summer, concentrations of all PPE were greater near developed areas than upstream of development. At sites downstream of development and within the Athabasca Delta, concentrations of all PPE except beryllium and selenium remained greater than upstream of development. Concentrations of some PPE at one location in Lake Athabasca near Fort Chipewyan were also greater than concentration in the Athabasca River upstream of development. Canada's or Alberta's guidelines for the protection of aquatic life were exceeded for seven PPE—cadmium, copper, lead, mercury, nickel, silver, and zinc—in melted snow and/or water collected near or downstream of development.

Diaz, Arturo; Wang, Xiaofeng; Ahlquist, Paul

doi: N/Apmid: 20805477

Positive-strand RNA viruses replicate their genomes on membranes with virus-induced rearrangements such as single- or double-membrane vesicles, but the mechanisms of such rearrangements, including the role of host proteins, are poorly understood. Brome mosaic virus (BMV) RNA synthesis occurs in ≈70 nm, negatively curved endoplasmic reticulum (ER) membrane invaginations induced by multifunctional BMV protein 1a. We show that BMV RNA replication is inhibited 80–90% by deleting the reticulon homology proteins (RHPs), a family of membrane-shaping proteins that normally induce and stabilize positively curved peripheral ER membrane tubules. In RHP-depleted cells, 1a localized normally to perinuclear ER membranes and recruited the BMV 2apol polymerase. However, 1a failed to induce ER replication compartments or to recruit viral RNA templates. Partial RHP depletion allowed formation of functional replication vesicles but reduced their diameter by 30–50%. RHPs coimmunoprecipitated with 1a and 1a expression redirected >50% of RHPs from peripheral ER tubules to the interior of BMV-induced RNA replication compartments on perinuclear ER. Moreover, RHP-GFP fusions retained 1a interaction but shifted 1a-induced membrane rearrangements from normal vesicles to double membrane layers, a phenotype also induced by excess 1a-interacting 2apol. Thus, RHPs interact with 1a, are incorporated into RNA replication compartments, and are required for multiple 1a functions in replication compartment formation and function. The results suggest possible RHP roles in the bodies and necks of replication vesicles.

Chiang, Po-Min; Ling, Jonathan; Jeong, Yun Ha; Price, Donald L.; Aja, Susan M.; Wong, Philip C.

doi: N/Apmid: 20660762

Tat activating regulatory DNA-binding protein (Tardbp or TDP-43), a highly conserved metazoan DNA/RNA binding protein thought to be involved in RNA transcription and splicing, has been linked to the pathophysiology of amyotrophic lateral sclerosis and frontotemporal lobar degeneration and is essential for early embryonic development. However, neither the physiological role of TDP-43 in the adult nor its downstream targets are well defined. To address these questions, we developed conditional Tardbp-KO mice and embryonic stem (ES) cell models. Here, we show that postnatal deletion of Tardbp in mice caused dramatic loss of body fat followed by rapid death. Moreover, conditional Tardbp-KO ES cells failed to proliferate. Importantly, high-throughput DNA sequencing analysis on the transcriptome of ES cells lacking Tardbp revealed a set of downstream targets of TDP-43. We show that Tbc1d1, a gene known to mediate leanness and linked to obesity, is down-regulated in the absence of TDP-43. Collectively, our results establish that TDP-43 is critical for fat metabolism and ES cell survival.

Snyder, Solomon H.; Gadalla, Moataz M.; Prabhakar, Nanduri R.

doi: N/Apmid: 20807753

Olson and Perry ( 1) commented on our recent article “H 2S mediates O 2 sensing in the carotid body” ( 2), noting that they published a study relevant to hypoxia and H 2S ( 3). To understand the relationship of the two studies, we will summarize work from our laboratories bearing on H 2S as a gasotransmitter in blood vessels ( 4) and the carotid body ( 2). Because of its chemical reactivity, H 2S is known to affect multiple biological systems, including blood vessels. Whether endogenously produced H 2S is a …

Saffo, Mary Beth; McCoy, Adam M.; Rieken, Christopher; Slamovits, Claudio H.

doi: N/Apmid: 20736348

With malaria parasites (Plasmodium spp.), Toxoplasma, and many other species of medical and veterinary importance its iconic representatives, the protistan phylum Apicomplexa has long been defined as a group composed entirely of parasites and pathogens. We present here a report of a beneficial apicomplexan: the mutualistic marine endosymbiont Nephromyces. For more than a century, the peculiar structural and developmental features of Nephromyces, and its unusual habitat, have thwarted characterization of the phylogenetic affinities of this eukaryotic microbe. Using short-subunit ribosomal DNA (SSU rDNA) sequences as key evidence, with sequence identity confirmed by fluorescence in situ hybridization (FISH), we show that Nephromyces, originally classified as a chytrid fungus, is actually an apicomplexan. Inferences from rDNA data are further supported by the several apicomplexan-like structural features in Nephromyces, including especially the strong resemblance of Nephromyces infective stages to apicomplexan sporozoites. The striking emergence of the mutualistic Nephromyces from a quintessentially parasitic clade accentuates the promise of this organism, and the three-partner symbiosis of which it is a part, as a model for probing the factors underlying the evolution of mutualism, pathogenicity, and infectious disease.

Azar, Beth

doi: N/Apmid: 20713701

Until his senior year in high school, however, he was unsure about his future plans. “No one in my family had gone to college,” he recalls. “I had a vague notion that it was a possibility, but I thought it …

Chakrabortee, Sohini; Meersman, Filip; Kaminski Schierle, Gabriele S.; Bertoncini, Carlos W.; McGee, Brian; Kaminski, Clemens F.; Tunnacliffe, Alan

doi: N/Apmid: 20805515

Intrinsically disordered proteins (IDPs) lack well-defined structure but are widely represented in eukaryotic proteomes. Although the functions of most IDPs are not understood, some have been shown to have molecular recognition and/or regulatory roles where their disordered nature might be advantageous. Anhydrin is an uncharacterized IDP induced by dehydration in an anhydrobiotic nematode, Aphelenchus avenae. We show here that anhydrin is a moonlighting protein with two novel, independent functions relating to desiccation tolerance. First, it has a chaperone-like activity that can reduce desiccation-induced enzyme aggregation and inactivation in vitro. When expressed in a human cell line, anhydrin localizes to the nucleus and reduces the propensity of a polyalanine expansion protein associated with oculopharyngeal muscular dystrophy to form aggregates. This in vivo activity is distinguished by a loose association of anhydrin with its client protein, consistent with a role as a molecular shield. In addition, anhydrin exhibits a second function as an endonuclease whose substrates include supercoiled, linear, and chromatin linker DNA. This nuclease activity could be involved in either repair of desiccation-induced DNA damage incurred during anhydrobiosis or in apoptotic or necrotic processes, for example, but it is particularly unexpected for anhydrin because IDP functions defined to date anticorrelate with enzyme activity. Enzymes usually require precise three-dimensional positioning of residues at the active site, but our results suggest this need not be the case. Anhydrin therefore extends the range of IDP functional categories to include catalysis and highlights the potential for the discovery of new functions in disordered proteomes.

Bray, Steven M.; Mulle, Jennifer G.; Dodd, Anne F.; Pulver, Ann E.; Wooding, Stephen; Warren, Stephen T.

doi: N/Apmid: 20798349

The Ashkenazi Jewish (AJ) population has long been viewed as a genetic isolate, yet it is still unclear how population bottlenecks, admixture, or positive selection contribute to its genetic structure. Here we analyzed a large AJ cohort and found higher linkage disequilibrium (LD) and identity-by-descent relative to Europeans, as expected for an isolate. However, paradoxically we also found higher genetic diversity, a sign of an older or more admixed population but not of a long-term isolate. Recent reports have reaffirmed that the AJ population has a common Middle Eastern origin with other Jewish Diaspora populations, but also suggest that the AJ population, compared with other Jews, has had the most European admixture. Our analysis indeed revealed higher European admixture than predicted from previous Y-chromosome analyses. Moreover, we also show that admixture directly correlates with high LD, suggesting that admixture has increased both genetic diversity and LD in the AJ population. Additionally, we applied extended haplotype tests to determine whether positive selection can account for the level of AJ-prevalent diseases. We identified genomic regions under selection that account for lactose and alcohol tolerance, and although we found evidence for positive selection at some AJ-prevalent disease loci, the higher incidence of the majority of these diseases is likely the result of genetic drift following a bottleneck. Thus, the AJ population shows evidence of past founding events; however, admixture and selection have also strongly influenced its current genetic makeup.

Valenza, Marta; Cattaneo, Elena

doi: N/Apmid: 20807740

The authors ( 1) suggested that SIRT2 inhibition may act through reduced sterol/cholesterol biosynthesis to curtail mutant huntingtin toxicity. Unfortunately, the effect of SIRT2 inhibitors (AK1 and AGK2 compounds) on in vivo sterol levels and cholesterol biosynthesis in their nonvertebrates’ models was not shown (figure 1 in ref. 1). Three-week-old primary striatal neuronal cultures carrying the N-terminal fragment of human huntingtin (Htt171-82Q) exhibited increased neuroprotection after exposure to AK1 and AGK2. However, gene expression profiles of cholesterol biosynthetic enzymes were evaluated …

Huynen, Leon; Gill, Brian J.; Millar, Craig D.; Lambert, David M.

doi: N/Apmid: 20805485

New Zealand's extinct flightless moa radiated rapidly into a large number of morphologically diverse species, which produced an equally large range of egg morphologies. The exact number of moa species, as well as the characteristics of the eggs they laid, remains contentious. Moreover, like most extinct species, we understand little about their nesting and incubation habits. We used a modified ancient DNA extraction procedure to recover exogenous mitochondrial and nuclear DNA from the inside and outside surfaces of moa eggs. We used sequences from the inside of 69 eggshells to directly assign these remains to seven of the 10 currently recognized moa species. In addition we were able to assign, to the species level, six of the rare reconstructed “whole” eggs. These molecular results enabled us to identify two distinct lineages within the genus Euryapteryx. Members of these lineages differed in eggshell thickness, with one lineage being characterized by a relatively thin eggshell. Unexpectedly, several thin-shelled eggs were also shown to belong to the heaviest moa of the genera Dinornis, Euryapteryx and Emeus, making these, to our knowledge, the most fragile of all avian eggs measured to date. Moreover, sex-specific DNA recovered from the outer surfaces of eggshells belonging to species of Dinornis and Euryapteryx suggest that these very thin eggs were likely to have been incubated by the lighter males. The thin nature of the eggshells of these larger species of moa, even if incubated by the male, suggests that egg breakage in these species would have been common if the typical contact method of avian egg incubation was used.