Further records of a new diatom species in the English Channel and North Sea: the importance of image-referenced data

Background In September 2015, an at the time undescribed, autotrophic taxon was discovered in the western English Channel (station L4) and also in the eastern English Channel and Celtic Sea during the Polarstern Cruise PS95 a month later. Subsequent investigations revealed further extensive records (going back to 1992) at stations in the English Channel and the southern North Sea (e.g. Helgoland Roads and Sylt Roads time series stations). Stations in the Northern North Sea have not recorded this distinct taxon. With the available records and crucially, the accompanying image metadata, we are able to chart a clear distribution record with occurrences being restricted to the southern North Sea and English Channel. Methods The biological data shown are from Lugol-fixed Utermöhl counts and investigations of live and Formalin-fixed net hauls (20 μm mesh size). All image material shown is available in the online repository Planktonnet (http://planktonnet.awi.de). Results We report the distribution, based on geo-referenced image records of an easily recognisable, yet taxonomically uncertain, autotrophic organism. Conclusions Distribution patterns of the unidentified autotrophic taxon suggests entry of this taxon into/out of the North Sea via the English Channel. Further investigations providing image-documented information over several years is clearly necessary to clarify its dynamics and ecological characteristics

The PD COMM trial: A protocol for the process evaluation of a randomised trial assessing the effectiveness of two types of SLT for people with Parkinson's disease

BACKGROUND: The PD COMM trial is a phase III multi-centre randomised controlled trial whose aim is to evaluate the effectiveness and cost-effectiveness of two approaches to speech and language therapy (SLT) compared with no SLT intervention (control) for people with Parkinson's disease who have self-reported or carer-reported problems with their speech or voice. Our protocol describes the process evaluation embedded within the outcome evaluation whose aim is to evaluate what happened at the time of the PD COMM intervention implementation and to provide findings that will assist in the interpretation of the PD COMM trial results. Furthermore, the aim of the PD COMM process evaluation is to investigate intervention complexity within a theoretical model of how the trialled interventions might work best and why. METHODS/DESIGN: Drawing from the Normalization Process Theory and frameworks for implementation fidelity, a mixed method design will be used to address process evaluation research questions. Therapists' and participants' perceptions and experiences will be investigated via in-depth interviews. Critical incident reports, baseline survey data from therapists, treatment record forms and home practice diaries also will be collected at relevant time points throughout the running of the PD COMM trial. Process evaluation data will be analysed independently of the outcome evaluation before the two sets of data are then combined. DISCUSSION: To date, there are a limited number of published process evaluation protocols, and few are linked to trials investigating rehabilitation therapies. Providing a strong theoretical framework underpinning design choices and being tailored to meet the complex characteristics of the trialled interventions, our process evaluation has the potential to provide valuable insight into which components of the interventions being delivered in PD COMM worked best (and what did not), how they worked well and why

Lee Silverman Voice Treatment versus standard speech and language therapy versus control in Parkinson's disease: a pilot randomised controlled trial (PD COMM pilot)

Background: Speech-related problems are common in Parkinson's disease (PD), but there is little evidence for the effectiveness of standard speech and language therapy (SLT) or Lee Silverman Voice Treatment (LSVT LOUD®). Methods: The PD COMM pilot was a three-arm, assessor-blinded, randomised controlled trial (RCT) of LSVT LOUD®, SLT and no intervention (1:1:1 ratio) to assess the feasibility and to inform the design of a full-scale RCT. Non-demented patients with idiopathic PD and speech problems and no SLT for speech problems in the past 2 years were eligible. LSVT LOUD® is a standardised regime (16 sessions over 4 weeks). SLT comprised individualised content per local practice (typically weekly sessions for 6-8 weeks). Outcomes included recruitment and retention, treatment adherence, and data completeness. Outcome data collected at baseline, 3, 6, and 12 months included patient-reported voice and quality of life measures, resource use, and assessor-rated speech recordings. Results: Eighty-nine patients were randomised with 90% in the therapy groups and 100% in the control group completing the trial. The response rate for Voice Handicap Index (VHI) in each arm was ≥ 90% at all time-points. VHI was highly correlated with the other speech-related outcome measures. There was a trend to improvement in VHI with LSVT LOUD® (difference at 3 months compared with control: - 12.5 points; 95% CI - 26.2, 1.2) and SLT (difference at 3 months compared with control: - 9.8 points; 95% CI - 23.2, 3.7) which needs to be confirmed in an adequately powered trial. Conclusion: Randomisation to a three-arm trial of speech therapy including a no intervention control is feasible and acceptable. Compliance with both interventions was good. VHI and other patient-reported outcomes were relevant measures and provided data to inform the sample size for a substantive trial. Trial registration: International Standard Randomised Controlled Trial Number Register: ISRCTN75223808. registered 22 March 2012

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

Background: The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results: The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions: ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf. comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.Blanca Postigo, JM.; Pascual Bañuls, L.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Cañizares Sales, J. (2011). Ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics. 12:1-8. doi:10.1186/1471-2164-12-285S1812Metzker ML: Sequencing technologies - the next generation. Nature Reviews Genetics. 2010, 11 (1): 31-46. 10.1038/nrg2626.454 sequencing. [ http://www.454.com/ ]Illumina Inc. [ http://www.illumina.com/ ]Flicek P, Birney E: Sense from sequence reads: methods for alignment and assembly (vol 6, pg S6, 2009). Nature Methods. 2010, 7 (6): 479-479.Chevreux B, Pfisterer T, Drescher B, Driesel AJ, Muller WEG, Wetter T, Suhai S: Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs. Genome Research. 2004, 14 (6): 1147-1159. 10.1101/gr.1917404.Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology. 2009, 10 (3):Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data P: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.1000 Genomes. A deep Catalog of Human Genetic Variation. [ http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 ]The seqanswers internet forum. [ http://seqanswers.com/ ]Blankenberg D, Taylor J, Schenck I, He JB, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Ross CH, Nekrutenko A: A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Research. 2007, 17 (6): 960-964. 10.1101/gr.5578007.CloVR Automated Sequence Analysis from Your Desktop. [ http://clovr.org/ ]Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG: Next generation transcriptomes for next generation genomes using est2assembly. Bmc Bioinformatics. 2009, 10:Applied Biosystems by life technologies. [ http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing.html ]Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang HY, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, dePamphilis CW: Comparison of next generation sequencing technologies for transcriptome characterization. Bmc Genomics. 2009, 10:Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, Marshall Graves JA, Woods GM, Hanon GJ, Papenfuss AT: The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer. Science. 2010, 327 (5961): 84-87. 10.1126/science.1180616.Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA: Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. Bmc Genomics. 2010, 11:Babik W, Stuglik M, Qi W, Kuenzli M, Kuduk K, Koteja P, Radwan J: Heart transcriptome of the bank vole (Myodes glareolus): towards understanding the evolutionary variation in metabolic rate. BMC Genomics. 2010, 11: 390-10.1186/1471-2164-11-390.Miller JC, Tanksley SD: RFLP analysis of phylogenetic-relationships and genetic-variation in the genus Lycopersicon. Theoretical and Applied Genetics. 1990, 80 (4): 437-448.Williams CE, Stclair DA: Phenetic relationships and levels of variability detected by restriction-fragment-length-polymorphism and random amplified polymorphic DNA analysis of cultivated and wild accessions of Lycopersicon-esculentum. Genome. 1993, 36 (3): 619-630. 10.1139/g93-083.Rick CM: Tomato, Lycopersicon esculentum (Solanaceae). Evolution of crop plants. Edited by: Simmonds NW. 1976, London: Longman Group, 268-273.Labate JA, Baldo AM: Tomato SNP discovery by EST mining and resequencing. Molecular Breeding. 2005, 16 (4): 343-349. 10.1007/s11032-005-1911-5.Yano K, Watanabe M, Yamamoto N, Maeda F, Tsugane T, Shibata D: Expressed sequence tags (EST) database of a miniature tomato cultivar, Micro-Tom. Plant and Cell Physiology. 2005, 46: S139-S139.Jimenez-Gomez JM, Maloof JN: Sequence diversity in three tomato species: SNPs, markers, and molecular evolution. Bmc Plant Biology. 2009, 9:Yang WC, Bai XD, Kabelka E, Eaton C, Kamoun S, van der Knaap E, Francis D: Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags. Molecular Breeding. 2004, 14 (1): 21-34.Van Deynze A, Stoffel K, Buell CR, Kozik A, Liu J, van der Knaap E, Francis D: Diversity in conserved genes in tomato. Bmc Genomics. 2007, 8:Sim SC, Robbins MD, Chilcott C, Zhu T, Francis DM: Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L.) reveals patterns of SNP variation associated with breeding. Bmc Genomics. 2009, 10:Bioinformatics at COMAV. [ http://bioinf.comav.upv.es/ngs_backbone/index.html ]Broad institute. [ http://www.broadinstitute.org/igv ]Bioinformatics at COMAV. [ http://bioinf.comav.upv.es/ngs_backbone/install.html ]Github social coding. [ http://github.com/JoseBlanca/franklin ]Chou HH, Holmes MH: DNA sequence quality trimming and vector removal. Bioinformatics. 2001, 17 (12): 1093-1104. 10.1093/bioinformatics/17.12.1093.Picard. [ http://picard.sourceforge.net/index.shtml ]McKenna A, Hanna M, Banks E, Sivachenko A, Citulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research. 2010, 20: 1297-1303. 10.1101/gr.107524.110.Sol Genomics Network. [ ftp://ftp.solgenomics.net/ ]NCBI Genbank. [ http://www.ncbi.nlm.nih.gov/genbank/ ]Gundry CN, Vandersteen JG, Reed GH, Pryor RJ, Chen J, Wittwer CT: Amplicon melting analysis with labeled primers: A closed-tube method for differentiating homozygotes and heterozygotes. Clinical Chemistry. 2003, 49 (3): 396-406. 10.1373/49.3.396

Impact of short-term dietary modification on postprandial oxidative stress

<p>Abstract</p> <p>Background</p> <p>We have recently reported that short-term (21-day) dietary modification in accordance with a stringent vegan diet (i.e., a Daniel Fast) lowers blood lipids as well as biomarkers of oxidative stress. However, this work only involved measurements obtained in a fasted state. In the present study, we determined the postprandial response to a high-fat milkshake with regards to blood triglycerides (TAG), biomarkers of oxidative stress, and hemodynamic variables before and following a 21-day Daniel Fast.</p> <p>Methods</p> <p>Twenty-two subjects (10 men and 12 women; aged 35 ± 3 years) completed a 21-day Daniel Fast. To induce oxidative stress, a milkshake (fat = 0.8 g·kg^-1; carbohydrate = 1.0 g·kg^-1; protein = 0.25 g·kg^-1) was consumed by subjects on day one and day 22 in a rested and 12-hour fasted state. Before and at 2 and 4 h after consumption of the milkshake, heart rate (HR) and blood pressure were measured. Blood samples were also collected at these times and analyzed for TAG, malondialdehyde (MDA), hydrogen peroxide (H₂O₂), advanced oxidation protein products (AOPP), nitrate/nitrite (NOx), and Trolox Equivalent Antioxidant Capacity (TEAC).</p> <p>Results</p> <p>A time effect was noted for HR (<it>p </it>= 0.006), with values higher at 2 hr post intake of the milkshake as compared to pre intake (<it>p </it>< 0.05). Diastolic blood pressure was lower post fast as compared to pre fast (<it>p </it>= 0.02), and a trend for lower systolic blood pressure was noted (<it>p </it>= 0.07). Time effects were noted for TAG (<it>p </it>= 0.001), MDA (<it>p </it>< 0.0001), H₂O₂(<it>p </it>< 0.0001), AOPP (<it>p </it>< 0.0001), and TEAC (<it>p </it>< 0.0001); all concentrations were higher at 2 h and 4 h post intake compared to pre intake, except for TEAC, which was lower at these times (<it>p </it>< 0.05). A condition effect was noted for NOx (<it>p </it>= 0.02), which was higher post fast as compared to pre fast. No pre/post fast × time interactions were noted (<it>p </it>> 0.05), with the area under the curve from pre to post fast reduced only slightly for TAG (11%), MDA (11%), H₂O₂(8%), and AOPP (12%), with a 37% increase noted for NOx.</p> <p>Conclusion</p> <p>Partaking in a 21-day Daniel Fast does not result in a statistically significant reduction in postprandial oxidative stress. It is possible that a longer time course of adherence to the Daniel Fast eating plan may be needed to observe significant findings.</p

Thermography imaging during static and controlled thermoregulation in complex regional pain syndrome type 1: diagnostic value and involvement of the central sympathetic system

BACKGROUND: Complex Regional Pain Syndrome type 1 (CRPS1) is a clinical diagnosis based on criteria describing symptoms of the disease. The main aim of the present study was to compare the sensitivity and specificity of calculation methods used to assess thermographic images (infrared imaging) obtained during temperature provocation. The secondary objective was to obtain information about the involvement of the sympathetic system in CRPS1. METHODS: We studied 12 patients in whom CRPS1 was diagnosed according to the criteria of Bruehl. High and low whole body cooling and warming induced and reduced sympathetic vasoconstrictor activity. The degree of vasoconstrictor activity in both hands was monitored using a videothermograph. The sensitivity and specificity of the calculation methods used to assess the thermographic images were calculated. RESULTS: The temperature difference between the hands in the CRPS patients increases significantly when the sympathetic system is provoked. At both the maximum and minimum vasoconstriction no significant differences were found in fingertip temperatures between both hands. CONCLUSION: The majority of CRPS1 patients do not show maximal obtainable temperature differences between the involved and contralateral extremity at room temperature (static measurement). During cold and warm temperature challenges this temperature difference increases significantly. As a result a higher sensitivity and specificity could be achieved in the diagnosis of CRPS1. These findings suggest that the sympathetic efferent system is involved in CRPS1

A study assessing the association of glycated hemoglobin a1C (HbA1C) associated variants with HbA1C, chronic kidney disease and diabetic retinopathy in populations of asian ancestry

10.1371/journal.pone.0079767PLoS ONE811-POLN

The Fischer 344 Rat Reflects Human Susceptibility to Francisella Pulmonary Challenge and Provides a New Platform for Virulence and Protection Studies

Background: The pathogenesis of Francisella tularensis, the causative agent of tularemia, has been primarily characterized in mice. However, the high degree of sensitivity of mice to bacterial challenge, especially with the human virulent strains of F. tularensis, limits this animal model for screening of defined attenuated vaccine candidates for protection studies. Methods and Findings: We analyzed the susceptibility of the Fischer 344 rat to pulmonary (intratracheal) challenge with three different subspecies (subsp) of F. tularensis that reflect different levels of virulence in humans, and characterized the bacterial replication profile in rat bone marrow-derived macrophages (BMDM). In contrast to the mouse, Fischer 344 rats exhibit a broader range of sensitivity to pulmonary challenge with the human virulent subsp. tularensis and holarctica. Unlike mice, Fischer rats exhibited a high degree of resistance to pulmonary challenge with LVS (an attenuated derivative o

The steady-state transcriptome of the four major life-cycle stages of Trypanosoma cruzi

<p>Abstract</p> <p>Background</p> <p>Chronic chagasic cardiomyopathy is a debilitating and frequently fatal outcome of human infection with the protozoan parasite, <it>Trypanosoma cruzi</it>. Microarray analysis of gene expression during the <it>T. cruzi </it>life-cycle could be a valuable means of identifying drug and vaccine targets based on their appropriate expression patterns, but results from previous microarray studies in <it>T. cruzi </it>and related kinetoplastid parasites have suggested that the transcript abundances of most genes in these organisms do not vary significantly between life-cycle stages.</p> <p>Results</p> <p>In this study, we used whole genome, oligonucleotide microarrays to globally determine the extent to which <it>T. cruzi </it>regulates mRNA relative abundances over the course of its complete life-cycle. In contrast to previous microarray studies in kinetoplastids, we observed that relative transcript abundances for over 50% of the genes detected on the <it>T. cruzi </it>microarrays were significantly regulated during the <it>T. cruzi </it>life-cycle. The significant regulation of 25 of these genes was confirmed by quantitative reverse-transcriptase PCR (qRT-PCR). The <it>T. cruzi </it>transcriptome also mirrored published protein expression data for several functional groups. Among the differentially regulated genes were members of paralog clusters, nearly 10% of which showed divergent expression patterns between cluster members.</p> <p>Conclusion</p> <p>Taken together, these data support the conclusion that transcript abundance is an important level of gene expression regulation in <it>T. cruzi</it>. Thus, microarray analysis is a valuable screening tool for identifying stage-regulated <it>T. cruzi </it>genes and metabolic pathways.</p