Numerous potentially functional but non-genic conserved sequences on human chromosome 21

The use of comparative genomics to infer genome function relies on the understanding of how different components of the genome change over evolutionary time. The aim of such comparative analysis is to identify conserved, functionally transcribed sequences such as protein-coding genes and non-coding RNA genes, and other functional sequences such as regulatory regions, as well as other genomic features. Here, we have compared the entire human chromosome 21 with syntenic regions of the mouse genome, and have identified a large number of conserved blocks of unknown function. Although previous studies have made similar observations, it is unknown whether these conserved sequences are genes or not. Here we present an extensive experimental and computational analysis of human chromosome 21 in an effort to assign function to sequences conserved between human chromosome 21 (ref. 8) and the syntenic mouse regions. Our data support the presence of a large number of potentially functional non-genic sequences, probably regulatory and structural. The integration of the properties of the conserved components of human chromosome 21 to the rapidly accumulating functional data for this chromosome will improve considerably our understanding of the role of sequence conservation in mammalian genomes.     

Novelty,coherence, and Mendeleev’s periodic table

Predictivism is the view that successful predictions of “novel” evidence carry more confirmational weight than accommodations of already known evidence. Novelty, in this context, has traditionally been conceived of as temporal novelty. However temporal predictivism has been criticized for lacking a rationale: why should the time order of theory and evidence matter? Instead, it has been proposed, novelty should be construed in terms of use-novelty, according to which evidence is novel if it was not used in the construction of a theory. Only if evidence is use-novel can it fully support the theory entailing it. As I point out in this paper, the writings of the most influential proponent of use-novelty contain a weaker and a stronger version of use-novelty. However both versions, I argue, are problematic. With regard to the appraisal of Mendeleev’ periodic table, the most contentious historical case in the predictivism debate, I argue that temporal predictivism is indeed supported, although in ways not previously appreciated. On the basis of this case, I argue for a form of so-called symptomatic predictivism according to which temporally novel predictions carry more confirmational weight only insofar as they reveal the theory’s presumed coherence of facts as real.     

The stoichiometry of peptide-heparan sulfate binding as a determinant of uptake efficiency of cell-penetrating peptides

Binding to negatively charged heparan sulfates (HS) at the cell surface is considered the first step in the internalization of cationic cell-penetrating peptides (CPPs). However, little is known about the relation of the characteristics of the HS-CPP interaction such as affinity, stoichiometry, and clustering with uptake. In this study, we investigated a collection of mutants of a cyclic CPP derived from human lactoferrin with respect to HS binding and uptake. The thermodynamic parameters of HS binding were determined by isothermal titration calorimetry, clustering of HS was investigated by dynamic light scattering, and cellular uptake by flow cytometry and confocal microscopy. Whereas mutations of non-arginine amino acids that are conserved across lactoferrins of different mammalia only had a minor effect on uptake efficiency, changes in the number of arginine residues influenced the uptake significantly. In general, introduction of arginine residues and cyclization improved the HS affinity and the ability to cluster HS. In particular, there was a strong negative correlation between stoichiometry and uptake, indicating that crosslinking of HS is the driving force for the uptake of arginine-rich CPPs. Using glycan microarrays presenting a collection of synthetic HS, we show that a minimal chain length of HS is required for peptide binding.     

Vascular growth factors in neuropsychiatry

Recent advances in understanding the cellular and molecular basis of psychiatric illnesses have shed light on the important role played by trophic factors in modulating functional parameters associated with disease causality and drug action. Disease mechanisms are now thought to involve multiple cell types, including neurons and endothelial cells. These functionally distinct but interactively coupled cell types engage in cellular cross talk via shared and common signaling molecules. Dysregulation in their cellular signaling pathways influences brain function and alters behavioral performance. Multifunctional trophic factors such as VEGF and EPO that possess both neurotrophic and angiogenic actions are of particular interest due to their ability to rescue structural and plasticity deficits in neurons and vasculature. Obtaining insight into the behavioral, cellular and molecular actions of multi-functional trophic factors has the potential to open new and transformative therapeutic approaches.     

Comprehensive list by habitat of algae of Utah, USA.

A list of the algal species that have been reported from the state of Utah is presented. Also listed are the habitats from which these algae were collected. A total of nearly 1,900 taxa have been identified to the species level or below. Diatoms comprise the largest group, with nearly 1,000 taxa, followed by the green algae with over 550 taxa.     

A comparison of epiphytic diatom assemblages on living and dead stems of the common grass Phragmites australis

Diatoms epiphytic on Phragmites australis (Cav.) Trin. ex Steaded stems were collected from a single clone at the southern end of Provo Bay, Utah Lake, Utah. Diatom populations from both living and dead stem sections were analyzed. Species diversity in each sample was high, indicating that the stems provide a relatively stable habitat for diatom epiphytes. Of the 23 genera found, only Gomphonema and Navicula showed significant trends toward stem preference. The diatoms in this study support the current view that Utah Lake is a slightly saline, eutrophic system.     

Lichens of soil crust communities in the Intermountain Area of the western United States

Lichens are common components of microbiotic soil crusts. A total of 34 species from 17 genera are reported from soil crust communities throughout the Intermountain Area. Distribution of terricolous lichens is determined by various physical and biological factors: physical and chemical characteristics of the soil, moisture regimes, temperature, insolation, and development and composition of the vascular plant community. Some species demonstrate a broad ecological amplitude while others have a more restricted distribution. All growth forms are represented; however, the vast majority of soil crust lichens are squamulose (minutely foliose). Fruticose species are least abundant. In exposed, middle-elevation sites vagrant (detached) species are common. This paper describes and discusses terricolous lichen communities of desert habitats of the intermountain western United States. Effects of various human-related activities including grazing, wildfire, air pollution, and recreation vehicles on soil crust lichens are discussed. Gypsoplaca macrophylla (Zahlbr.) Timdal, a rare squamulose lichen which occurs on gypsifersous soils, was recently collected in Emery County, Utah, and is reported as new to the state.     

Contours and Tight Clusters

Nested clusters arise independently in graph partitioning and in the study of contours. We take a step toward unifying these two instances of nested clusters. We show that the graph theoretical tight clusters introduced by Dress, Steel, Moulton and Wu in 2010 are a special case of nested clusters associated to contours.     

Purification of 2-deoxy-2-dansylamido-D-glucose by affinity chromatography on a lectin-loaded agarose column

Summary A method is demonstrated to purify 2-substituted derivatives of glucose and sterically related sugars by affinity chromatography on Con A-sepharose. The method seems to be of rather general applicability.