A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria

<p>Abstract</p> <p>Background</p> <p>Non-coding RNAs (ncRNA) are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the <it>Prochlorococcus/Synechococcus </it>group of marine cyanobacteria.</p> <p>Results</p> <p>Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of <it>Prochlorococcus</it>, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16–20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'.</p> <p>Conclusion</p> <p>Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of <it>E. coli </it>and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.</p

A systematic review of methods to immobilise breast tissue during adjuvant breast irradiation

Greater use of 3D conformal, Intensity Modulated Radiotherapy (IMRT) and external beam partial breast irradiation following local excision (LE) for breast cancer has necessitated a review of the effectiveness of immobilisation methods to stabilise breast tissue. To identify the suitability of currently available breast (rather than thorax) immobilisation techniques an appraisal of the literature was undertaken. The aim was to identify and evaluate the benefit of additional or novel immobilisation approaches (beyond the standard supine, single arm abducted and angled breast board technique adopted in most radiotherapy departments). A database search was supplemented with an individual search of key radiotherapy peer-reviewed journals, author searching, and searching of the grey literature. A total of 27 articles met the inclusion criteria. The review identified good reproducibility of the thorax using the standard supine arm-pole technique. Reproducibility with the prone technique appears inferior to supine methods (based on data from existing randomised controlled trials). Assessing the effectiveness of additional breast support devices (such as rings or thermoplastic material) is hampered by small sample sizes and a lack of randomised data for comparison. Attention to breast immobilisation is recommended, as well as agreement on how breast stability should be measured using volumetric imaging. Keywords: Breast, immobilisation, positioning, reproducibility, review.</p

Dynamic orifice area variations in functional mitral regurgitation: In vivoreproduction and mechanistic insights

Aims: The spinocerebellar ataxia type 2 (SCA2), type 3 (SCA3) and type 7 (SCA7) are clinically characterized by progressive and severe ataxic symptoms, dysarthria, dysphagia, oculomotor impairments, pyramidal and extrapyramidal manifestations and sensory deficits. Although recent clinical studies reported additional disease signs suggesting involvement of the brainstem auditory system, this has never been studied in detail in SCA2, SCA3 or SCA7. Methods: We performed a detailed pathoanatomical investigation of unconventionally thick tissue sections through the auditory brainstem nuclei (that is, nucleus of the inferior colliculus, nuclei of the lateral lemniscus, superior olive, cochlear nuclei) and auditory brainstem fibre tracts (that is, lateral lemniscus, trapezoid body, dorsal acoustic stria, cochlear portion of the vestibulocochlear nerve) of clinically diagnosed and genetically confirmed SCA2, SCA3 and SCA7 patients. Results: Examination of unconventionally thick serial brainstem sections stained for lipofuscin pigment and Nissl material revealed a consistent and widespread involvement of the auditory brainstem nuclei in the SCA2, SCA3 and SCA7 patients studied. Serial brainstem tissue sections stained for myelin showed loss of myelinated fibres in two of the auditory brainstem fibre tracts (that is, lateral lemniscus, trapezoid body) in a subset of patients. Conclusions: The involvement of the auditory brainstem system offers plausible explanations for the auditory impairments detected in some of our and other SCA2, SCA3 and SCA7 patients upon bedside examination or neurophysiological investigation. However, further clinical studies are required to resolve the striking discrepancy between the consistent involvement of the brainstem auditory system observed in this study and the comparatively low frequency of reported auditory impairments in SCA2, SCA3 and SCA7 patients

Reproducibility of patient setup by surface image registration system in conformal radiotherapy of prostate cancer

<p>Abstract</p> <p>Background</p> <p>The reproducibility of patient setup for radiotherapy is based on various methods including external markers, X-rays with planar or computerized image acquisition, and, more recently, surface matching imaging. We analyzed the setup reproducibility of 16 patients affected by prostate cancer who underwent conformal radiotherapy with curative intent by using a surface image registration system.</p> <p>Methods</p> <p>We analyzed the setup reproducibility of 16 patients affected by prostate cancer candidates for conformal radiotherapy by using a surface image registration system. At the initial setup, EPID images were compared with DRRs and a reference 3D surface image was obtained by the AlignRT system (Vision RT, London, UK). Surface images were acquired prior to every subsequent setup procedure. EPID acquisition was repeated when errors > 5 mm were reported.</p> <p>Results</p> <p>The mean random and systematic errors were 1.2 ± 2.3 mm and 0.3 ± 3.0 mm along the X axis, 0.0 ± 1.4 mm and 0.5 ± 2.0 mm along the Y axis, and 2.0 ± 1.8 mm and -0.7 ± 2.4 mm along the Z axis respectively. The positioning error detected by AlignRT along the 3 axes X, Y, and Z exceeded the value of 5 mm in 14.1%, 2.0%, and 5.1% measurements and the value of 3 mm in 36.9%, 13.6% and 27.8% measurements, respectively. Correlation factors calculated by linear regression between the errors measured by AlignRT and EPID ranged from 0.77 to 0.92 with a mean of 0.85 and SD of 0.13. The setup measurements by surface imaging are highly reproducible and correlate with the setup errors detected by EPID.</p> <p>Conclusion</p> <p>Surface image registration system appears to be a simple, fast, non-invasive, and reproducible method to analyze the set-up alignment in 3DCRT of prostate cancer patients.</p

Rfam: Wikipedia, clans and the “decimal” release

The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models. In this contribution, we discuss the pros and cons of using the online encyclopedia, Wikipedia, as a source of community‐derived annotation. We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk

Intra-fraction setup variability: IR optical localization vs. X-ray imaging in a hypofractionated patient population

<p>Abstract</p> <p>Background</p> <p>The purpose of this study is to investigate intra-fraction setup variability in hypo-fractionated cranial and body radiotherapy; this is achieved by means of integrated infrared optical localization and stereoscopic kV X-ray imaging.</p> <p>Method and Materials</p> <p>We analyzed data coming from 87 patients treated with hypo-fractionated radiotherapy at cranial and extra-cranial sites. Patient setup was realized through the ExacTrac X-ray 6D system (BrainLAB, Germany), consisting of 2 infrared TV cameras for external fiducial localization and X-ray imaging in double projection for image registration. Before irradiation, patients were pre-aligned relying on optical marker localization. Patient position was refined through the automatic matching of X-ray images to digitally reconstructed radiographs, providing 6 corrective parameters that were automatically applied using a robotic couch. Infrared patient localization and X-ray imaging were performed at the end of treatment, thus providing independent measures of intra-fraction motion.</p> <p>Results</p> <p>According to optical measurements, the size of intra-fraction motion was (<it>median ± quartile</it>) 0.3 ± 0.3 mm, 0.6 ± 0.6 mm, 0.7 ± 0.6 mm for cranial, abdominal and lung patients, respectively. X-ray image registration estimated larger intra-fraction motion, equal to 0.9 ± 0.8 mm, 1.3 ± 1.2 mm, 1.8 ± 2.2 mm, correspondingly.</p> <p>Conclusion</p> <p>Optical tracking highlighted negligible intra-fraction motion at both cranial and extra-cranial sites. The larger motion detected by X-ray image registration showed significant inter-patient variability, in contrast to infrared optical tracking measurement. Infrared localization is put forward as the optimal strategy to monitor intra-fraction motion, featuring robustness, flexibility and less invasivity with respect to X-ray based techniques.</p

Compound-specific carbon and nitrogen isotopic compositions of chlorophyll a and its derivatives reveal the eutrophication history of Lake Zurich (Switzerland)

© 2016 Elsevier B.V. To reconstruct the impact of eutrophication on phototrophic communities and the biogeochemical cycling of carbon and nitrogen in the surface water, we investigated the distributions and carbon and nitrogen isotopic compositions (d13C and d15N values) of chlorins in the sediments of Lake Zurich. The chlorin distributions were dominated by chlorophyll a (Chl a) and its derivatives, which reflect rapid degradation to the pheopigments in the water column and sediments of the lake. The d13C values of these sedimentary chlorins followed the historical trends of eutrophication and reoligotrophication, except in the surface sediments, which were characterised by higher relative contributions of aged, redeposited organic matter (OM). The d13C values of the sedimentary chlorins together with bulk sediment d13C values and C/N ratios indicate that the phototrophic communities in the lake used a 13C-depleted carbon source, which is mainly of aquatic origin. The d15N values of chlorins reflect the predominance of nitrate assimilating phototrophs, especially the non-N2-fixing cyanobacterium Planktothrix rubescens prevalent during sediment deposition. Shifts in d15N values of Chl a followed mostly the trends in eutrophication and reoligotrophication, but were also affected by community assemblage shifts to diatoms and/or other cyanobacteria at the end of the 19th century and during the eutrophication maximum in the 1970s.The lower d15NChl-a values in the surface sediments coincide with increasing nitrogen to phosphorus ratios and reduced water column mixing that characterise the recent reoligotrophication period and may explain the predominance of P. rubescens in Lake Zurich. In contrast, the higher contributions of laterally transported OM explains the large offset of d15N values of the pheopigments relative to Chl a, which is supported by the high radiocarbon age of the surface sediments

Biological evaluation of a novel nitroimidazooxazole derivative, IIIM-MCD-019 against Mycobacterium tuberculosis and its in vivo efficacy

Dysphagia, which can lead to nutritional deficiencies, weight loss and dehydration, represents a risk factor for aspiration pneumonia. Although clinical studies have reported the occurrence of dysphagia in patients with spinocerebellar ataxia type 2 (SCA2), type 3 (SCA3), type 6 (SCA6) and type 7 (SCA7), there are neither detailed clinical records concerning the kind of ingestive malfunctions which contribute to dysphagia nor systematic pathoanatomical studies of brainstem regions involved in the ingestive process. In the present study we performed a systematic post mortem study on thick serial tissue sections through the ingestion-related brainstem nuclei of 12 dysphagic patients who suffered from clinically diagnosed and genetically confirmed spinocerebellar ataxias assigned to the CAG-repeat or polyglutamine diseases (two SCA2, seven SCA3, one SCA6 and two SCA7 patients) and evaluated their medical records. Upon pathoanatomical examination in all of the SCA2, SCA3, SCA6 and SCA7 patients, a widespread neurodegeneration of the brainstem nuclei involved in the ingestive process was found. The clinical records revealed that all of the SCA patients were diagnosed with progressive dysphagia and showed dysfunctions detrimental to the preparatory phase of the ingestive process, as well as the lingual, pharyngeal and oesophageal phases of swallowing. The vast majority of the SCA patients suffered from aspiration pneumonia, which was the most frequent cause of death in our sample. The findings of the present study suggest (i) that dysphagia in SCA2, SCA3, SCA6 and SCA7 patients may be associated with widespread neurodegeneration of ingestion-related brainstem nuclei; (ii) that dysphagic SCA2, SCA3, SCA6 and SCA7 patients may suffer from dysfunctions detrimental to all phases of the ingestive process; and (iii) that rehabilitative swallow therapy which takes specific functional consequences of the underlying brainstem lesions into account might be helpful in preventing aspiration pneumonia, weight loss and dehydration in SCA2, SCA3, SCA6 and SCA7 patients