Microbial Transport, Survival, and Succession in a Sequence of Buried Sediments

Abstract Two chronosequences of unsaturated, buried loess sediments, ranging in age from <10,000 years to >1 million years, were investigated to reconstruct patterns of microbial ecological succession that have occurred since sediment burial. The relative importance of microbial transport and survival to succession was inferred from sediment ages, porewater ages, patterns of abundance (measured by direct counts, counts of culturable cells, and total phospholipid fatty acids), activities (measured by radiotracer and enzyme assays), and community composition (measured by phospholipid fatty acid patterns and Biolog substrate usage). Core samples were collected at two sites 40 km apart in the Palouse region of eastern Washington State, near the towns of Washtucna and Winona. The Washtucna site was flooded multiple times during the Pleistocene by glacial outburst floods; the Winona site elevation is above flood stage. Sediments at the Washtucna site were collected from near surface to 14.9 m depth, where the sediment age was approximately 250 ka and the porewater age was 3700 years; sample intervals at the Winona site ranged from near surface to 38 m (sediment age: approximately 1 Ma; porewater age: 1200 years). Microbial abundance and activities declined with depth at both sites; however, even the deepest, oldest sediments showed evidence of viable microorganisms. Same-age sediments had equal quantities of microorganisms, but different community types. Differences in community makeup between the two sites can be attributed to differences in groundwater recharge and paleoflooding. Estimates of the microbial community age can be constrained by porewater and sediment ages. In the shallower sediments (<9 m at Washtucna, <12 m at Winona), the microbial communities are likely similar in age to the groundwater; thus, microbial succession has been influenced by recent transport of microorganisms from the surface. In the deeper sediments, the populations may be considerably older than the porewater ages, since microbial transport is severely restricted in unsaturated sediments. This is particularly true at the Winona site, which was never flooded.     

The Genetic Correlation between Height and IQ: Shared Genes or Assortative Mating?

Traits that are attractive to the opposite sex are often positively correlated when scaled such that scores increase with attractiveness, and this correlation typically has a genetic component. Such traits can be genetically correlated due to genes that affect both traits (“pleiotropy”) and/or because assortative mating causes statistical correlations to develop between selected alleles across the traits (“gametic phase disequilibrium”). In this study, we modeled the covariation between monozygotic and dizygotic twins, their siblings, and their parents (total N = 7,905) to elucidate the nature of the correlation between two potentially sexually selected traits in humans: height and IQ. Unlike previous designs used to investigate the nature of the height–IQ correlation, the present design accounts for the effects of assortative mating and provides much less biased estimates of additive genetic, non-additive genetic, and shared environmental influences. Both traits were highly heritable, although there was greater evidence for non-additive genetic effects in males. After accounting for assortative mating, the correlation between height and IQ was found to be almost entirely genetic in nature. Model fits indicate that both pleiotropy and assortative mating contribute significantly and about equally to this genetic correlation.     

Kinetic evidence that Glut4 follows different endocytic pathways than the receptors for transferrin and alpha2-macroglobulin

Insulin regulates glucose uptake through effects on the trafficking of the glucose transporter Glut4. To investigate the degree of overlap between Glut4 and the general endocytic pathways, the kinetics of trafficking of Glut4 and the receptors for transferrin (Tf) and α(2)-macroglobulin (α-2-M; LRP-1) were compared using quantitative flow cytometric assays. Insulin increased the exocytic rate constant (k(ex)) for both Glut4 and Tf. However, the k(ex) of Glut4 was 5-15 times slower than Tf in both basal and insulin-stimulated cells. The endocytic rate constant (k(en)) of Glut4 was also five times slower than Tf. Insulin did not affect the k(en) of either protein. In basal cells, the k(en) for α-2-M/LRP-1 was similar to Glut4 but 5-fold slower than Tf. Insulin increased k(en) for α-2-M/LRP-1 by 30%. In contrast, the k(ex) for LRP-1 was five times faster than Glut4 in basal cells, and insulin did not increase this rate constant. Thus, although there is overlap in the protein machineries/compartments utilized, the differences in trafficking kinetics indicate that Glut4, the Tf receptor, and LRP-1 are differentially processed both within the cell and at the plasma membrane. It has been reported that insulin decreases the k(en) of Glut4 in adipocytes. However, the effect of exocytosis on the "internalization" assays was not considered. Because it is counterintuitive, the effect of exocytosis on these assays is often overlooked in endocytosis studies. Using mathematical modeling and simulation, we show that the reported decrease in Glut4 k(en) can be entirely accounted for by the well established increase in Glut4 k(ex).     

Potential impact of the leaf‐cutting ant Acromyrmex lobicornis on conifer plantations in northern Patagonia,Argentina

• 1 The economic losses associated with crop damage by invasive pests can be minimized by recognizing their potential impact before they spread into new areas or crops.
• 2 We experimentally evaluated the preferences of the leaf‐cutting ant Acromyrmex lobicornis (Hymenoptera: Formicidae) for the most common conifer species commercially planted in northern Patagonia, Argentina. The areas of potential forest interest in this region and the geographical range of this ant overlap. We performed field preference tests and monitored the level of ant herbivory on planted conifer seedlings next to nests.
• 3 Acromyrmex lobicornis preferred some conifer species and avoided foraging on others. Pseudotsuga menziesii and Austrocedrus chilensis were the less preferred species, Pinus ponderosa and Pinus contorta were the most preferred by A. lobicornis.
• 4 The item mostly selected by ants was young needles from P. contorta. This species was also the pine mostly defoliated. Seedlings without ant‐exclusion showed a mean±SE of 60±5% defoliation during the sampling period. Pinus ponderosa was less defoliated; control seedlings showed a mean±SE of 8.5±1% of leaf damage in the sampling period.
• 5 The present study shows how the use of simple field tests of leaf‐cutting ant preferences could allow an improved selection of appropriate conifer species for future plantations in areas where leaf‐cutting ants are present.

     

Functional outcome of B cell activation by chromatin immune complex engagement of the B cell receptor and TLR9

We have previously shown that rheumatoid factors produced by Fas-deficient autoimmune-prone mice typically bind autologous IgG2a with remarkably low affinity. Nevertheless, B cells representative of this rheumatoid factor population proliferate vigorously in response to IgG2a/chromatin immune complexes through a mechanism dependent on the sequential engagement of the BCR and TLR9. To more precisely address the role of both receptors in this response, we analyzed the signaling pathways activated in AM14 B cells stimulated with these complexes. We found that the BCR not only serves to direct the chromatin complex to an internal compartment where it can engage TLR9 but also transmits a suboptimal signal that in combination with the signals emanating from TLR9 leads to NF-kappaB activation and proliferation. Importantly, engagement of both receptors leads to the up-regulation of a group of gene products, not induced by the BCR or TLR9 alone, that include IL-2. These data indicate that autoreactive B cells, stimulated by a combination of BCR and TLR9 ligands, acquire functional properties that may contribute to the activation of additional cells involved in the autoimmune disease process.     

Behavioural response of the woodwasp Sirex noctilio to volatile emissions of its fungal symbiont

The wood‐boring wasp, Sirex noctilio, is a global invasive pest that infects and kills pine trees by inoculating spores of a symbiotic fungus (Amylostereum areolatum) at oviposition. Wasp larvae depend on fungal growth to feed, while the fungus relies on female wasps to initially condition the pine tree by inoculating a phytotoxic venom and for dispersal. Wasp larvae use the fungus as an external gut for the digestion of lignocellulosic compounds resulting in a strong correlation between fungal growth inside the wood and wasp fitness. This study explores the hypothesis that female wasps will use fungal volatiles as a synomone in the process of locating suitable oviposition areas (i.e. trees). Using a Y‐tube olfactometer, adult female wasp behaviour was assessed towards fungal and pine tree volatiles (i.e. positive control). Our results are the first to demonstrate attraction of female S. noctilio towards volatiles of their fungal symbiont. Furthermore, the positive response towards these volatiles seems to be stronger than the response to a known attractant (i.e. pine volatiles). These results could be an important contribution to improving baits for monitoring and control purposes. Further work is needed, mainly oriented towards the identification of the volatiles that trigger the observed attraction response and their possible synergistic effects with tree volatiles.     

Predicted protein-protein interactions in the moss Physcomitrella patens: a new bioinformatic resource

Background

Physcomitrella patens, a haploid dominant plant, is fast becoming a useful molecular genetics and bioinformatics tool due to its key phylogenetic position as a bryophyte in the post-genomic era. Genome sequences from select reference species were compared bioinformatically to Physcomitrella patens using reciprocal blasts with the InParanoid software package. A reference protein interaction database assembled using MySQL by compiling BioGrid, BIND, DIP, and Intact databases was queried for moss orthologs existing for both interacting partners. This method has been used to successfully predict interactions for a number of angiosperm plants.

Results

The first predicted protein-protein interactome for a bryophyte based on the interolog method contains 67,740 unique interactions from 5,695 different Physcomitrella patens proteins. Most conserved interactions among proteins were those associated with metabolic processes. Over-represented Gene Ontology categories are reported here.

Conclusion

Addition of moss, a plant representative 200 million years diverged from angiosperms to interactomic research greatly expands the possibility of conducting comparative analyses giving tremendous insight into network evolution of land plants. This work helps demonstrate the utility of “guilt-by-association” models for predicting protein interactions, providing provisional roadmaps that can be explored using experimental approaches. Included with this dataset is a method for characterizing subnetworks and investigating specific processes, such as the Calvin-Benson-Bassham cycle.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0524-1) contains supplementary material, which is available to authorized users.     

Linkage confirms canine pkd1 orthologue as a candidate for bull terrier polycystic kidney disease

Bull terrier polycystic kidney disease (BTPKD) is a Mendelian disorder with many features reminiscent of human autosomal dominant polycystic disease, the latter disease being due to mutations at PKD1 and PKD2 loci. We investigated the role of the canine pkd1 orthologue in BTPKD via linkage analysis of a large kindred in which the disorder is segregating. Twelve microsatellite markers around the canine pkd1 locus (CFA6) were amplified from the genomic DNA of 20 affected and 16 unaffected bull terriers. An additional 28 affected dogs were genotyped at five key microsatellites. A highly significant multi-point LOD score that peaked over the canine pkd1 locus was observed (LOD = 6.59, best two-point LOD score LOD = 6.02), implicating this as the BTPKD locus.