Probing Circadian Clock-Steroid Receptor Interactions in GnRH Neurons

Endogenous circadian clock regulation is essential to normal rhythmicity, particularly the timing of hormone release in the brain. In the context of mammalian reproduction, a surge of a specific hormone, gonadotrophin-releasing hormone (GnRH), initiates a surge of luteinizing hormone (LH) from the pituitary gland, which is required for ovulation in females. Ordinarily, GnRH is secreted in a pulsatile pattern distinct from the surging that promotes ovulation. These surges occur with an approximately 24-hour release pattern and require elevated levels of ovarian estradiol (E2), the most common form of estrogen in human mammals, originating from the granulosa cells of the developing follicle. GnRH neurons express the estrogen receptor isoform estrogen receptor β (ERβ). Currently, little is known about mechanisms underlying GnRH/LH surge timing and how E2 acts directly on GnRH neurons. To better understand how endogenous clocks interact with sex-steroid hormone signalling, we explored protein-protein interactions between ERβ and the circadian clock transcription factor BMAL1 in multiple representative cell lines, in both the absence and presence of E2. It was hypothesized that direct protein-protein interactions may exist among clock components and ERβ in immortalized GnRH neurons (GT1-7 cell lines), exhibiting altered interactions in the presence of E2. Co-Immunoprecipitation (Co-IP) and Western blot procedures provided unclear results as some data supported the hypothesis, while other data contradict it

Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the "targeted" clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production

An Integrated Content and Metadata based Retrieval System for Art

In this paper we describe aspects of the Artiste project to develop a distributed content and metadata based analysis, retrieval and navigation system for a number of major European Museums. In particular, after a brief overview of the complete system, we describe the design and evaluation of some of the image analysis algorithms developed to meet the specific requirements of the users from the museums. These include a method for retrievals based on sub images, retrievals based on very low quality images and retrieval using craquelure type

The Chlamydomonas genome project: A decade on

The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its genome project was initiated an iterative process of improvements to the genome and gene predictions has propelled this organism to the forefront of the omics era. Housed at Phytozome, the plant genomics portal of the Joint Genome Institute (JGI), the most up-to-date genomic data include a genome arranged on chromosomes and high-quality gene models with alternative splice forms supported by an abundance of whole transcriptome sequencing (RNA-Seq) data. We present here the past, present, and future of Chlamydomonas genomics. Specifically, we detail progress on genome assembly and gene model refinement, discuss resources for gene annotations, functional predictions, and locus ID mapping between versions and, importantly, outline a standardized framework for naming genes

Genome Improvement at JGI-HAGSC

Since the completion of the sequencing of the human genome, the JGI has rapidly expanded its scientific goals in several DOE mission-relevant areas. At the JGI-HAGSC, we have kept pace with this rapid expansion of projects with our focus on assessing, assembling, improving and finishing eukaryotic whole genome shotgun (WGS) projects for which the shotgun sequence is generated at the Production Genomic Facility (JGI-PGF). We follow this by combining the draft WGS with genomic resources generated at JGI-HAGSC or in collaborator laboratories (including BAC end sequences, genetic maps and FLcDNA sequences) to produce an improved draft sequence. For eukaryotic genomes important to the DOE mission, we then add further information from directed experiments to produce reference genomic sequences that are publicly available for any scientific researcher. Also, we have continued our program for producing BAC-based finished sequence, both for adding information to JGI genome projects and for small BAC-based sequencing projects proposed through any of the JGI sequencing programs. We have now built our computational expertise in WGS assembly and analysis and have moved eukaryotic genome assembly from the JGI-PGF to JGI-HAGSC. We have concentrated our assembly development work on large plant genomes and complex fungal and algal genomes

Voluntary versus ABC breath-hold in the context of VMAT for breast and locoregional lymph node radiotherapy including the internal mammary chain

Background: Deep-inspiration breath-hold (DIBH) reduces radiation dose to the heart in patients undergoing locoregional breast radiotherapy. In the context of tangential irradiation of the breast/ chest wall, a voluntary breath hold (vDIBH) technique has been shown to be as reproducible as a machine-assisted breath hold technique using the active breathing co-ordinator (ABCTM, Elekta, Crawley, UK, ABC_DIBH). This study compares set-up reproducibility for vDIBH versus ABC_DIBH in patients undergoing volumetric-modulated arc radiotherapy (VMAT) for breast cancer, both with and without wax bolus. Method: Patients with breast cancer requiring pan regional lymph node VMAT +/� wax bolus in breathhold were CT scanned in vDIBH and ABC_DIBH. Patients were randomised to receive one technique for fractions 1–7 and the other for fractions 8–15. Daily cone beam computed tomography (CBCT) was performed and registered to planning-CT using bony anatomy. Within-patient comparisons of mean daily chest wall position were made using a paired t-test. Population, systematic (P) and random errors (a) were estimated. Intrafraction reproducibility was assessed by comparing chest wall position and diaphragm movement between consecutive breath holds on CBCT. Results: 16 patients were recruited. All completed treatment with both techniques (9 patients with wax bolus, 7 patients without). CBCT derived P were 2.1–6.4 mm (ABC_DIBH) and 2.1–4.9 mm (vDIBH), a were 1.7–2.6 mm (ABC_DIBH) and 2.2–2.7 mm (vDIBH) and mean daily chest wall displacements (MD) were 0.0–1.5 mm (ABC_DIBH) and - 0.1–1.6 vDIBH (all p non-significant). Chest wall and diaphragm position was equivalent between consecutive breath holds in ABC and vDIBH (median difference 1.0 mm and 0.8 mm respectively, non p significant) demonstrating equivalent intrafraction reproducibility. Conclusion: This study demonstrates that a simple voluntary breath hold technique is feasible in combination with VMAT (+/� bolus) and is as reproducible as ABC_DIBH with VMAT for the irradiation of the breast and axillary and IMC lymph nodes in breast cancer patients

Complete Plastome Sequences from Glycine syndetika, and Six Additional Perennial Wild Relatives of Soybean

Organelle sequences have a long history of utility in phylogenetic analyses. Chloroplast sequences when combined with nuclear data can help resolve relationships among flowering plant genera, and within genera incongruence can point to reticulate evolution. Plastome sequences are becoming plentiful because they are increasingly easier to obtain. Complete plastome sequences allow us to detect rare rearrangements and test the tempo of sequence evolution. Chloroplast sequences are generally considered a nuisance to be kept to a minimum in bacterial artificial chromosome libraries. Here, we sequenced two bacterial artificial chromosomes per species to generate complete plastome sequences from seven species. The plastome sequences from Glycine syndetika and six other perennial Glycine species are similar in arrangement and gene content to the previously published soybean plastome. Repetitive sequences were detected in high frequencies as in soybean, but further analysis showed that repeat sequence numbers are inflated. Previous chloroplast-based phylogenetic trees for perennial Glycine were incongruent with nuclear gene\u2013based phylogenetic trees. We tested whether the hypothesis of introgression was supported by the complete plastomes. Alignment of complete plastome sequences and Bayesian analysis allowed us to date putative hybridization events supporting the hypothesis of introgression and chloroplast \u201ccapture.\u201

London governance and the politics of neighbourhood planning: a case for investigation

The Localism Act 2011 has successfully devolved planning powers to over 2,500 English communities, involving 14 million people, with over 700 ‘made’ neighbourhood plans legitimised by referendum. In London, however, there are less than one-tenth of the made plans than in the rest of England. Institutional resistance and policy choices may be implicated. Two national studies of neighbourhood planning are reviewed. The role of the local authority is found to be a crucial factor in determining progress, and issues of social deprivation and unequal access are highlighted. Theorisation is considered by reference to a range of academic studies of localism and neighbourhood planning. Distinctions made between ‘representative’ and ‘community’ localism, and objections to anti-political effects, are noted. There has been remarkably little research into borough governance and neighbourhood planning in the capital. Based upon evidence of anomalous and differentiated governance practice, a study in London is called for

Real-time intrafraction motion monitoring in external beam radiotherapy

© 2019 Institute of Physics and Engineering in Medicine. Radiotherapy (RT) aims to deliver a spatially conformal dose of radiation to tumours while maximizing the dose sparing to healthy tissues. However, the internal patient anatomy is constantly moving due to respiratory, cardiac, gastrointestinal and urinary activity. The long term goal of the RT community to 'see what we treat, as we treat' and to act on this information instantaneously has resulted in rapid technological innovation. Specialized treatment machines, such as robotic or gimbal-steered linear accelerators (linac) with in-room imaging suites, have been developed specifically for real-time treatment adaptation. Additional equipment, such as stereoscopic kilovoltage (kV) imaging, ultrasound transducers and electromagnetic transponders, has been developed for intrafraction motion monitoring on conventional linacs. Magnetic resonance imaging (MRI) has been integrated with cobalt treatment units and more recently with linacs. In addition to hardware innovation, software development has played a substantial role in the development of motion monitoring methods based on respiratory motion surrogates and planar kV or Megavoltage (MV) imaging that is available on standard equipped linacs. In this paper, we review and compare the different intrafraction motion monitoring methods proposed in the literature and demonstrated in real-time on clinical data as well as their possible future developments. We then discuss general considerations on validation and quality assurance for clinical implementation. Besides photon RT, particle therapy is increasingly used to treat moving targets. However, transferring motion monitoring technologies from linacs to particle beam lines presents substantial challenges. Lessons learned from the implementation of real-time intrafraction monitoring for photon RT will be used as a basis to discuss the implementation of these methods for particle RT