A photometricity and extinction monitor at the Apache Point Observatory

An unsupervised software ``robot'' that automatically and robustly reduces and analyzes CCD observations of photometric standard stars is described. The robot measures extinction coefficients and other photometric parameters in real time and, more carefully, on the next day. It also reduces and analyzes data from an all-sky $10 \mu m$ camera to detect clouds; photometric data taken during cloudy periods are automatically rejected. The robot reports its findings back to observers and data analysts via the World-Wide Web. It can be used to assess photometricity, and to build data on site conditions. The robot's automated and uniform site monitoring represents a minimum standard for any observing site with queue scheduling, a public data archive, or likely participation in any future National Virtual Observatory.Comment: accepted for publication in A

First principles theory of fluctuations in vortex liquids and solids

Consistent perturbation theory for thermodynamical quantities in type II superconductors in magnetic field at low temperatures is developed. It is complementary to the existing expansion valid at high temperatures. Magnetization and specific heat are calculated to two loop order and compare well to existing Monte Carlo simulations and experiments.Comment: 3 .ps fig. In press Phys. Rev.

The differential effect of instructions on dysphoric and nondysphoric persons

The experimenters investigated whether dysphoric and nondysphoric persons differentially exhibited the traditional instruction-induced schedule-insensitivity effect (rule-governed behavior). Dysphoric and nondysphoric participants were given instructions to perform a matching-to-sample task (four blocks, 40 trials each). The instructions in the first half of the study were correct and in the second half, incorrect. Participants were assigned to one of two instructional control conditions in which they read the instruction either privately (tracking condition) or out loud to the experimenter (pliance condition). Dysphoric individuals demonstrated greater schedule sensitivity (less rule-governed behavior) than did nondysphoric persons. No other differences were found. Results indicate that deficits in rule-governed behavior may contribute to depression; however, this experiment did not incorporate procedures to directly test the role of rule-governed experiential avoidance

Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus

Multiple discrete regions at 8q24 were recently shown to contain alleles that predispose to many cancers including prostate, breast, and colon. These regions are far from any annotated gene and their biological activities have been unknown. Here we profiled a 5-megabase chromatin segment encompassing all the risk regions for RNA expression, histone modifications, and locations occupied by RNA polymerase II and androgen receptor (AR). This led to the identification of several transcriptional enhancers, which were verified using reporter assays. Two enhancers in one risk region were occupied by AR and responded to androgen treatment; one contained a single nucleotide polymorphism (rs11986220) that resides within a FoxA1 binding site, with the prostate cancer risk allele facilitating both stronger FoxA1 binding and stronger androgen responsiveness. The study reported here exemplifies an approach that may be applied to any risk-associated allele in non-protein coding regions as it emerges from genome-wide association studies to better understand the genetic predisposition of complex diseases

Biomolecular condensates formed by designer minimalistic peptides

Inspired by the role of intracellular liquid-liquid phase separation (LLPS) in formation of membraneless organelles, there is great interest in developing dynamic compartments formed by LLPS of intrinsically disordered proteins (IDPs) or short peptides. However, the molecular mechanisms underlying the formation of biomolecular condensates have not been fully elucidated, rendering on-demand design of synthetic condensates with tailored physico-chemical functionalities a significant challenge. To address this need, here we design a library of LLPS-promoting peptide building blocks composed of various assembly domains. We show that the LLPS propensity, dynamics, and encapsulation efficiency of compartments can be tuned by changes to the peptide composition. Specifically, with the aid of Raman and NMR spectroscopy, we show that interactions between arginine and aromatic amino acids underlie droplet formation, and that both intra- and intermolecular interactions dictate droplet dynamics. The resulting sequence-structure-function correlation could support the future development of compartments for a variety of applications

The Cysteine-Rich Interdomain Region from the Highly Variable Plasmodium falciparum Erythrocyte Membrane Protein-1 Exhibits a Conserved Structure

Plasmodium falciparum malaria parasites, living in red blood cells, express proteins of the erythrocyte membrane protein-1 (PfEMP1) family on the red blood cell surface. The binding of PfEMP1 molecules to human cell surface receptors mediates the adherence of infected red blood cells to human tissues. The sequences of the 60 PfEMP1 genes in each parasite genome vary greatly from parasite to parasite, yet the variant PfEMP1 proteins maintain receptor binding. Almost all parasites isolated directly from patients bind the human CD36 receptor. Of the several kinds of highly polymorphic cysteine-rich interdomain region (CIDR) domains classified by sequence, only the CIDR1α domains bind CD36. Here we describe the CD36-binding portion of a CIDR1α domain, MC179, as a bundle of three α-helices that are connected by a loop and three additional helices. The MC179 structure, containing seven conserved cysteines and 10 conserved hydrophobic residues, predicts similar structures for the hundreds of CIDR sequences from the many genome sequences now known. Comparison of MC179 with the CIDR domains in the genome of the P. falciparum 3D7 strain provides insights into CIDR domain structure. The CIDR1α three-helix bundle exhibits less than 20% sequence identity with the three-helix bundles of Duffy-binding like (DBL) domains, but the two kinds of bundles are almost identical. Despite the enormous diversity of PfEMP1 sequences, the CIDR1α and DBL protein structures, taken together, predict that a PfEMP1 molecule is a polymer of three-helix bundles elaborated by a variety of connecting helices and loops. From the structures also comes the insight that DBL1α domains are approximately 100 residues larger and that CIDR1α domains are approximately 100 residues smaller than sequence alignments predict. This new understanding of PfEMP1 structure will allow the use of better-defined PfEMP1 domains for functional studies, for the design of candidate vaccines, and for understanding the molecular basis of cytoadherence

Saving sage-grouse from the trees: A proactive solution to reducing a key threat to a candidate species

Conservation investment in management of at-risk species can be less costly than a delay-and-repair approach implemented after species receive legal protection. The United States Endangered Species Act candidate species designation represents an opportunity to implement proactive management to avoid future listing. Such efforts require substantial investments, and the challenge becomes one of optimization of limited conservation funds to maximize return. Focusing on conifer encroachment threats to greater sage-grouse (Centrocercus urophasianus), we demonstrated an approach that links species demographics with attributes of conservation threats to inform targeting of investments. We mapped conifer stand characteristics using spatial wavelet analysis, and modeled lek activity as a function of conifer-related and additional lek site covariates using random forests. We applied modeling results to identify leks of high management potential and to estimate management costs. Results suggest sage-grouse incur population-level impacts at very low levels of encroachment, and leks were less likely to be active where smaller trees were dispersed. We estimated costs of prevention (treating active leks in jeopardy) and restoration (treating inactive leks with recolonization potential) management across the study area (2.5 million ha) at a total of US$17.5 million, which is within the scope of landscape-level conservation already implemented. An annual investment of US$8.75 million can potentially address encroachment issues near all known Oregon leks within the next decade. Investments in proactive conservation with public and private landowners can increase ecosystem health to benefit species conservation and sustainable land uses, replace top-down regulatory approaches, and prevent conservation reliance of at-risk species.Keywords: Conifer encroachment, Spatial wavelet analysis, Sage-Grouse Initiative, Random forest models, Ecological economics, Juniperus occidentalis, Proactive managementKeywords: Conifer encroachment, Spatial wavelet analysis, Sage-Grouse Initiative, Random forest models, Ecological economics, Juniperus occidentalis, Proactive managemen