Quantum measurement of a rapidly rotating spin qubit in diamond.

A controlled qubit in a rotating frame opens new opportunities to probe fundamental quantum physics, such as geometric phases in physically rotating frames, and can potentially enhance detection of magnetic fields. Realizing a single qubit that can be measured and controlled during physical rotation is experimentally challenging. We demonstrate quantum control of a single nitrogen-vacancy (NV) center within a diamond rotated at 200,000 rpm, a rotational period comparable to the NV spin coherence time T2. We stroboscopically image individual NV centers that execute rapid circular motion in addition to rotation and demonstrate preparation, control, and readout of the qubit quantum state with lasers and microwaves. Using spin-echo interferometry of the rotating qubit, we are able to detect modulation of the NV Zeeman shift arising from the rotating NV axis and an external DC magnetic field. Our work establishes single NV qubits in diamond as quantum sensors in the physically rotating frame and paves the way for the realization of single-qubit diamond-based rotation sensors.

HCV Prevalence in Asian Americans in California.

The World Health Organization estimates that 170 million persons are infected with HCV worldwide, but only 22 million are from the Americas and Europe, compared to 94 million from Asia. HCV prevalence in the general US population is 1.6 %, but data for Asian Americans are limited. Our goal was to examine HCV prevalence in Asian Americans in a large ethnically diverse patient cohort seeking primary care at a free clinic in Northern California. A total of 1347 consecutive patients were seen from September 2009 to October 2012 and were studied via individual chart review using case report forms. HCV infection was defined as positive HCV antibody (anti-HCV) or HCV RNA by PCR. 699 out of 1347 patients were screened for HCV. Asian Americans comprised 57.2 % of these patients and 29 (4.1 %) patients tested positive for HCV. Of these 29 HCV-positive patients, 22 (75.9 %) were Asian, yielding a prevalence of 5.5 % for Asians and 2.3 % for non-Asians (P = 0.038). The highest HCV prevalence was seen in Vietnamese patients at 7.9 %, and 6.0 % in Chinese patients. Of the HCV-positive Asians, none had a history of intravenous drug use (IVDU), tattoos, or sexual exposure. On multivariate analysis, significant independent predictors for positive HCV infection were male gender (OR 2.53, P = 0.02) and presence of known risk factors (OR 21.1, P < 0.001). However, older age and Asian ethnicity were found to be significant predictors of HCV infection (OR 1.03, P = 0.05 and 2.31, P = 0.066, respectively). In our study, HCV prevalence in patients seeking routine primary care was 5.5 % in Asian Americans, which was over double the prevalence for non-Asians at 2.3 %. Known risk factors were also notably absent in Asian patients with HCV infection. The high prevalence of HCV in Asian-Americans is likely reflective of the higher prevalence of HCV in their countries of origin in Asia. Asian-Americans immigrants from endemic countries are at higher risk of HCV infection and should be screened for HCV, regardless of their exposure risk profile.

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.

Repetitive sequences are biologically and clinically important because they can influence traits and disease, but repeats are challenging to analyse using short-read sequencing technology. We present a tool for genotyping microsatellite repeats called RepeatSeq, which uses Bayesian model selection guided by an empirically derived error model that incorporates sequence and read properties. Next, we apply RepeatSeq to high-coverage genomes from the 1000 Genomes Project to evaluate performance and accuracy. The software uses common formats, such as VCF, for compatibility with existing genome analysis pipelines. Source code and binaries are available at http://github.com/adaptivegenome/repeatseq.

Analysis of microsatellite variation in Drosophila melanogaster with population-scale genome sequencing.

Genome sequencing technologies promise to revolutionize our understanding of genetics, evolution, and disease by making it feasible to survey a broad spectrum of sequence variation on a population scale. However, this potential can only be realized to the extent that methods for extracting and interpreting distinct forms of variation can be established. The error profiles and read length limitations of early versions of next-generation sequencing technologies rendered them ineffective for some sequence variant types, particularly microsatellites and other tandem repeats, and fostered the general misconception that such variants are inherently inaccessible to these platforms. At the same time, tandem repeats have emerged as important sources of functional variation. Tandem repeats are often located in and around genes, and frequent mutations in their lengths exert quantitative effects on gene function and phenotype, rapidly degrading linkage disequilibrium between markers and traits. Sensitive identification of these variants in large-scale next-gen sequencing efforts will enable more comprehensive association studies capable of revealing previously invisible associations. We present a population-scale analysis of microsatellite repeats using whole-genome data from 158 inbred isolates from the Drosophila Genetics Reference Panel, a collection of over 200 extensively phenotypically characterized isolates from a single natural population, to uncover processes underlying repeat mutation and to enable associations with behavioral, morphological, and life-history traits. Analysis of repeat variation from next-generation sequence data will also enhance studies of genome stability and neurodegenerative diseases.

Identification and characterization of a strict and a promiscuous N-acetylglucosamine-1-P uridylyltransferase in Arabidopsis.

UDP-GlcNAc is an essential precursor for glycoprotein and glycolipid synthesis. In the present study, a functional nucleotidyltransferase gene from Arabidopsis encoding a 58.3 kDa GlcNAc1pUT-1 (N-acetylglucosamine-1-phosphate uridylyltransferase) was identified. In the forward reaction the enzyme catalyses the formation of UDP-N-acetylglucosamine and PPi from the respective monosaccharide 1-phosphate and UTP. The enzyme can utilize the 4-epimer UDP-GalNAc as a substrate as well. The enzyme requires divalent ions (Mg2+ or Mn2+) for activity and is highly active between pH 6.5 and 8.0, and at 30-37 degrees C. The apparent Km values for the forward reaction were 337 microM (GlcNAc-1-P) and 295 microM (UTP) respectively. Another GlcNAc1pUT-2, which shares 86% amino acid sequence identity with GlcNAc1pUT-1, was found to convert, in addition to GlcNAc-1-P and GalNAc-1-P, Glc-1-P into corresponding UDP-sugars, suggesting that subtle changes in the UT family cause different substrate specificities. A three-dimensional protein structure model using the human AGX1 as template showed a conserved catalytic fold and helped identify key conserved motifs, despite the high sequence divergence. The identification of these strict and promiscuous gene products open a window to identify new roles of amino sugar metabolism in plants and specifically their role as signalling molecules. The ability of GlcNAc1pUT-2 to utilize three different substrates may provide further understanding as to why biological systems have plasticity.

Phylogenetic Relationships and Functional Genes: Distribution of a Gene (mnxG) encoding a putative manganese-oxidizing enzyme in Bacillus species.

Several Bacillus and Paenibacillus species were isolated from Fe and Mn oxide minerals precipitating at a deep subsurface oxic-anoxic interface at Henderson Molybdenum Mine, Empire, CO. The isolates were investigated for their Mn(II)-oxidizing potential and interrogated for possession of the mnxG gene, a gene that codes for a putative Mn(II)-oxidizing enzyme in Bacillus species. Seven of eight Bacillus species were capable of Mn(II) oxidation; however, the mnxG gene was detected in only one isolate. Using sequences of known Bacillus species both with and without amplifiable mnxG genes and Henderson Mine isolates, the 16S rRNA and mnxG gene phylogenies were compared to determine if 16S rRNA sequences could be used to predict the presence or absence of an amplifiable mnxG gene within the genomes of the isolates. We discovered a strong correspondence between 16S rRNA sequence similarity and the presence/absence of an amplifiable mnxG gene in the isolates. The data revealed a complex phylogenetic distribution of the mnxG gene in which vertical inheritance and gene loss influence the distribution of the gene among the Bacillus species included in this study. Comparisons of 16S rRNA and functional gene phylogenies can be used as a tool to aid in unraveling the history and dispersal of the mnxG gene within the Bacillus clade.

Disturbance and patch-specific responses: the interactive effects of woody debris and floods on lotic invertebrates.

Disturbance may play an important role in generating patterns of abundance and distribution of biotic assemblages, particularly if its impact differs among habitat patches. Despite much speculation concerning the probable importance of spatial variation in the response of stream fauna to flooding, empirical work on patch-specific responses to spates is largely lacking. Floods typically reduce the abundance of lotic invertebrates dramatically in open-channel areas. We conducted a set of experiments to determine if faunal abundances are less affected in patches more sheltered due to the presence of woody debris dams. Specifically, we tested two hypotheses using chironomids and copepods living in a warmwater, 4th order stream: (1) the effect of flooding on the fauna varies between patches associated with debris dams versus the open channel, and (2) the absence of woody debris in a stream impedes faunal recovery throughout the channel following floods. We tested the first hypothesis by quantifying faunal abundances prior to, during, and following two floods in four patch types: mid-channel sandy patches distant from dams, coarse sediments associated with dams, fine sediments associated with dams, and leafy debris in dams. The second hypothesis was tested by removing all of the woody debris from two stretches of the stream and comparing the impact of a flood on fauna in debris-removed versus control stretches. Across all of the eight study dams, there were patchspecific faunal responses to two floods. Removal of woody debris from the stream did not prevent faunal recovery throughout the channel; however, the presence of woody debris dams did confer greater resistance of fauna to floods (as measured by no decrease in abundance during flooding) in two patch types. Abundances of chironomids and, to a lesser extent, copepods in the leafy debris of dams and in fine sediment patches associated with some dams either did not change or increased during floods, despite the fact that abundances in the dominant patch type of the stream (the sandy mid-channel) were reduced by 75-95%. All instances of faunal increase were limited to fine sediment patches associated with dams, thus entire dams cannot be labeled as flow refugia per se. Statistically, we distinguished fine patches which accumulated animals during floods from the other fine patches based on two physical attributes. Patches accumulating animals were all characterized by low water flux and nearbed flow, which likely contributed to the retention and/or passive deposition of animals. Whole dam attributes (e.g. dam size or complexity) were not useful in predicting which of the dams would accumulate animals in their fine sediments during flooding. Although structural complexity - here in the form of wood and leafy debris - is clearly important in generating biotic pattern in many ecosystems, our work underscores the need to understand what processes are responsible for the link between physical structure and biotic pattern.