RNA-guided genetic silencing systems in bacteria and archaea

Clustered regularly interspaced short palindromic repeat (CRISPR) are essential components of nucleic-acid-based adaptive immune systems that are widespread in bacteria and archaea. Similar to RNA interference (RNAi) pathways in eukaryotes, CRISPR-mediated immune systems rely on small RNAs for sequence-specific detection and silencing of foreign nucleic acids, including viruses and plasmids. However, the mechanism of RNA-based bacterial immunity is distinct from RNAi. Understanding how small RNAs are used to find and destroy foreign nucleic acids will provide new insights into the diverse mechanisms of RNA-controlled genetic silencing systems.     

An abundance of small exoplanets around stars with a wide range of metallicities

The abundance of heavy elements (metallicity) in the photospheres of stars similar to the Sun provides a 'fossil' record of the chemical composition of the initial protoplanetary disk. Metal-rich stars are much more likely to harbour gas giant planets, supporting the model that planets form by accumulation of dust and ice particles. Recent ground-based surveys suggest that this correlation is weakened for Neptunian-sized planets. However, how the relationship between size and metallicity extends into the regime of terrestrial-sized exoplanets is unknown. Here we report spectroscopic metallicities of the host stars of 226 small exoplanet candidates discovered by NASA's Kepler mission, including objects that are comparable in size to the terrestrial planets in the Solar System. We find that planets with radii less than four Earth radii form around host stars with a wide range of metallicities (but on average a metallicity close to that of the Sun), whereas large planets preferentially form around stars with higher metallicities. This observation suggests that terrestrial planets may be widespread in the disk of the Galaxy, with no special requirement of enhanced metallicity for their formation.     

Reconstructing Native American population history

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.     

A new analytical framework for the understanding of Diophantus’s Arithmetica I–III

This study is the foundation of a new interpretation of the introduction and the three first books of Diophantus’s Arithmetica, one that opens the way to a historically correct contextualization of the work. Its purpose, as indicated in the title, is to renew the traditional discussion on the methods of problem-solving used by Diophantus, through the detailed exposition of a new analytical framework that aims to give an account of the coherence and progressive nature of the material included in the three first books of the Arithmetica. One outcome of this new ‘toolbox’ is a new conspectus of the problems and solutions contained in the latter, which is presented in appendix. The first part of the article clarifies, as a necessary preliminary, the key notions and terminology underlying our analysis. Among these new concepts is the notion of “method of invention,” which accounts in general for any way, by which “positions” (hypostaseis) are used in the Arithmetica. The next part proposes a complete inventory of the various methods of invention found in the three first books. Finally the last part presents the above mentioned conspectus and proposes a series of preliminary conclusions that can be drawn from it.     

Base excision repair and design of small molecule inhibitors of human DNA polymerase β

Base excision repair (BER) can protect a cell after endogenous or exogenous genotoxic stress, and a deficiency in BER can render a cell hypersensitive to stress-induced apoptotic and necrotic cell death, mutagenesis, and chromosomal rearrangements. However, understanding of the mammalian BER system is not yet complete as it is extraordinarily complex and has many back-up processes that complement a deficiency in any one step. Due of this lack of information, we are unable to make accurate predictions on therapeutic approaches targeting BER. A deeper understanding of BER will eventually allow us to conduct more meaningful clinical interventions. In this review, we will cover historical and recent information on mammalian BER and DNA polymerase β and discuss approaches toward development and use of small molecule inhibitors to manipulate BER. With apologies to others, we will emphasize results obtained in our laboratory and those of our collaborators.     

Invasion and stabilization of recent beaches by salt grass ( Distichilis spicata ) at Mono Lake, Mono County, California

Invasion of plant species onto recently exposed beaches of Mono Lake, California, was documented. Three vegetation zones were evident on these beaches. The first was formed entirely of annual species. The second was composed of annuals mixed with salt grass, and the third was formed entirely of salt grass. Stabilization of these beaches was accomplished by the aggressive growth of salt grass rhizomes.         

Soil algae of cryptogamic crusts from the Uintah Basin, Utah, U.S.A.

The algal flora of selected soils in the Uintah Basin, Uintah County, Utah, was studied. A total of 45 species was identified from the top soils of three different vascular plant habitats. The soil algal flora was dominated in biomass by filamentous Cyanophyta, including Microcoleus vaginatus, Phormidium minnesotense, and three species of Nostoc . These algae formed the algal matrix of the soil within which other Cyanophyta as well as Chlorophyta, Bacillariophyta, and Euglenophyta occurred.         

Three new records for diatoms from the Great Basin, USA

Three diatom species recently collected from Great Basin localities represent new records of these taxa from this region of western North America. Cocconeis scutellum   Ehr. and Melosira dubia   Kuetz. were collected from a thermal spring in Tooele County, Utah. Nitzschia hustedtiana   Salah was collected from newly flooded marshes at the south end of the Great Salt Lake, Tooele Countv, Utah.     

New records of diatoms from Blue Lake Warm Spring, Tooele County, Utah

Blue Lake Warm Spring in Tooele County, Utah, contains a rich diatom flora with a significant number of taxa that are unusual in this region. We have identified a total of 136 taxa in our samples from this locality, several of which are new records for Utah and North America.         

The bacterium Thioploca ingrica on wet walls in Zion National Park, Utah

Hanging gardens and wet wall habitats have been studied for the past several years in many arid regions of the Intermountain West. One unusual large wet wall habitat in Zion National Park was found to be covered with a mucilaginous red-colored growth of the filamentous gliding bacterium Thioploca ingrica Visloukh. This is the only habitat we have examined where the predominant matrix-forming organism was a bacterium rather than an alga.