The transcriptome and proteome of the diatom Thalassiosira pseudonana reveal a diverse phosphorus stress response

© The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS One 7 (2012): e33768, doi:10.1371/journal.pone.0033768.Phosphorus (P) is a critical driver of phytoplankton growth and ecosystem function in the ocean. Diatoms are an abundant class of marine phytoplankton that are responsible for significant amounts of primary production. With the control they exert on the oceanic carbon cycle, there have been a number of studies focused on how diatoms respond to limiting macro and micronutrients such as iron and nitrogen. However, diatom physiological responses to P deficiency are poorly understood. Here, we couple deep sequencing of transcript tags and quantitative proteomics to analyze the diatom Thalassiosira pseudonana grown under P-replete and P-deficient conditions. A total of 318 transcripts were differentially regulated with a false discovery rate of <0.05, and a total of 136 proteins were differentially abundant (p<0.05). Significant changes in the abundance of transcripts and proteins were observed and coordinated for multiple biochemical pathways, including glycolysis and translation. Patterns in transcript and protein abundance were also linked to physiological changes in cellular P distributions, and enzyme activities. These data demonstrate that diatom P deficiency results in changes in cellular P allocation through polyphosphate production, increased P transport, a switch to utilization of dissolved organic P through increased production of metalloenzymes, and a remodeling of the cell surface through production of sulfolipids. Together, these findings reveal that T. pseudonana has evolved a sophisticated response to P deficiency involving multiple biochemical strategies that are likely critical to its ability to respond to variations in environmental P availability.This research was supported by the National Science Foundation (NSF) Environmental Genomics and NSF Biological Oceanography Program through grant OCE-0723667 to Dr. Dyhrman, Dr. Jenkins, Dr. Saito, and Dr. Rynearson, the NSF Chemical Oceanography Program through grant OCE-0549794 to Dr. Dyhrman and OCE-0526800 to Dr. Jenkins, the G. B. Moore Foundation and OCE-0752291 to Dr. Saito, NSF-EPSCoR (NSF-0554548 & NSF-1004057) to the University of Rhode Island, the Center for Microbial Oceanography: Research and Education, and the Joint Genome Institute/DOE Community Sequencing Program (CSP795793) to Dr. Jenkins, Dr. Dyhrman, Dr. Rynearson and Dr. Saito

Balance Rehabilitation Unit (BRU TM) posturography in relapsing-remitting multiple sclerosis

OBJECTIVE: To evaluate balance control with Balance Rehabilitation Unit (BRU TM) posturography in patients with multiple sclerosis (MS). METHOD: A cross controlled study was performed including 39 relapsing-remitting multiple sclerosis patients with scores less than or equal to 4 in the Expanded Disability Status Scale (EDSS), and a homogeneous control group consisting of 65 healthy individuals, matched by the age and gender. The experimental group was distributed according to the EDSS scale scores in 0-2.5 and 3-4. To assess the vestibular system function, the patients underwent a neurotological evaluation, including posturography of the Balance Rehabilitation Unit (BRU TM). RESULTS: Statistically significant differences were observed when comparing the values of the sway velocity and the ellipse area of the MS 0-2.5 group with the control and the MS 3-4 group with the control. A statistically significant difference was verified between the MS 0-2.5 and the MS 3-4 groups in the condition 3 ellipse area values. CONCLUSION: The evaluation of the balance control with posturography of Balance Rehabilitation Unit (BRU TM) enables the identification of abnormalities of the sway velocity and confidential ellipse in patients with relapsing-remitting multiple sclerosis

Gene Expression Signatures of Radiation Response Are Specific, Durable and Accurate in Mice and Humans

Background: Previous work has demonstrated the potential for peripheral blood (PB) gene expression profiling for the detection of disease or environmental exposures. Methods and Findings: We have sought to determine the impact of several variables on the PB gene expression profile of an environmental exposure, ionizing radiation, and to determine the specificity of the PB signature of radiation versus other genotoxic stresses. Neither genotype differences nor the time of PB sampling caused any lessening of the accuracy of PB signatures to predict radiation exposure, but sex difference did influence the accuracy of the prediction of radiation exposure at the lowest level (50 cGy). A PB signature of sepsis was also generated and both the PB signature of radiation and the PB signature of sepsis were found to be 100 % specific at distinguishing irradiated from septic animals. We also identified human PB signatures of radiation exposure and chemotherapy treatment which distinguished irradiated patients and chemotherapy-treated individuals within a heterogeneous population with accuracies of 90 % and 81%, respectively. Conclusions: We conclude that PB gene expression profiles can be identified in mice and humans that are accurate i

Lexical access speed and the development of phonological recoding during immediate serial recall

A recent Registered Replication Report (RRR) of the development of verbal rehearsal during serial recall revealed that children verbalized at younger ages than previously thought, but did not identify sources of individual differences. Here, we use mediation analysis to reanalyze data from the 934 children ranging from 5 to 10 years old from the RRR for that purpose. From ages 5 to 7, the time taken for a child to label pictures (i.e. isolated naming speed) predicted the child’s spontaneous use of labels during a visually presented serial reconstruction task, despite no need for spoken responses. For 6- and 7-year-olds, isolated naming speed also predicted recall. The degree to which verbalization mediated the relation between isolated naming speed and recall changed across development. All relations dissipated by age 10. The same general pattern was observed in an exploratory analysis of delayed recall for which greater demands are placed on rehearsal for item maintenance. Overall, our findings suggest that spontaneous phonological recoding during a standard short-term memory task emerges around age 5, increases in efficiency during the early elementary school years, and is sufficiently automatic by age 10 to support immediate serial recall in most children. Moreover, the findings highlight the need to distinguish between phonological recoding and rehearsal in developmental studies of short-term memory

Balance training program is highly effective in improving functional status and reducing the risk of falls in elderly women with osteoporosis: a randomized controlled trial

INTRODUCTION: The purpose of this study was to investigate the effect of a 12-month Balance Training Program on balance, mobility and falling frequency in women with osteoporosis. METHODS: Sixty-six consecutive elderly women were selected from the Osteometabolic Disease Outpatient Clinic and randomized into 2 groups: the ‘Intervention’, submitted for balance training; and the ‘Control’, without intervention. Balance, mobility and falling frequency were evaluated before and at the end of the trial, using the Berg Balance Scale (BBS), the Clinical Test Sensory Interaction Balance (CTSIB) and the Timed “Up & Go” Test (TUGT). Intervention used techniques to improve balance consisting of a 1-hour session each week and a home-based exercise program. RESULTS: Sixty women completed the study and were analyzed. The BBS difference was significant higher in the Intervention group compared to Control (5.5 ± 5.67 vs −0.5 ± 4.88 score, p < 0.001). Similarly, the number of patients in the Intervention group presented improvement in two conditions of CTSIB compared to Control (eyes closed and unstable surface condition: 13 vs one patient, p < 0.001 and eyes open, visual conflict and unstable surface condition: 12 vs one patient, p < 0.001). Additionally, the differences between the TUGT were reduced in the Intervention group compared to Control (−3.65 ± 3.61 vs 2.27 ± 7.18 seconds, p< 0.001). Notably, this improvement was paralleled by a reduction in the number of falls/patient in the Intervention group compared to Control (−0.77 ± 1.76 vs 0.33 ± 0.96, p = 0.018). CONCLUSION: This longitudinal prospective study demonstrated that an intervention using balance training is effective in improving functional and static balance, mobility and falling frequency in elderly women with osteoporosis

A metric space for Type Ia supernova spectra

We develop a new framework for use in exploring Type Ia supernovae (SNe Ia) spectra. Combining principal component analysis (PCA) and partial least square (PLS) analysis we are able to establish correlations between the principal components (PCs) and spectroscopic/photometric SNe Ia features. The technique was applied to ∼120 SN and ∼800 spectra from the Nearby Supernova Factory. The ability of PCA to group together SNe Ia with similar spectral features, already explored in previous studies, is greatly enhanced by two important modifications: (1) the initial data matrix is built using derivatives of spectra over the wavelength, which increases the weight of weak lines and discards extinction, and (2) we extract time evolution information through the use of entire spectral sequences concatenated in each line of the input data matrix. These allow us to define a stable PC parameter space which can be used to characterize synthetic SN Ia spectra by means of real SN features. Using PLS, we demonstrate that the information from important previously known spectral indicators (namely the pseudo-equivalent width of Si II 5972 Å/Si II 6355 Å and the line velocity of S II 5640 Å/Si II 6355 Å) at a given epoch is contained within the PC space and can be determined through a linear combination of the most important PCs. We also show that the PC space encompasses photometric features like B/V magnitudes, B − V colours and SALT2 parameters c and x1. The observed colours and magnitudes, which are heavily affected by extinction, cannot be reconstructed using this technique alone. All the above-mentioned applications allowed us to construct a metric space for comparing synthetic SN Ia spectra with observations

Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification

<p>Abstract</p> <p>Background</p> <p>Large-scale compilation of gene expression microarray datasets across diverse biological phenotypes provided a means of gathering a priori knowledge in the form of identification and annotation of bimodal genes in the human and mouse genomes. These switch-like genes consist of 15% of known human genes, and are enriched with genes coding for extracellular and membrane proteins. It is of interest to determine the prediction potential of bimodal genes for class discovery in large-scale datasets.</p> <p>Results</p> <p>Use of a model-based clustering algorithm accurately classified more than 400 microarray samples into 19 different tissue types on the basis of bimodal gene expression. Bimodal expression patterns were also highly effective in differentiating between infectious diseases in model-based clustering of microarray data. Supervised classification with feature selection restricted to switch-like genes also recognized tissue specific and infectious disease specific signatures in independent test datasets reserved for validation. Determination of "on" and "off" states of switch-like genes in various tissues and diseases allowed for the identification of activated/deactivated pathways. Activated switch-like genes in neural, skeletal muscle and cardiac muscle tissue tend to have tissue-specific roles. A majority of activated genes in infectious disease are involved in processes related to the immune response.</p> <p>Conclusion</p> <p>Switch-like bimodal gene sets capture genome-wide signatures from microarray data in health and infectious disease. A subset of bimodal genes coding for extracellular and membrane proteins are associated with tissue specificity, indicating a potential role for them as biomarkers provided that expression is altered in the onset of disease. Furthermore, we provide evidence that bimodal genes are involved in temporally and spatially active mechanisms including tissue-specific functions and response of the immune system to invading pathogens.</p