Linkage of plasma Abeta42 to a quantitative locus on chromosome 10 in late-onset Alzheimer's disease pedigrees

Plasma Abeta42 (amyloid beta42 peptide) is invariably elevated in early-onset familial Alzheimer's disease (AD), and it is also increased in the first-degree relatives of patients with typical late-onset AD (LOAD). To detect LOAD loci that increase Abeta42, we used plasma Abeta42 as a surrogate trait and performed linkage analysis on extended AD pedigrees identified through a LOAD patient with extremely high plasma Abeta. Here, we report linkage to chromosome 10 with a maximal lod score of 3.93 at 81 centimorgans close to D10S1225. Remarkably, linkage to the same region was obtained independently in a genome-wide screen of LOAD sibling pairs. These results provide strong evidence for a novel LOAD locus on chromosome 10 that acts to increase Abeta.

Gene-expression variation within and among human populations

Understanding patterns of gene-expression variation within and among human populations will provide important insights into the molecular basis of phenotypic diversity and the interpretation of patterns of expression variation in disease. However, little is known about how gene-expression variation is apportioned within and among human populations. Here, we characterize patterns of natural gene-expression variation in 16 individuals of European and African ancestry. We find extensive variation in gene-expression levels and estimate that approximately 83% of genes are differentially expressed among individuals and that approximately 17% of genes are differentially expressed among populations. By decomposing total gene-expression variation into within- versus among-population components, we find that most expression variation is due to variation among individuals rather than among populations, which parallels observations of extant patterns of human genetic variation. Finally, we performed allele-specific quantitative polymerase chain reaction to demonstrate that cis-regulatory variation in the lymphocyte adaptor protein (SH2B adapter protein 3) contributes to differential expression between European and African samples. These results provide the first insight into how human population structure manifests itself in gene-expression levels and will help guide the search for regulatory quantitative trait loci.

Health care utilization in males with obstructive sleep apnea syndrome two years after diagnosis and treatment

OBJECTIVE

To document changes in health care utilization (physician claims and hospitalizations) two years after diagnosis and treatment of patients with OSAS.

DESIGN

Prospective observational cohort study.

SETTING

The study was done in the Canadian Province of Manitoba. OSAS patients were selected from a University-based sleep disorders center. Control subjects were selected from the general population.

PATIENTS AND CONTROLS

There were 344 OSAS patients on whom there was utilization data for the period of the study. They were matched to controls from the general population by gender, age, and geographic location.

MEASUREMENTS AND RESULTS

The difference in physician claims between the patients and their matched controls two years after diagnosis and treatment ($174+/-32.4 (SE) per year in Canadian dollars) was significantly less than the difference in the year before diagnosis ($260+/-35.7 (SE), p=0.038). Examining the subgroups of patients adhering (PAT) or not adhering (PNAT) to treatment revealed that the changes were only significant in the patients adhering to treatment. Hospital stays for the entire OSAS group decreased from 1.27 days+0.25(SE) per patient per year one year before diagnosis to 0.54+0.13 per patient per year (p=0.01). The changes in the PAT group (1.25+0.28 per patient per year one year before diagnosis to 0.53+0.14 per patient per year (p=0.034) were significant while in the PNAT group they were not.

CONCLUSIONS

Adherence to treatment in patients with OSAS results in a significant reduction in physician claims and hospital stays.

Reproducibility of CT Radiomic Features within the Same Patient: Influence of Radiation Dose and CT Reconstruction Settings

Background Results of recent phantom studies show that variation in CT acquisition parameters and reconstruction techniques may make radiomic features largely nonreproduceable and of limited use for prognostic clinical studies. Purpose To investigate the effect of CT radiation dose and reconstruction settings on the reproducibility of radiomic features, as well as to identify correction factors for mitigating these sources of variability. Materials and Methods This was a secondary analysis of a prospective study of metastatic liver lesions in patients who underwent staging with single-energy dual-source contrast material-enhanced staging CT between September 2011 and April 2012. Technique parameters were altered, resulting in 28 CT data sets per patient that included different dose levels, section thicknesses, kernels, and reconstruction algorithm settings. By using a training data set (n = 76), reproducible intensity, shape, and texture radiomic features (reproducibility threshold, R2 ≥ 0.95) were selected and correction factors were calculated by using a linear model to convert each radiomic feature to its estimated value in a reference technique. By using a test data set (n = 75), the reproducibility of hierarchical clustering based on 106 radiomic features measured with different CT techniques was assessed. Results Data in 78 patients (mean age, 60 years ± 10; 33 women) with 151 liver lesions were included. The percentage of radiomic features deemed reproducible for any variation of the different technical parameters was 11% (12 of 106). Of all technical parameters, reconstructed section thickness had the largest impact on the reproducibility of radiomic features (12.3% [13 of 106]) if only one technical parameter was changed while all other technical parameters were kept constant. The results of the hierarchical cluster analysis showed improved clustering reproducibility when reproducible radiomic features with dedicated correction factors were used (ρ = 0.39-0.71 vs ρ = 0.14-0.47). Conclusion Most radiomic features are highly affected by CT acquisition and reconstruction settings, to the point of being nonreproducible. Selecting reproducible radiomic features along with study-specific correction factors offers improved clustering reproducibility. © RSNA, 2019 Online supplemental material is available for this article. See also the editorial by Sosna in this issue.

Health care utilization in the 10 years prior to diagnosis in obstructive sleep apnea syndrome patients

Obstructive sleep apnea syndrome (OSAS) patients may have symptoms for years prior to recognition of their disorder, or they may be treated for the associated comorbidities. We hypothesized that such patients would be heavy consumers of health care resources for several years prior to diagnosis. We therefore compared health service utilization for a 10-year interval prior to diagnosis of 181 OSA patients to those of randomly selected age-, gender-, and geographically matched controls from the general population. OSAS patients used approximately twice as many health care services (as defined by physician claims and overnight stays in hospital) in the 10 years prior to their initial diagnostic evaluation for apnea. Physician claims for the OSA patients totaled $686,365 ($3972 per patient), compared to $356,376 ($1969 per patient) for the controls for the 10-year period examined in this study. Use of health services was significantly higher in 7 of 10 years prior to diagnosis. The OSAS patients also had more overnight hospitalizations: they spent 1118 nights (6.2 per patient) in hospital vs 676 nights (3.7 per patient) for controls in the decade prior to diagnosis. We conclude that by the time patients are finally diagnosed for sleep apnea, they have already been heavy users of health services for several years. It is possible that our findings reflect not OSAS per se, but the presence of some of the risk factors that predispose to OSAS, such as obesity, alcohol usage and perhaps tobacco consumption.

Local regulatory variation in Saccharomyces cerevisiae

Naturally occurring sequence variation that affects gene expression is an important source of phenotypic differences among individuals within a species. We and others have previously shown that such regulatory variation can occur both at the same locus as the gene whose expression it affects (local regulatory variation) and elsewhere in the genome at trans-acting factors. Here we present a detailed analysis of genome-wide local regulatory variation in Saccharomyces cerevisiae. We used genetic linkage analysis to show that nearly a quarter of all yeast genes contain local regulatory variation between two divergent strains. We measured allele-specific expression in a diploid hybrid of the two strains for 77 genes showing strong self-linkage and found that in 52%–78% of these genes, local regulatory variation acts directly in cis. We also experimentally confirmed one example in which local regulatory variation in the gene AMN1 acts in trans through a feedback loop. Genome-wide sequence analysis revealed that genes subject to local regulatory variation show increased polymorphism in the promoter regions, and that some but not all of this increase is due to polymorphisms in predicted transcription factor binding sites. Increased polymorphism was also found in the 3′ untranslated regions of these genes. These findings point to the importance of cis-acting variation, but also suggest that there is a diverse set of mechanisms through which local variation can affect gene expression levels.

Variation in DNA sequences in and around a gene can contribute to differences between individuals by affecting the gene's expression. The authors have used a variety of methods to characterize this local DNA sequence variation on a large scale in two strains of the budding yeast Saccharomyces cerevisiae. Their results suggest that the expression levels of a sizeable fraction of genes are affected by local sequence variation. Many local variants alter the expression of only one of two copies of a gene in diploid hybrid yeast, but other local variants can affect both copies equally. The authors also found that sequence variation in particular regions of DNA near genes, both upstream and downstream of coding sequences and especially in transcription factor binding sites, is most likely to affect gene expression. These results provide a detailed view of local sequence variation that affects the expression of nearby genes in S. cerevisiae.

Simultaneous genotyping, gene-expression measurement, and detection of allele-specific expression with oligonucleotide arrays

Oligonucleotide microarrays provide a high-throughput method for exploring genomes. In addition to their utility for gene-expression analysis, oligonucleotide-expression arrays have also been used to perform genotyping on genomic DNA. Here, we show that in segregants from a cross between two unrelated strains of Saccharomyces cerevisiae, high-quality genotype data can also be obtained when mRNA is hybridized to an oligonucleotide-expression array. We were able to identify and genotype nearly 1000 polymorphisms at an error rate close to 3% in segregants and at an error rate of 7% in diploid strains, a performance comparable to methods using genomic DNA. In addition, we demonstrate how simultaneous genotyping and gene-expression profiling can reveal cis-regulatory variation by screening hundreds of genes for allele-specific expression. With this method, we discovered 70 ORFs with evidence for preferential expression of one allele in a diploid hybrid of two S. cerevisiae strains.

LI-RADS Treatment Response Algorithm: Performance and Diagnostic Accuracy

Background In 2017, the Liver Imaging Reporting and Data System (LI-RADS) included an algorithm for the assessment of hepatocellular carcinoma (HCC) treated with local-regional therapy. The aim of the algorithm was to enable standardized evaluation of treatment response to guide subsequent therapy. However, the performance of the algorithm has not yet been validated in the literature. Purpose To evaluate the performance of the LI-RADS 2017 Treatment Response algorithm for assessing the histopathologic viability of HCC treated with bland arterial embolization. Materials and Methods This retrospective study included patients who underwent bland arterial embolization for HCC between 2006 and 2016 and subsequent liver transplantation. Three radiologists independently assessed all treated lesions by using the CT/MRI LI-RADS 2017 Treatment Response algorithm. Radiology and posttransplant histopathology reports were then compared. Lesions were categorized on the basis of explant pathologic findings as either completely (100%) or incompletely (<100%) necrotic, and performance characteristics and predictive values for the LI-RADS Treatment Response (LR-TR) Viable and Nonviable categories were calculated for each reader. Interreader association was calculated by using the Fleiss κ. Results A total of 45 adults (mean age, 57.1 years ± 8.2; 13 women) with 63 total lesions were included. For predicting incomplete histopathologic tumor necrosis, the accuracy of the LR-TR Viable category for the three readers was 60%-65%, and the positive predictive value was 86%-96%. For predicting complete histopathologic tumor necrosis, the accuracy of the LR-TR Nonviable category was 67%-71%, and the negative predictive value was 81%-87%. By consensus, 17 (27%) of 63 lesions were categorized as LR-TR Equivocal, and 12 of these lesions were incompletely necrotic. Interreader association for the LR-TR category was moderate (κ = 0.55; 95% confidence interval: 0.47, 0.67). Conclusion The Liver Imaging Reporting and Data System 2017 Treatment Response algorithm had high predictive value and moderate interreader association for the histopathologic viability of hepatocellular carcinoma treated with bland arterial embolization when lesions were assessed as Viable or Nonviable. © RSNA, 2019 Online supplemental material is available for this article. See also the editorial by Gervais in this issue.

A mobile ELF4 delivers circadian temperature information from shoots to roots

The circadian clock is synchronized by environmental cues, mostly by light and temperature. Explaining how the plant circadian clock responds to temperature oscillations is crucial to understanding plant responsiveness to the environment. Here, we found a prevalent temperature-dependent function of the Arabidopsis clock component EARLY FLOWERING 4 (ELF4) in the root clock. Although the clocks in roots are able to run in the absence of shoots, micrografting assays and mathematical analyses show that ELF4 moves from shoots to regulate rhythms in roots. ELF4 movement does not convey photoperiodic information, but trafficking is essential for controlling the period of the root clock in a temperature-dependent manner. Low temperatures favour ELF4 mobility, resulting in a slow-paced root clock, whereas high temperatures decrease movement, leading to a faster clock. Hence, the mobile ELF4 delivers temperature information and establishes a shoot-to-root dialogue that sets the pace of the clock in roots.

The LI-RADS Version 2018 MRI Treatment Response Algorithm: Evaluation of Ablated Hepatocellular Carcinoma

Background The Liver Imaging Reporting and Data System (LI-RADS) treatment response algorithm (TRA) is used to assess presumed hepatocellular carcinoma (HCC) after local-regional therapy, but its performance has not been extensively assessed. Purpose To assess the performance of LI-RADS version 2018 TRA in the evaluation of HCC after ablation. Materials and Methods In this retrospective study, patients who underwent ablation therapy for presumed HCC followed by liver transplantation between January 2011 and December 2015 at a single tertiary care center were identified. Lesions were categorized as completely (100%) or incompletely (≤99%) necrotic based on transplant histology. Three radiologists assessed pre- and posttreatment MRI findings using LI-RADS version 2018 and the TRA, respectively. Interreader agreement was assessed by using the Fleiss κ test. Performance characteristics for predicting necrosis category based on LI-RADS treatment response (LR-TR) category (viable or nonviable) were calculated by using generalized mixed-effects models to account for clustering by subject. Results A total of 36 patients (mean age, 58 years ± 5 [standard deviation]; 32 men) with 53 lesions was included. Interreader agreement for pretreatment LI-RADS category was 0.40 (95% confidence interval [CI]: 0.15, 0.67; P < .01) and was lower than the interreader agreement for TRA category (κ = 0.71; 95% CI: 0.59, 0.84; P < .01). After accounting for clustering by subject, sensitivity of tumor necrosis across readers ranged from 40% to 77%, and specificity ranged from 85% to 97% when LR-TR equivocal assessments were treated as nonviable. When LR-TR equivocal assessments were treated as viable, sensitivity of tumor necrosis across readers ranged from 81% to 87%, and specificity ranged from 81% to 85% across readers. Six (11%) of 53 treated lesions were LR-TR equivocal by consensus, with most (five of six) incompletely necrotic at histopathology. Conclusion The Liver Imaging Reporting and Data System treatment response algorithm can be used to predict viable or nonviable hepatocellular carcinoma after ablation. Most ablated lesions rated as treatment response equivocal were incompletely necrotic at histopathology. © RSNA, 2019 Online supplemental material is available for this article. See also the editorial by Do and Mendiratta-Lala in this issue.

Fine mapping of the alpha-T catenin gene to a quantitative trait locus on chromosome 10 in late-onset Alzheimer's disease pedigrees

Using plasma amyloid beta protein (Abeta42) levels as an intermediate, quantitative phenotype for late onset Alzheimer's disease (LOAD), we previously obtained significant linkage at approximately 80 cM on chromosome 10. Linkage to the same region was obtained independently in a study of affected LOAD sib-pairs. Together, these two studies provide strong evidence for a novel LOAD locus on chromosome 10 that acts to increase Abeta42. VR22 is a large (1.7 Mb) gene located at 80 cM that encodes alpha-T catenin, which is a binding partner of beta catenin. This makes VR22 an attractive candidate gene because beta catenin interacts with presenilin 1, which has many mutations that elevate Abeta42 and cause early onset familial AD. We identified two intronic VR22 SNPs (4360 and 4783) in strong linkage disequilibrium (LD) that showed highly significant association (P=0.0001 and 0.0006) with plasma Abeta42 in 10 extended LOAD families. This association clearly contributed to the linkage at approximately 80 cM because the lod scores decreased when linkage analysis was performed conditional upon the VR22 association. This association replicated in another independent set of 12 LOAD families (P=0.04 for 4783 and P=0.08 for 4360). Bounding of the association region using multiple SNPs showed VR22 to be the only confirmed gene within the region of association. These findings indicate that VR22 has variant(s) which influence Abeta42 and contribute to the previously reported linkage for plasma Abeta42 in LOAD families.

Inherited variation in gene expression

Variation in gene expression constitutes an important source of biological variability within and between populations that is likely to contribute significantly to phenotypic diversity. Recent conceptual, technical, and methodological advances have enabled the genome-scale dissection of transcriptional variation. Here, we outline common approaches for detecting gene expression quantitative trait loci, and summarize the insights gleaned from these studies regarding the genetic architecture of transcriptional variation and the nature of regulatory alleles. Particular emphasis is placed on human studies, and we discuss experimental designs that ensure that increasingly large and complex studies continue to advance our understanding of gene expression variation. We conclude by discussing the evolution of gene expression levels, and we explore prospects for leveraging new technological developments to investigate inherited variation in gene expression in even greater depth.

Elevated amyloid β protein (Aβ42) and late onset Alzheimer's disease are associated with single nucleotide polymorphisms in the urokinase-type plasminogen activator gene

Plasma amyloid beta protein (Abeta42) levels and late onset Alzheimer's disease (LOAD) have been linked to the same region on chromosome 10q. The PLAU gene within this region encodes urokinase-type plasminogen activator, which converts plasminogen to plasmin. Abeta aggregates induce PLAU expression thereby increasing plasmin, which degrades both aggregated and non-aggregated forms of Abeta. We evaluated single nucleotide polymorphisms (SNPs) in PLAU for association with Abeta42 and LOAD. PLAU SNP compound genotypes composed of haplotype pairs showed significant association with AD in three independent case-control series. PLAU SNP haplotypes associated significantly with plasma Abeta42 in 10 extended LOAD families. One of the SNPs analyzed was a missense C/T polymorphism in exon 6 of PLAU (PLAU_1=rs2227564), which causes a proline to leucine change (P141L). We analyzed PLAU_1 for association with AD in six case-control series and 24 extended LOAD families. The CT and TT PLAU_1 genotypes showed association (P=0.05) with an overall estimated odds ratio of 1.2 (1.0-1.5). The CT and TT genotypes of PLAU_1 were also associated with significant age-dependent elevation of plasma Abeta42 in 24 extended LOAD families (P=0.0006). In knockout mice lacking the PLAU gene, plasma--but not brain--Abeta42 as well as Abeta40 was significantly elevated, also in an age-dependent manner. The PLAU_1 associations were independent of the associations we found among plasma Abeta42, LOAD and variants in the IDE or VR22 region. These results provide strong evidence that PLAU or a nearby gene is involved in the development of LOAD. PLAU_1 is a plausible pathogenic mutation that could act by increasing Abeta42, but additional biological experiments are required to show this definitively.

The evolution of gene expression QTL in Saccharomyces cerevisiae

Understanding the evolutionary forces that influence patterns of gene expression variation will provide insights into the mechanisms of evolutionary change and the molecular basis of phenotypic diversity. To date, studies of gene expression evolution have primarily been made by analyzing how gene expression levels vary within and between species. However, the fundamental unit of heritable variation in transcript abundance is the underlying regulatory allele, and as a result it is necessary to understand gene expression evolution at the level of DNA sequence variation. Here we describe the evolutionary forces shaping patterns of genetic variation for 1206 cis-regulatory QTL identified in a cross between two divergent strains of Saccharomyces cerevisiae. We demonstrate that purifying selection against mildly deleterious alleles is the dominant force governing cis-regulatory evolution in S. cerevisiae and estimate the strength of selection. We also find that essential genes and genes with larger codon bias are subject to slightly stronger cis-regulatory constraint and that positive selection has played a role in the evolution of major trans-acting QTL.

Genetic variation in LPAL2, LPA, and PLG predicts plasma lipoprotein(a) level and carotid artery disease risk

BACKGROUND AND PURPOSE

lipoprotein(a) [Lp(a)] level is an established risk factor for coronary artery disease and has been implicated in carotid artery disease (CAAD). The relationship between genetic variation in the LPA gene region and CAAD risk remains unknown.

METHODS

we genotyped single nucleotide polymorphisms (SNPs) in the LPAL2, LPA, and PLG regions in 530 individuals with severe CAAD and 770 controls and kringle IV type 2 (KIV2) repeat length in a subset of 90 individuals.

RESULTS

nine SNPs collectively accounted for 30% of the variance in Lp(a) level. Six SNPs were associated with Lp(a) level after accounting for KIV2 copy number, and the dominant KIV2 allele combined with these markers explained 60% of the variance in Lp(a) level. Five SNPs, including rs10455872, which had an odds ratio of 2.1 per minor allele and haplotypes formed by rs10455872, rs6919346, and rs3123629, were significant predictors of CAAD. After accounting for Lp(a) level, all evidence of CAAD-genotype association in the LPA region was eliminated.

CONCLUSIONS

LPA region SNPs capture some but not all of the effect of KIV2 repeat length on Lp(a) level. There are associations between LPA region SNPs and CAAD that appear to be attributable to effects on Lp(a) level.

Genome-wide scans for loci under selection in humans

Natural selection, which can be defined as the differential contribution of genetic variants to future generations, is the driving force of Darwinian evolution. Identifying regions of the human genome that have been targets of natural selection is an important step in clarifying human evolutionary history and understanding how genetic variation results in phenotypic diversity, it may also facilitate the search for complex disease genes. Technological advances in high-throughput DNA sequencing and single nucleotide polymorphism genotyping have enabled several genome-wide scans of natural selection to be undertaken. Here, some of the observations that are beginning to emerge from these studies will be reviewed, including evidence for geographically restricted selective pressures (ie local adaptation) and a relationship between genes subject to natural selection and human disease. In addition, the paper will highlight several important problems that need to be addressed in future genome-wide studies of natural selection.

Lead poisoning in rural Scotland

Nine people from four families living in rural parts of Scotland have been found to suffer from clinical or biochemical effects of lead poisoning. Five had symptoms and four had unequivocal evidence of excessive lead exposure. The source of lead has been traced to the domestic water supply which in all cases was grossly contaminated with lead acquired from lead plumbing systems, including lead storage tanks. Clinical improvement followed the replacement of lead piping in two families studied. Lead poisoning is a possible cause of chronic ill health in areas of plumbosolvent water.

Myoelectric prostheses for below-elbow amputees: the Trent experience

Experience of myoelectric prostheses for unilateral below-elbow amputees in a large region of Great Britain is presented. Of the cases considered, 14 were adults and 29 were 16 years of age or less. The rejection rate was 25% overall but it was lower in adults, at 17%. Comparisons with published data and other aspects of myoelectric prostheses are discussed. Just over half the 37 amputees interviewed were independent in activities of daily living; independence was more common in the adults, at 77%. A very large proportion of myoelectric prosthesis users also used body-powered prostheses, demonstrating a need for both types of prosthesis for optimum rehabilitation. It is recommended that myoelectric prosthetic programmes should be carried out from specialized centres with comprehensive facilities for this expensive rehabilitation aid.

Analysis of recently identified dyslipidemia alleles reveals two loci that contribute to risk for carotid artery disease

Background

Genome-wide association studies have identified numerous single nucleotide polymorphisms (SNPs) affecting high density lipoprotein (HDL) or low density lipoprotein (LDL) cholesterol levels; these SNPs may contribute to the genetic basis of vascular diseases.

Results

We assessed the impact of 34 SNPs at 23 loci on dyslipidemia, key lipid sub-phenotypes, and severe carotid artery disease (CAAD) in a case-control cohort. The effects of these SNPs on HDL and LDL were consistent with those previously reported, and we provide unbiased estimates of the percent variance in HDL (3.9%) and LDL (3.3%) explained by genetic risk scores. We assessed the effects of these SNPs on HDL subfractions, apolipoprotein A-1, LDL buoyancy, apolipoprotein B, and lipoprotein (a) and found that rs646776 predicts apolipoprotein B level while rs2075650 predicts LDL buoyancy. Finally, we tested the role of these SNPs in conferring risk for ultrasonographically documented CAAD stenosis status. We found that two loci, chromosome 1p13.3 near CELSR2 and PSRC1 which contains rs646776, and 19q13.2 near TOMM40 and APOE which contains rs2075650, harbor risk alleles for CAAD.

Conclusion

Our analysis of 34 SNPs contributing to dyslipidemia at 23 loci suggests that genetic variation in the 1p13.3 region may increase risk of CAAD by increasing LDL particle number, whereas variation in the 19q13.2 region may increase CAAD risk by promoting formation of smaller, denser LDL particles.

Focusing on the nuclear and subnuclear dynamics of light and circadian signalling

Circadian clocks provide organisms the ability to synchronize their internal physiological responses with the external environment. This process, termed entrainment, occurs through the perception of internal and external stimuli. As with other organisms, in plants, the perception of light is a critical for the entrainment and sustainment of circadian rhythms. Red, blue, far-red, and UV-B light are perceived by the oscillator through the activity of photoreceptors. Four classes of photoreceptors signal to the oscillator: phytochromes, cryptochromes, UVR8, and LOV-KELCH domain proteins. In most cases, these photoreceptors localize to the nucleus in response to light and can associate to subnuclear structures to initiate downstream signalling. In this review, we will highlight the recent advances made in understanding the mechanisms facilitating the nuclear and subnuclear localization of photoreceptors and the role these subnuclear bodies have in photoreceptor signalling, including to the oscillator. We will also highlight recent progress that has been made in understanding the regulation of the nuclear and subnuclear localization of components of the plant circadian clock.

Genomewide evolutionary rates in laboratory and wild yeast

As wild organisms adapt to the laboratory environment, they become less relevant as biological models. It has been suggested that a commonly used S. cerevisiae strain has rapidly accumulated mutations in the lab. We report a low-to-intermediate rate of protein evolution in this strain relative to wild isolates.

Making the clock tick: the transcriptional landscape of the plant circadian clock

Circadian clocks are molecular timekeepers that synchronise internal physiological processes with the external environment by integrating light and temperature stimuli. As in other eukaryotic organisms, circadian rhythms in plants are largely generated by an array of nuclear transcriptional regulators and associated co-regulators that are arranged into a series of interconnected molecular loops. These transcriptional regulators recruit chromatin-modifying enzymes that adjust the structure of the nucleosome to promote or inhibit DNA accessibility and thus guide transcription rates. In this review, we discuss the recent advances made in understanding the architecture of the Arabidopsis oscillator and the chromatin dynamics that regulate the generation of rhythmic patterns of gene expression within the circadian clock.