Secondary siRNAs result from unprimed RNA synthesis and form a distinct class

In Caenorhabditis elegans, an effective RNA interference (RNAi) response requires the production of secondary short interfering RNAs (siRNAs) by RNA-directed RNA polymerases (RdRPs). We cloned secondary siRNAs from transgenic C. elegans lines expressing a single 22-nucleotide primary siRNA. Several secondary siRNAs start a few nucleotides downstream of the primary siRNA, indicating that non-RISC (RNA-induced silencing complex)-cleaved mRNAs are substrates for secondary siRNA production. In lines expressing primary siRNAs with single-nucleotide mismatches, secondary siRNAs do not carry the mismatch but contain the nucleotide complementary to the mRNA. We infer that RdRPs perform unprimed RNA synthesis. Secondary siRNAs are only of antisense polarity, carry 5' di- or triphosphates, and are only in the minority associated with RDE-1, the RNAi-specific Argonaute protein. Therefore, secondary siRNAs represent a distinct class of small RNAs. Their biogenesis depends on RdRPs, and we propose that each secondary siRNA is an individual RdRP product.     

Radioactive elements on Mercury's surface from MESSENGER: implications for the planet's formation and evolution

The MESSENGER Gamma-Ray Spectrometer measured the average surface abundances of the radioactive elements potassium (K, 1150 ± 220 parts per million), thorium (Th, 220 ± 60 parts per billion), and uranium (U, 90 ± 20 parts per billion) in Mercury's northern hemisphere. The abundance of the moderately volatile element K, relative to Th and U, is inconsistent with physical models for the formation of Mercury requiring extreme heating of the planet or its precursor materials, and supports formation from volatile-containing material comparable to chondritic meteorites. Abundances of K, Th, and U indicate that internal heat production has declined substantially since Mercury's formation, consistent with widespread volcanism shortly after the end of late heavy bombardment 3.8 billion years ago and limited, isolated volcanic activity since.     

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum

Flow cytometry is an essential tool for dissecting the functional complexity of hematopoiesis. We used single-cell "mass cytometry" to examine healthy human bone marrow, measuring 34 parameters simultaneously in single cells (binding of 31 antibodies, viability, DNA content, and relative cell size). The signaling behavior of cell subsets spanning a defined hematopoietic hierarchy was monitored with 18 simultaneous markers of functional signaling states perturbed by a set of ex vivo stimuli and inhibitors. The data set allowed for an algorithmically driven assembly of related cell types defined by surface antigen expression, providing a superimposable map of cell signaling responses in combination with drug inhibition. Visualized in this manner, the analysis revealed previously unappreciated instances of both precise signaling responses that were bounded within conventionally defined cell subsets and more continuous phosphorylation responses that crossed cell population boundaries in unexpected manners yet tracked closely with cellular phenotype. Collectively, such single-cell analyses provide system-wide views of immune signaling in healthy human hematopoiesis, against which drug action and disease can be compared for mechanistic studies and pharmacologic intervention.     

Conserved eukaryotic fusogens can fuse viral envelopes to cells

Caenorhabditis elegans proteins AFF-1 and EFF-1 [C. elegans fusion family (CeFF) proteins] are essential for developmental cell-to-cell fusion and can merge insect cells. To study the structure and function of AFF-1, we constructed vesicular stomatitis virus (VSV) displaying AFF-1 on the viral envelope, substituting the native fusogen VSV glycoprotein. Electron microscopy and tomography revealed that AFF-1 formed distinct supercomplexes resembling pentameric and hexameric "flowers" on pseudoviruses. Viruses carrying AFF-1 infected mammalian cells only when CeFFs were on the target cell surface. Furthermore, we identified fusion family (FF) proteins within and beyond nematodes, and divergent members from the human parasitic nematode Trichinella spiralis and the chordate Branchiostoma floridae could also fuse mammalian cells. Thus, FF proteins are part of an ancient family of cellular fusogens that can promote fusion when expressed on a viral particle.     

Impact of land-use type and harvesting on population structure of a non-timber forest product-providing tree in a semi-arid savanna, West Africa

Non-timber forest products (NTFPs) strongly contribute to livelihood security in the semi-arid tropics. Main factors determining the populations of NTFP-providing species are human activities. This study examined the impact of land-use, combined with rates and patterns of debarking and chopping on a NTFP-providing tree (Anogeissus leiocarpa) in Burkina Faso. We compared stands in a protected area (W National Park) with those of its surrounding communal area (fallows, croplands) in order to (i) obtain an indication on the status of the population, (ii) assess its harvesting tolerance, (iii) estimate the sustainability of present management, and (iv) derive which additional management strategies may foster its conservation. Our results reveal that the stands of A. leiocarpa are in healthy states in fallows and in the park. In croplands, the absence of saplings gives evidence of a declining population. Nearly all individuals of A. leiocarpa were harvested in croplands and fallows, while the number of harvested individuals in the park was negligible. Intensity of debarking and chopping was tree size-specific. The sprouting ability significantly increased with higher chopping intensity. We conclude that despite the land-use impact and the intense harvesting, stands of A. leiocarpa are still well preserved due to the species life history (fast growing and high sprouting) and due to indirect positive influences of human activities by providing better environmental conditions for its recruitment. Thus, the population of A. leiocarpa is not at risk to over-harvesting and land-use even though it is not protected.     

Factors related to the distribution and prevalence of the fungal pathogen Batrachochytrium dendrobatidis in Rana cascadae and other amphibians in the Klamath Mountains

The fungal pathogen Batrachochytrium dendrobatidis (Bd), which causes the disease chytridiomycosis, has been associated with declines and extinctions of montane amphibians worldwide. To gain insight into factors affecting its distribution and prevalence we focus on the amphibian community of the Klamath Mountains in northwest California. The Cascades frog (Rana cascadae), one of the most common amphibians in these mountains, experienced increased mortality as a result of Bd exposure in laboratory trials and has experienced recent, dramatic declines in other parts of California. We surveyed 112 sites in the Klamaths, all of which supported R. cascadae between 1999 and 2002, for amphibians and Bd to (1) determine the distribution of Bd, (2) evaluate changes in the distribution of R. cascadae, and (3) assess associations between potential biotic and abiotic drivers and Bd infection. Bd was widely distributed in the Klamath Mountains – we detected the pathogen at 64% of sites. R. cascadae was found at 79% of sites, and was often infected with Bd. These results suggest that Bd has not caused dramatic declines in R. cascadae in the Klamaths in recent years. Subadult R. cascadae had a higher Bd prevalence than other R. cascadae life stages (subadults: 36%, adults: 25%, metamorphs: 4%, larvae: 1%), and while the probability of infection decreased over the season for adults, it did not for subadults, suggesting that subadults may be more vulnerable to chytridiomycosis than other R. cascadae life stages. Bd prevalence in R. cascadae was highest early in the season at high-elevation sites, which may indicate that populations inhabiting high elevation sites may have a greater risk of being affected by chytridiomycosis. Three other common amphibian species also tested positive for Bd: Pacific chorus frog (Pseudacris regilla), western toad (Anaxyrus boreas), and rough-skinned newt (Taricha granulosa).     

Influence of agricultural soils on the growth and reproduction of the bio-indicator Folsomia candida

Soil organisms have been recommended as bio-indicators of soil quality due to their sensitivity to anthropogenic influences and their high degree of site-specificity. The objectives of this study were to determine if the relationship between the soil Collembola, Folsomia candida, and forest soil could be extended to other soils and, if not, to determine the relationship between its life parameters and soils from the different phases of an agricultural rotation sequence. A comparison of growth, reproduction and survival of 1 day old neonates and 10 day old juveniles subjected to a series of different soils (composted manure, pasture soil, forest soil, sand alone, and sand supplemented with yeast) established that the association between F. candida and forest soil quality cannot be automatically transferred to soils from other ecosystems. The test also showed that neonate (1 d) individuals were more sensitive to the different soil treatments than 10 d old juveniles and should be used in future tests. On this basis, neonate F. candida individuals were used to determine if the species could be employed to characterize the agricultural soils from the different phases of an organic or conventional rotation sequence. Results demonstrated that changes in body growth and reproduction constituted suitable criteria to characterize the soil quality of these different phases. The research required to develop these results as a standard bio-indicator test of agricultural soil quality is discussed.