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1.  The adhesion of mussel foot protein-3 to TiO2 surfaces: the effect of pH 
Biomacromolecules  2013;14(4):1072-1077.
The underwater adhesion of marine mussels relies on mussel foot proteins (mfps) rich in the catecholic amino acid 3, 4-dihydroxyphenylalanine (Dopa). As a side-chain, Dopa is capable of strong bidentate interactions with a variety of surfaces, including many minerals and metal oxides. Titanium is among the most widely used medical implant material and quickly forms a TiO2 passivation layer under physiological conditions. Understanding the binding mechanism of Dopa to TiO2 surfaces is therefore of considerable theoretical and practical interest. Using a surface forces apparatus, we explored the force-distance profiles and adhesion energies of mussel foot protein 3 (mfp-3) to TiO2 surfaces at three different pHs (pH3, 5.5 and 7.5). At pH3, mfp-3 showed the strongest adhesion force on TiO2, with an adhesion energy of ~ −7.0 mJ/m2. Increasing the pH gives rise to two opposing effects: (1) increased oxidation of Dopa, thus decreasing availability for the Dopa-mediated adhesion, and (2) increased bidentate Dopa-Ti coordination, leading to the further stabilization of the Dopa group and thus an increasing of adhesion force. Both effects were reflected in the resonance-enhanced Raman spectra obtained at the three deposition pHs. The two competing effects give rise to a higher adhesion force of mfp-3 on TiO2 surface at pH 7.5 than at pH 5.5. Our results suggest that Dopa-containing proteins and synthetic polymers have great potential as coating materials for medical implant materials, particularly if redox activity can be controlled.
doi:10.1021/bm301908y
PMCID: PMC3635841  PMID: 23452271
2.  Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture 
Berndt, Sonja I. | Gustafsson, Stefan | Mägi, Reedik | Ganna, Andrea | Wheeler, Eleanor | Feitosa, Mary F. | Justice, Anne E. | Monda, Keri L. | Croteau-Chonka, Damien C. | Day, Felix R. | Esko, Tõnu | Fall, Tove | Ferreira, Teresa | Gentilini, Davide | Jackson, Anne U. | Luan, Jian’an | Randall, Joshua C. | Vedantam, Sailaja | Willer, Cristen J. | Winkler, Thomas W. | Wood, Andrew R. | Workalemahu, Tsegaselassie | Hu, Yi-Juan | Lee, Sang Hong | Liang, Liming | Lin, Dan-Yu | Min, Josine L. | Neale, Benjamin M. | Thorleifsson, Gudmar | Yang, Jian | Albrecht, Eva | Amin, Najaf | Bragg-Gresham, Jennifer L. | Cadby, Gemma | den Heijer, Martin | Eklund, Niina | Fischer, Krista | Goel, Anuj | Hottenga, Jouke-Jan | Huffman, Jennifer E. | Jarick, Ivonne | Johansson, Åsa | Johnson, Toby | Kanoni, Stavroula | Kleber, Marcus E. | König, Inke R. | Kristiansson, Kati | Kutalik, Zoltán | Lamina, Claudia | Lecoeur, Cecile | Li, Guo | Mangino, Massimo | McArdle, Wendy L. | Medina-Gomez, Carolina | Müller-Nurasyid, Martina | Ngwa, Julius S. | Nolte, Ilja M. | Paternoster, Lavinia | Pechlivanis, Sonali | Perola, Markus | Peters, Marjolein J. | Preuss, Michael | Rose, Lynda M. | Shi, Jianxin | Shungin, Dmitry | Smith, Albert Vernon | Strawbridge, Rona J. | Surakka, Ida | Teumer, Alexander | Trip, Mieke D. | Tyrer, Jonathan | Van Vliet-Ostaptchouk, Jana V. | Vandenput, Liesbeth | Waite, Lindsay L. | Zhao, Jing Hua | Absher, Devin | Asselbergs, Folkert W. | Atalay, Mustafa | Attwood, Antony P. | Balmforth, Anthony J. | Basart, Hanneke | Beilby, John | Bonnycastle, Lori L. | Brambilla, Paolo | Bruinenberg, Marcel | Campbell, Harry | Chasman, Daniel I. | Chines, Peter S. | Collins, Francis S. | Connell, John M. | Cookson, William | de Faire, Ulf | de Vegt, Femmie | Dei, Mariano | Dimitriou, Maria | Edkins, Sarah | Estrada, Karol | Evans, David M. | Farrall, Martin | Ferrario, Marco M. | Ferrières, Jean | Franke, Lude | Frau, Francesca | Gejman, Pablo V. | Grallert, Harald | Grönberg, Henrik | Gudnason, Vilmundur | Hall, Alistair S. | Hall, Per | Hartikainen, Anna-Liisa | Hayward, Caroline | Heard-Costa, Nancy L. | Heath, Andrew C. | Hebebrand, Johannes | Homuth, Georg | Hu, Frank B. | Hunt, Sarah E. | Hyppönen, Elina | Iribarren, Carlos | Jacobs, Kevin B. | Jansson, John-Olov | Jula, Antti | Kähönen, Mika | Kathiresan, Sekar | Kee, Frank | Khaw, Kay-Tee | Kivimaki, Mika | Koenig, Wolfgang | Kraja, Aldi T. | Kumari, Meena | Kuulasmaa, Kari | Kuusisto, Johanna | Laitinen, Jaana H. | Lakka, Timo A. | Langenberg, Claudia | Launer, Lenore J. | Lind, Lars | Lindström, Jaana | Liu, Jianjun | Liuzzi, Antonio | Lokki, Marja-Liisa | Lorentzon, Mattias | Madden, Pamela A. | Magnusson, Patrik K. | Manunta, Paolo | Marek, Diana | März, Winfried | Mateo Leach, Irene | McKnight, Barbara | Medland, Sarah E. | Mihailov, Evelin | Milani, Lili | Montgomery, Grant W. | Mooser, Vincent | Mühleisen, Thomas W. | Munroe, Patricia B. | Musk, Arthur W. | Narisu, Narisu | Navis, Gerjan | Nicholson, George | Nohr, Ellen A. | Ong, Ken K. | Oostra, Ben A. | Palmer, Colin N.A. | Palotie, Aarno | Peden, John F. | Pedersen, Nancy | Peters, Annette | Polasek, Ozren | Pouta, Anneli | Pramstaller, Peter P. | Prokopenko, Inga | Pütter, Carolin | Radhakrishnan, Aparna | Raitakari, Olli | Rendon, Augusto | Rivadeneira, Fernando | Rudan, Igor | Saaristo, Timo E. | Sambrook, Jennifer G. | Sanders, Alan R. | Sanna, Serena | Saramies, Jouko | Schipf, Sabine | Schreiber, Stefan | Schunkert, Heribert | Shin, So-Youn | Signorini, Stefano | Sinisalo, Juha | Skrobek, Boris | Soranzo, Nicole | Stančáková, Alena | Stark, Klaus | Stephens, Jonathan C. | Stirrups, Kathleen | Stolk, Ronald P. | Stumvoll, Michael | Swift, Amy J. | Theodoraki, Eirini V. | Thorand, Barbara | Tregouet, David-Alexandre | Tremoli, Elena | Van der Klauw, Melanie M. | van Meurs, Joyce B.J. | Vermeulen, Sita H. | Viikari, Jorma | Virtamo, Jarmo | Vitart, Veronique | Waeber, Gérard | Wang, Zhaoming | Widén, Elisabeth | Wild, Sarah H. | Willemsen, Gonneke | Winkelmann, Bernhard R. | Witteman, Jacqueline C.M. | Wolffenbuttel, Bruce H.R. | Wong, Andrew | Wright, Alan F. | Zillikens, M. Carola | Amouyel, Philippe | Boehm, Bernhard O. | Boerwinkle, Eric | Boomsma, Dorret I. | Caulfield, Mark J. | Chanock, Stephen J. | Cupples, L. Adrienne | Cusi, Daniele | Dedoussis, George V. | Erdmann, Jeanette | Eriksson, Johan G. | Franks, Paul W. | Froguel, Philippe | Gieger, Christian | Gyllensten, Ulf | Hamsten, Anders | Harris, Tamara B. | Hengstenberg, Christian | Hicks, Andrew A. | Hingorani, Aroon | Hinney, Anke | Hofman, Albert | Hovingh, Kees G. | Hveem, Kristian | Illig, Thomas | Jarvelin, Marjo-Riitta | Jöckel, Karl-Heinz | Keinanen-Kiukaanniemi, Sirkka M. | Kiemeney, Lambertus A. | Kuh, Diana | Laakso, Markku | Lehtimäki, Terho | Levinson, Douglas F. | Martin, Nicholas G. | Metspalu, Andres | Morris, Andrew D. | Nieminen, Markku S. | Njølstad, Inger | Ohlsson, Claes | Oldehinkel, Albertine J. | Ouwehand, Willem H. | Palmer, Lyle J. | Penninx, Brenda | Power, Chris | Province, Michael A. | Psaty, Bruce M. | Qi, Lu | Rauramaa, Rainer | Ridker, Paul M. | Ripatti, Samuli | Salomaa, Veikko | Samani, Nilesh J. | Snieder, Harold | Sørensen, Thorkild I.A. | Spector, Timothy D. | Stefansson, Kari | Tönjes, Anke | Tuomilehto, Jaakko | Uitterlinden, André G. | Uusitupa, Matti | van der Harst, Pim | Vollenweider, Peter | Wallaschofski, Henri | Wareham, Nicholas J. | Watkins, Hugh | Wichmann, H.-Erich | Wilson, James F. | Abecasis, Goncalo R. | Assimes, Themistocles L. | Barroso, Inês | Boehnke, Michael | Borecki, Ingrid B. | Deloukas, Panos | Fox, Caroline S. | Frayling, Timothy | Groop, Leif C. | Haritunian, Talin | Heid, Iris M. | Hunter, David | Kaplan, Robert C. | Karpe, Fredrik | Moffatt, Miriam | Mohlke, Karen L. | O’Connell, Jeffrey R. | Pawitan, Yudi | Schadt, Eric E. | Schlessinger, David | Steinthorsdottir, Valgerdur | Strachan, David P. | Thorsteinsdottir, Unnur | van Duijn, Cornelia M. | Visscher, Peter M. | Di Blasio, Anna Maria | Hirschhorn, Joel N. | Lindgren, Cecilia M. | Morris, Andrew P. | Meyre, David | Scherag, André | McCarthy, Mark I. | Speliotes, Elizabeth K. | North, Kari E. | Loos, Ruth J.F. | Ingelsson, Erik
Nature genetics  2013;45(5):501-512.
Approaches exploiting extremes of the trait distribution may reveal novel loci for common traits, but it is unknown whether such loci are generalizable to the general population. In a genome-wide search for loci associated with upper vs. lower 5th percentiles of body mass index, height and waist-hip ratio, as well as clinical classes of obesity including up to 263,407 European individuals, we identified four new loci (IGFBP4, H6PD, RSRC1, PPP2R2A) influencing height detected in the tails and seven new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3, ZZZ3) for clinical classes of obesity. Further, we show that there is large overlap in terms of genetic structure and distribution of variants between traits based on extremes and the general population and little etiologic heterogeneity between obesity subgroups.
doi:10.1038/ng.2606
PMCID: PMC3973018  PMID: 23563607
4.  Helping Patients Simplify and Safely Use Complex Prescription Regimens 
Archives of internal medicine  2011;171(4):300-305.
Background
There is considerable variability in the manner in which prescriptions are written by physicians and transcribed by pharmacists, resulting in patient misunderstanding of label instructions. A ‘universal medication schedule’ (UMS) was recently proposed for standardizing prescribing practices to four daily time intervals thereby helping patients simplify and safely use their medicine. We investigated whether patients consolidate their medications, or if there is evidence of unnecessary regimen complexity that would support standardization.
Methods
Structured interviews were conducted with 464 adults ages 55–74 who were receiving care at either an academic general medicine practice or one of three federally qualified health centers in Chicago, Illinois. Subjects were given a hypothetical, seven-drug medication regimen and asked to demonstrate how and when they would take all of the medicine in a 24-hour period. The regimen could be consolidated into four dosing episodes per day. The primary outcome was the number of times per day individuals would take medicine. Root causes for patients complicating the regimen (> four times a day) were examined.
Results
Participants on average identified six times in 24 hours to take the seven drugs (SD=1.8; range 3 to 14). One third (29.3%) found seven or more times per day to take their medicine, while only 14.9% organized the regimen into four or fewer times a day. In multivariable analysis, low literacy was an independent predictor of more times per day for dosing out the regimen (β=0.67; 95% Confidence Interval 0.12 to 1.22, p=0.018). Instructions for two of the drugs were identical, yet 31% of patients did not dose these medicines at the same time. Another set of drugs had similar instructions with the primary exception of one having the added instruction to take “with food and water”. Half (49.5%) of participants dosed these medicines at different times. When medicines had variable expressions of the same dose frequency (“every 12 hours” vs. “twice daily”), 79.0% did not consolidate the medicines.
Conclusion
Many patients, especially those with limited literacy, do not consolidate prescription regimens in the most efficient manner, which could impede adherence. Standardized instructions proposed with the UMS and other task-centered strategies could potentially help patients routinely organize and take medication regimens.
doi:10.1001/archinternmed.2011.39
PMCID: PMC3968427  PMID: 21357804
Prescription; medication; health literacy; dosing; instructions; standardization; elderly
5.  Stream Macroinvertebrate Response Models for Bioassessment Metrics: Addressing the Issue of Spatial Scale 
PLoS ONE  2014;9(3):e90944.
We developed independent predictive disturbance models for a full regional data set and four individual ecoregions (Full Region vs. Individual Ecoregion models) to evaluate effects of spatial scale on the assessment of human landscape modification, on predicted response of stream biota, and the effect of other possible confounding factors, such as watershed size and elevation, on model performance. We selected macroinvertebrate sampling sites for model development (n = 591) and validation (n = 467) that met strict screening criteria from four proximal ecoregions in the northeastern U.S.: North Central Appalachians, Ridge and Valley, Northeastern Highlands, and Northern Piedmont. Models were developed using boosted regression tree (BRT) techniques for four macroinvertebrate metrics; results were compared among ecoregions and metrics. Comparing within a region but across the four macroinvertebrate metrics, the average richness of tolerant taxa (RichTOL) had the highest R2 for BRT models. Across the four metrics, final BRT models had between four and seven explanatory variables and always included a variable related to urbanization (e.g., population density, percent urban, or percent manmade channels), and either a measure of hydrologic runoff (e.g., minimum April, average December, or maximum monthly runoff) and(or) a natural landscape factor (e.g., riparian slope, precipitation, and elevation), or a measure of riparian disturbance. Contrary to our expectations, Full Region models explained nearly as much variance in the macroinvertebrate data as Individual Ecoregion models, and taking into account watershed size or elevation did not appear to improve model performance. As a result, it may be advantageous for bioassessment programs to develop large regional models as a preliminary assessment of overall disturbance conditions as long as the range in natural landscape variability is not excessive.
doi:10.1371/journal.pone.0090944
PMCID: PMC3968005  PMID: 24675770
6.  LacR Mutations Are Frequently Observed in Streptococcus intermedius and Are Responsible for Increased Intermedilysin Production and Virulence 
Infection and Immunity  2013;81(9):3276-3286.
Streptococcus intermedius secretes a human-specific cytolysin, intermedilysin (ILY), which is considered to be the major virulence factor of this pathogen. We screened for a repressor of ily expression by using random gene disruption in a low-ILY-producing strain (PC574). Three independent high-ILY-producing colonies that had plasmid insertions within a gene that has high homology to lacR were isolated. Validation of these observations was achieved through disruption of lacR in strain PC574 with an erythromycin cassette, which also led to higher hemolytic activity, increased transcription of ily, and higher cytotoxicity against HepG2 cells, compared to the parental strain. The direct binding of LacR within the ily promoter region was shown by a biotinylated DNA probe pulldown assay, and the amount of ILY secreted into the culture supernatant by PC574 cells was increased by adding lactose or galactose to the medium as a carbon source. Furthermore, we examined lacR nucleotide sequences and the hemolytic activity of 50 strains isolated from clinical infections and 7 strains isolated from dental plaque. Of the 50 strains isolated from infections, 13 showed high ILY production, 11 of these 13 strains had one or more point mutations and/or an insertion mutation in LacR, and almost all mutations were associated with a marked decline in LacR function. These results strongly suggest that mutation in lacR is required for the overproduction of ILY, which is associated with an increase in pathogenicity of S. intermedius.
doi:10.1128/IAI.00638-13
PMCID: PMC3754192  PMID: 23798532
7.  Literacy and Race as Risk Factors to Low Rates of Advance Directives Among Older Adults 
Background
Advance directives are documented instructions by a patient to ensure their medical care preferences are fulfilled in the event they cannot communicate with clinicians or family members.
Objectives
The current study examined the relationship between literacy and other patient level factors on having an advance directive.
Design
Face-to-face structured interview.
Setting
Participants were recruited from either an academic general internal medicine clinic or one of four federally qualified health centers in Chicago.
Participants
784 adults ages 55 to 74.
Measurements
Assessment of participant literacy, sociodemographic factors, and having an advance directive for medical care.
Results
Having an advanced directive was reported by 12.4% of subjects with low literacy, 26.6% of those with marginal literacy, and 49.5% of those with adequate literacy (p<0.001). In multivariable analyses, both literacy and race were independently associated with a lower likelihood of having an advance directive. Specifically, people with limited literacy and African Americans were less likely to have an advance directive (RR, 0.45; 95% CI, 0.22–0.95; RR, 0.64; 95% CI: 0.47–0.88, respectively). Exploratory analyses exhibited that there was not a significant interaction between the effect of literacy and race.
Conclusion
Limited literacy and African American race were significant risk factors to not having an advance directive in this cohort of older patients. Literacy and race likely represent two separate but important causal pathways that need to be understood to improve how the health care system ascertains and protects patients’ advanced care preferences.
doi:10.1111/jgs.12134
PMCID: PMC3891653  PMID: 23379361
Literacy; Advance Directive; End of Life Decisions; Race
8.  StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics 
F1000Research  2014;2:248.
Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. ”provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month”. The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages.
doi:10.12688/f1000research.2-248.v2
PMCID: PMC3938176  PMID: 24627795
9.  Adhesion of mussel foot proteins to different substrate surfaces 
Mussel foot proteins (mfps) have been investigated as a source of inspiration for the design of underwater coatings and adhesives. Recent analysis of various mfps by a surface forces apparatus (SFA) revealed that mfp-1 functions as a coating, whereas mfp-3 and mfp-5 resemble adhesive primers on mica surfaces. To further refine and elaborate the surface properties of mfps, the force–distance profiles of the interactions between thin mfp (i.e. mfp-1, mfp-3 or mfp-5) films and four different surface chemistries, namely mica, silicon dioxide, polymethylmethacrylate and polystyrene, were measured by an SFA. The results indicate that the adhesion was exquisitely dependent on the mfp tested, the substrate surface chemistry and the contact time. Such studies are essential for understanding the adhesive versatility of mfps and related/similar adhesion proteins, and for translating this versatility into a new generation of coatings and (including in vivo) adhesive materials.
doi:10.1098/rsif.2012.0759
PMCID: PMC3565691  PMID: 23173195
mussel foot proteins; coatings and adhesives; molecular interactions; surface forces; bioadhesion
10.  Hydrophobic enhancement of Dopa-mediated adhesion in a mussel foot protein 
Dopa (3,4-dihydroxyphenylalanine) is recognized as a key chemical signature of mussel adhesion and has been adopted into diverse synthetic polymer systems. Dopa’s notorious susceptibility to oxidation, however, poses significant challenges to the practical translation of mussel adhesion. Using a Surface Forces Apparatus to investigate the adhesion of Mfp3 (mussel foot protein 3) slow, a hydrophobic protein variant of the Mfp3 family in the plaque, we have discovered a subtle molecular strategy correlated with hydrophobicity that appears to compensate for Dopa instability. At pH 3, where Dopa is stable, Mfp3 slow like Mfp3 fast adhesion to mica is directly proportional to the mol% of Dopa present in the protein. At pH 5.5 and 7.5, however, loss of adhesion in Mfp3 slow was less than half that occurring in Mfp3 fast, purportedly because Dopa in Mfp3 slow is less prone to oxidation. Indeed, cyclic voltammetry showed that the oxidation potential of Dopa in Mfp3 slow is significantly higher than in Mfp3 fast at pH 7.5. A much greater difference between the two variants was revealed in the interaction energy of two symmetric Mfp3 slow films (Ead = −3 mJ/m2). This energy corresponds to the energy of protein cohesion which is notable for its reversibility and pH-independence. Exploitation of aromatic hydrophobic sequences to protect Dopa against oxidation as well as to mediate hydrophobic and H-bonding interactions between proteins provides new insights for developing effective artificial underwater adhesives.
doi:10.1021/ja309590f
PMCID: PMC3587158  PMID: 23214725
11.  Physical activity and health-related quality of life among physiotherapists: a cross sectional survey in an Australian hospital and health service 
Background
Physiotherapists are a professional group with a high rate of attrition and at high risk of musculoskeletal disorders. The purpose of this investigation was to examine the physical activity levels and health-related quality of life of physiotherapists working in metropolitan clinical settings in an Australian hospital and health service. It was hypothesized that practicing physiotherapists would report excellent health-related quality of life and would already be physically active. Such a finding would add weight to a claim that general physical activity conditioning strategies may not be useful for preventing musculoskeletal disorders among active healthy physiotherapists, but rather, future investigations should focus on the development and evaluation of role specific conditioning strategies.
Methods
A questionnaire was completed by 44 physiotherapists from three inpatient units and three ambulatory clinics (63.7% response rate). Physical activity levels were reported using the Active Australia Survey. Health-related quality of life was examined using the EQ-5D instrument. Physical activity and EQ-5D data were examined using conventional descriptive statistics; with domain responses for the EQ-5D presented in a frequency histogram.
Results
The majority of physiotherapists in this sample were younger than 30 years of age (n = 25, 56.8%) consistent with the presence of a high attrition rate. Almost all respondents exceeded minimum recommended physical activity guidelines (n = 40, 90.9%). Overall the respondents engaged in more vigorous physical activity (median = 180 minutes) and walking (median = 135 minutes) than moderate exercise (median = 35 minutes) each week. Thirty-seven (84.1%) participants reported no pain or discomfort impacting their health-related quality of life, with most (n = 35,79.5%) being in full health.
Conclusions
Physical-conditioning based interventions for the prevention of musculoskeletal disorders among practicing physiotherapists may be better targeted to role or task specific conditioning rather than general physical conditioning among this physically active population. It is plausible that an inherent attrition of physiotherapists may occur among those not as active or healthy as therapists who cope with the physical demands of clinical practice. Extrapolation of findings from this study may be limited due to the sample characteristics. However, this investigation addressed the study objectives and has provided a foundation for larger scale longitudinal investigations in this field.
doi:10.1186/1745-6673-9-1
PMCID: PMC3896696  PMID: 24405934
Physical activity; Work related musculoskeletal disorders; Physiotherapists; Prevention; Injury; Attrition; Quality of life; Workforce; Australian
12.  Pleiotropic and isoform-specific functions for Pitx2 in superior colliculus and hypothalamic neuronal development 
Transcriptional regulation of gene expression during development is critical for proper neuronal differentiation and migration. Alternative splicing and differential isoform expression have been demonstrated for most mammalian genes, but their specific contributions to gene function are not well understood. In mice, the transcription factor gene Pitx2 is expressed as three different isoforms (PITX2A, PITX2B, and PITX2C) which have unique amino termini and common DNA binding homeodomains and carboxyl termini. The specific roles of these isoforms in neuronal development are not known. Here we report the onset of Pitx2ab and Pitx2c isoform-specific expression by E9.5 in the developing mouse brain. Using isoform-specific Pitx2 deletion mouse strains, we show that collicular neuron migration requires PITX2AB and that collicular GABAergic differentiation and targeting of hypothalamic projections require unique Pitx2 isoform dosage. These results provide insights into Pitx2 dosage and isoform-specific requirements underlying midbrain and hypothalamic development.
doi:10.1016/j.mcn.2012.11.007
PMCID: PMC3540135  PMID: 23147109
migration; transcription factor; midbrain; isoform; differentiation; axon
13.  Sequencing quality assessment tools to enable data-driven informatics for high throughput genomics 
Frontiers in Genetics  2013;4:288.
The processes of quality assessment and control are an active area of research at The Genome Analysis Centre (TGAC). Unlike other sequencing centers that often concentrate on a certain species or technology, TGAC applies expertise in genomics and bioinformatics to a wide range of projects, often requiring bespoke wet lab and in silico workflows. TGAC is fortunate to have access to a diverse range of sequencing and analysis platforms, and we are at the forefront of investigations into library quality and sequence data assessment. We have developed and implemented a number of algorithms, tools, pipelines and packages to ascertain, store, and expose quality metrics across a number of next-generation sequencing platforms, allowing rapid and in-depth cross-platform Quality Control (QC) bioinformatics. In this review, we describe these tools as a vehicle for data-driven informatics, offering the potential to provide richer context for downstream analysis and to inform experimental design.
doi:10.3389/fgene.2013.00288
PMCID: PMC3865868  PMID: 24381581
quality control; sequence analysis; QC; NGS data analysis; bioinformatics tools; run statistics; quality assessment and improvement; contamination screening
14.  Improved performance of protected catecholic polysiloxanes for bio-inspired wet adhesion to surface oxides 
Journal of the American Chemical Society  2012;134(49):20139-20145.
A facile synthetic strategy for introducing catecholic moieties into polymeric materials based on a readily available precursor – eugenol – and efficient chemistries – tris(pentafluorophenyl)borane catalyzed silation and thiol-ene coupling is reported. Silyl-protection is shown to be critical for the oxidative stability of catecholic moieties during synthesis and processing which allows functionalized polysiloxane derivatives to be fabricated into 3-D microstructures as well as 2-D patterned surfaces. Deprotection gives stable catechol surfaces with adhesion to a variety of oxide surfaces being precisely tuned by the level of catechol incorporation. The advantage of silyl-protection for catechol functionalized polysiloxanes is demonstrated and represents a promising and versatile new platform for underwater surface treatments.
doi:10.1021/ja309044z
PMCID: PMC3521601  PMID: 23181614
Catechol; Deprotection; Polysiloxane; Wet adhesion; Lithography
15.  Acute stress causes rapid synaptic insertion of Ca2+-permeable AMPA receptors to facilitate long-term potentiation in the hippocampus 
Brain  2013;136(12):3753-3765.
The neuroendocrine response to episodes of acute stress is crucial for survival whereas the prolonged response to chronic stress can be detrimental. Learning and memory are particularly susceptible to stress with cognitive deficits being well characterized consequences of chronic stress. Although there is good evidence that acute stress can enhance cognitive performance, the mechanism(s) for this are unclear. We find that hippocampal slices, either prepared from rats following 30 min restraint stress or directly exposed to glucocorticoids, exhibit an N-methyl-d-aspartic acid receptor-independent form of long-term potentiation. We demonstrate that the mechanism involves an NMDA receptor and PKA-dependent insertion of Ca2+-permeable AMPA receptors into synapses. These then trigger the additional NMDA receptor-independent form of LTP during high frequency stimulation.
doi:10.1093/brain/awt293
PMCID: PMC3859225  PMID: 24271563
long-term potentiation; metaplasticity; glucocorticoids; glutamate receptor; calcium
16.  Withdrawal from Buprenorphine/Naloxone and Maintenance with a Natural Dopaminergic Agonist: A Cautionary Note 
Journal of addiction research & therapy  2013;4(2):10.4172/2155-6105.1000146.
Background
While numerous studies support the efficacy of methadone and buprenorphine for the stabilization and maintenance of opioid dependence, clinically significant opioid withdrawal symptoms occur upon tapering and cessation of dosage.
Methods
We present a case study of a 35 year old Caucasian female (Krissie) who was prescribed increasing dosages of prescription opioids after carpel tunnel surgery secondary to chronic pain from reflex sympathetic dystrophy and fibromyalgia. Over the next 5 years, daily dosage requirements increased to over 80 mg of Methadone and 300 ug/hr Fentanyl transdermal patches, along with combinations of 12–14 1600 mcg Actig lollipop and oral 100 mg Morphine and 30 mg oxycodone 1–2 tabs q4-6hr PRN for breakthrough pain. Total monthly prescription costs including supplemental benzodiazepines, hypnotics and stimulants exceeded $50,000. The patient was subsequently transferred to Suboxone® in 2008, and the dosage was gradually tapered until her admission for inpatient detoxification with KB220Z a natural dopaminergic agonist. We carefully documented her withdrawal symptoms when she precipitously stopped taking buprenorphine/naloxone and during follow-up while taking KB220Z daily. We also genotyped the patient using a reward gene panel including (9 genes 18 alleles): DRD 2,3,4; MOA-A; COMT; DAT1; 5HTTLLR; OPRM1; and GABRA3.
Findings
At 432 days post Suboxone® withdrawal the patient is being maintained on KB220Z, has been urine tested and is opioid free. Genotyping data revealed a moderate genetic risk for addiction showing a hypodopaminergic trait. This preliminary case data suggest that the daily use of KB220Z could provide a cost effective alternative substitution adjunctive modality for Suboxone®. We encourage double-blind randomized –placebo controlled studies to test the proposition that KB220Z may act as a putative natural opioid substitution maintenance adjunct.
doi:10.4172/2155-6105.1000146
PMCID: PMC3835595  PMID: 24273683
Buprenorphine/naloxone; Withdrawal; Natural dopaminergic agonist
17.  StatsDB: platform-agnostic storage and understanding of next generation sequencing run metrics 
F1000Research  2013;2:248.
Modern sequencing platforms generate enormous quantities of data in ever-decreasing amounts of time. Additionally, techniques such as multiplex sequencing allow one run to contain hundreds of different samples. With such data comes a significant challenge to understand its quality and to understand how the quality and yield are changing across instruments and over time. As well as the desire to understand historical data, sequencing centres often have a duty to provide clear summaries of individual run performance to collaborators or customers. We present StatsDB, an open-source software package for storage and analysis of next generation sequencing run metrics. The system has been designed for incorporation into a primary analysis pipeline, either at the programmatic level or via integration into existing user interfaces. Statistics are stored in an SQL database and APIs provide the ability to store and access the data while abstracting the underlying database design. This abstraction allows simpler, wider querying across multiple fields than is possible by the manual steps and calculation required to dissect individual reports, e.g. ”provide metrics about nucleotide bias in libraries using adaptor barcode X, across all runs on sequencer A, within the last month”. The software is supplied with modules for storage of statistics from FastQC, a commonly used tool for analysis of sequence reads, but the open nature of the database schema means it can be easily adapted to other tools. Currently at The Genome Analysis Centre (TGAC), reports are accessed through our LIMS system or through a standalone GUI tool, but the API and supplied examples make it easy to develop custom reports and to interface with other packages.
doi:10.12688/f1000research.2-248.v1
PMCID: PMC3938176  PMID: 24627795
18.  Spatial self-organization favors heterotypic cooperation over cheating 
eLife  2013;2:e00960.
Heterotypic cooperation—two populations exchanging distinct benefits that are costly to produce—is widespread. Cheaters, exploiting benefits while evading contribution, can undermine cooperation. Two mechanisms can stabilize heterotypic cooperation. In ‘partner choice’, cooperators recognize and choose cooperating over cheating partners; in ‘partner fidelity feedback’, fitness-feedback from repeated interactions ensures that aiding your partner helps yourself. How might a spatial environment, which facilitates repeated interactions, promote fitness-feedback? We examined this process through mathematical models and engineered Saccharomyces cerevisiae strains incapable of recognition. Here, cooperators and their heterotypic cooperative partners (partners) exchanged distinct essential metabolites. Cheaters exploited partner-produced metabolites without reciprocating, and were competitively superior to cooperators. Despite initially random spatial distributions, cooperators gained more partner neighbors than cheaters did. The less a cheater contributed, the more it was excluded and disfavored. This self-organization, driven by asymmetric fitness effects of cooperators and cheaters on partners during cell growth into open space, achieves assortment.
DOI: http://dx.doi.org/10.7554/eLife.00960.001
eLife digest
Cooperation between individuals of the same species, and also between different species, is known to be important in evolution. Large fish, for example, rely on small cleaner fish to remove parasites, while the small fish benefit from the nutrients in these parasites. However, cooperation can be undermined by other individuals or species who “cheat” by taking advantage of those who cooperate, without providing any benefits in return. For example, some cleaner fish cheat by biting off healthy tissue from their host, in addition to parasites.
Genetically-related individuals who cooperate by sharing identical benefits can combat cheaters by giving preferential treatment to their relatives (a process known as kin discrimination) or by staying close to the relatives to form clusters (kin fidelity). However, two genetically-unrelated populations that mutually cooperate by sharing different benefits cannot employ these methods to overcome cheaters. Instead they rely on either partner choice or partner fidelity feedback.
Partner choice – the approach adopted by cleaner fish and their hosts – relies on one population recognizing a signal from the other population and responding accordingly: for example, large fish observe cleaner fish and approach those that cooperate with their current host and avoid those that cheat. Partner fidelity feedback, on the other hand, relies on repeated interactions between the two populations providing an advantage in terms of evolutionary fitness to both: for example, organelles called mitochondria and chloroplasts live inside cells, helping the cells to harvest energy and providing energy for themselves and the host cells in the process. In some cases – such as the cooperation between figs and fig wasps, or between certain plants and the bacteria that fix nitrogen in their roots – researchers cannot agree if the populations are relying on partner choice or partner fidelity feedback.
Now Momeni et al. have used a combination of experiments on yeast and mathematical modeling to explore partner fidelity feedback in greater detail. They started by using genetic engineering techniques to produce two species of yeast that mutually cooperate, each providing a metabolite that is essential to the other, but are not able to recognize each other: this means that these populations cannot rely on partner choice to combat cheaters. Momeni et al. then observed how these two species interacted with each other and a third species of yeast that cheated by consuming one of the metabolites without releasing any metabolite of its own.
Momeni et al. found that as long as there was space for the yeast cells to grow into, the two species that cooperated self-organized into mixed clusters, with the cheating species being excluded from these clusters. The self-organization was driven by a positive feedback loop involving the two species that cooperated, with each species helping to increase the fitness of the other. The results of Momeni et al. demonstrate that it is possible for two genetically unrelated populations to cooperate and combat cheaters without the use of partner choice.
DOI: http://dx.doi.org/10.7554/eLife.00960.002
doi:10.7554/eLife.00960
PMCID: PMC3823188  PMID: 24220506
cooperation; self-organization; pattern formation; community ecology; mutualism; spatial structure; S. cerevisiae
19.  Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds 
BMC Genomics  2013;14:784.
Background
Obesity, excess fat tissue in the body, can underlie a variety of medical complaints including heart disease, stroke and cancer. The pig is an excellent model organism for the study of various human disorders, including obesity, as well as being the foremost agricultural species. In order to identify genetic variants associated with fatness, we used a selective genomic approach sampling DNA from animals at the extreme ends of the fat and lean spectrum using estimated breeding values derived from a total population size of over 70,000 animals. DNA from 3 breeds (Sire Line Large White, Duroc and a white Pietrain composite line (Titan)) was used to interrogate the Illumina Porcine SNP60 Genotyping Beadchip in order to identify significant associations in terms of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs).
Results
By sampling animals at each end of the fat/lean EBV (estimate breeding value) spectrum the whole population could be assessed using less than 300 animals, without losing statistical power. Indeed, several significant SNPs (at the 5% genome wide significance level) were discovered, 4 of these linked to genes with ontologies that had previously been correlated with fatness (NTS, FABP6, SST and NR3C2). Quantitative analysis of the data identified putative CNV regions containing genes whose ontology suggested fatness related functions (MCHR1, PPARα, SLC5A1 and SLC5A4).
Conclusions
Selective genotyping of EBVs at either end of the phenotypic spectrum proved to be a cost effective means of identifying SNPs and CNVs associated with fatness and with estimated major effects in a large population of animals.
doi:10.1186/1471-2164-14-784
PMCID: PMC3879217  PMID: 24225222
SNP; CNV; Pig; QuantiSNP; cnvPartition; Fatness; Obesity; Genotyping; GWAS
20.  Literacy, Cognitive Function, and Health: Results of the LitCog Study 
Journal of General Internal Medicine  2012;27(10):1300-1307.
ABSTRACT
BACKGROUND
Emerging evidence suggests the relationship between health literacy and health outcomes could be explained by cognitive abilities.
OBJECTIVE
To investigate to what degree cognitive skills explain associations between health literacy, performance on common health tasks, and functional health status.
DESIGN
Two face-to-face, structured interviews spaced a week apart with three health literacy assessments and a comprehensive cognitive battery measuring ‘fluid’ abilities necessary to learn and apply new information, and ‘crystallized’ abilities such as background knowledge.
SETTING
An academic general internal medicine practice and three federally qualified health centers in Chicago, Illinois.
PATIENTS
Eight hundred and eighty-two English-speaking adults ages 55 to 74.
MEASUREMENTS
Health literacy was measured using the Rapid Estimate of Adult Literacy in Medicine (REALM), Test of Functional Health Literacy in Adults (TOFHLA), and Newest Vital Sign (NVS). Performance on common health tasks were globally assessed and categorized as 1) comprehending print information, 2) recalling spoken information, 3) recalling multimedia information, 4) dosing and organizing medication, and 5) healthcare problem-solving.
RESULTS
Health literacy measures were strongly correlated with fluid and crystallized cognitive abilities (range: r = 0.57 to 0.77, all p < 0.001). Lower health literacy and weaker fluid and crystallized abilities were associated with poorer performance on healthcare tasks. In multivariable analyses, the association between health literacy and task performance was substantially reduced once fluid and crystallized cognitive abilities were entered into models (without cognitive abilities: β = −28.9, 95 % Confidence Interval (CI) -31.4 to −26.4, p; with cognitive abilities: β = −8.5, 95 % CI −10.9 to −6.0).
LIMITATIONS
Cross-sectional analyses, English-speaking, older adults only.
CONCLUSIONS
The most common measures used in health literacy studies are detecting individual differences in cognitive abilities, which may predict one’s capacity to engage in self-care and achieve desirable health outcomes. Future interventions should respond to all of the cognitive demands patients face in managing health, beyond reading and numeracy.
doi:10.1007/s11606-012-2079-4
PMCID: PMC3445686  PMID: 22566171
health literacy; cognitive abilities; health tasks; patient-reported outcomes; physical health; mental health
21.  Have We Hatched the Addiction Egg: Reward Deficiency Syndrome Solution System™ 
This article co-authored by a number of scientists, ASAM physicians, clinicians, treatment center owners, geneticists, neurobiologists, psychologists, social workers, criminologists, nurses, nutritionist, and students, is dedicated to all the people who have lost loved ones in substance-abuse and “reward deficiency syndrome” related tragedies. Why are we failing at reducing the incidence of ‘Bad Behaviors’? Are we aiming at the wrong treatment targets for behavioral disorders? We are proposing a paradigm shift and calling it “Reward Deficiency Solution System” providing evidence for its adoption.
doi:10.4172/2157-7412.1000136
PMCID: PMC3783340  PMID: 24077767
Reward Deficiency Syndrome (RDS) dopamine; Standard of Care; Addiction
22.  Mini-review: The role of redox in DOPA-mediated marine adhesion 
Biofouling  2012;28(8):865-877.
3, 4-Dihydroxyphenylanine (Dopa)-containing proteins are key to wet adhesion in mussels and possibly other sessile organisms also. However, Dopa-mediated adhesive bonding is a hard act to follow in that, at least in mussels, bonding depends on Dopa in both reduced and oxidized forms, for adhesion and cohesion, respectively. Given the vulnerability of Dopa to spontaneous oxidation, the most significant challenge to using it in practical adhesion is controlling Dopa redox in a temporally- and spatially defined manner. Mussels appear to achieve such control in their byssal attachment plaques, and factors involved in redox control can be measured with precision using redox probes such as the diphenylpicryl hydrazyl (DPPH) free radical. Understanding the specifics of natural redox control may provide fundamentally important insights for adhesive polymer engineering and antifouling strategies.
doi:10.1080/08927014.2012.719023
PMCID: PMC3463409  PMID: 22924420
Mytilus; byssus; 3, 4-dihydroxyphenylalanine; anti-oxidant; wet adhesion
23.  Nutrigenomic targeting of carbohydrate craving behavior: Can we manage obesity and aberrant craving behaviors with neurochemical pathway manipulation by Immunological Compatible Substances (nutrients) using a Genetic Positioning System (GPS) Map? 
Medical hypotheses  2009;73(3):427-434.
SUMMARY
Genetic mediated physiological processes that rely on both pharmacological and nutritional principles hold great promise for the successful therapeutic targeting of reduced carbohydrate craving, body-friendly fat loss, healthy body recomposition, and overall wellness. By integrating an assembly of scientific knowledge on inheritable characteristics and environmental mediators of gene expression, we review the relationship of genes, hormones, neurotransmitters, and nutrients as they correct unwanted weight gain coupled with unhappiness. In contrast to a simple one-locus, one-mechanism focus on pharmaceuticals alone, we hypothesize that the use of nutrigenomic treatment targeting multi-physiological neurological, immunological, and metabolic pathways will enable clinicians to intercede in the process of lipogenesis by promoting lipolysis while attenuating aberrant glucose cravings. In turn, this approach will enhance wellness in a safe and predictable manner through the use of a Genetic Positioning System (GPS) Map. The GPS Map, while presently incomplete, ultimately will serve not only as a blueprint for personalized medicine in the treatment of obesity, but also for the development of strategies for reducing many harmful addictive behaviors and promoting optimal health by using substances compatible with the body’s immune system.
doi:10.1016/j.mehy.2009.02.037
PMCID: PMC3758908  PMID: 19450935
24.  Knockdown of Human TCF4 Affects Multiple Signaling Pathways Involved in Cell Survival, Epithelial to Mesenchymal Transition and Neuronal Differentiation 
PLoS ONE  2013;8(8):e73169.
Haploinsufficiency of TCF4 causes Pitt-Hopkins syndrome (PTHS): a severe form of mental retardation with phenotypic similarities to Angelman, Mowat-Wilson and Rett syndromes. Genome-wide association studies have also found that common variants in TCF4 are associated with an increased risk of schizophrenia. Although TCF4 is transcription factor, little is known about TCF4-regulated processes in the brain. In this study we used genome-wide expression profiling to determine the effects of acute TCF4 knockdown on gene expression in SH-SY5Y neuroblastoma cells. We identified 1204 gene expression changes (494 upregulated, 710 downregulated) in TCF4 knockdown cells. Pathway and enrichment analysis on the differentially expressed genes in TCF4-knockdown cells identified an over-representation of genes involved in TGF-β signaling, epithelial to mesenchymal transition (EMT) and apoptosis. Among the most significantly differentially expressed genes were the EMT regulators, SNAI2 and DEC1 and the proneural genes, NEUROG2 and ASCL1. Altered expression of several mental retardation genes such as UBE3A (Angelman Syndrome), ZEB2 (Mowat-Wilson Syndrome) and MEF2C was also found in TCF4-depleted cells. These data suggest that TCF4 regulates a number of convergent signaling pathways involved in cell differentiation and survival in addition to a subset of clinically important mental retardation genes.
doi:10.1371/journal.pone.0073169
PMCID: PMC3751932  PMID: 24058414
25.  Adhesion of Mussel Foot Protein Mefp-5 to Mica: An Underwater Superglue† 
Biochemistry  2012;51(33):6511-6518.
Mussels have a remarkable ability to attach their holdfast, or byssus, opportunistically to a variety of substrata that are wet, saline, corroded, and/or fouled by biofilms. Mytilus edulis foot protein-5 (Mefp-5) is one of several proteins in the byssal adhesive plaque of the mussel M. edulis. The high content of 3,4 dihydroxyphenylalanine (Dopa) (~30 mol%) and its localization near the plaque-substrate interface have often prompted speculation that Mefp-5 plays a key role in adhesion. Using the surface forces apparatus, we show that on mica surfaces Mefp-5 achieves an adhesion energy approaching Ead = ~− 14 mJ/m2. This exceeds the adhesion energy of another interfacial protein, Mefp-3, by a factor of 4–5 and is greater than the adhesion between highly oriented monolayers of biotin and streptavidin. The adhesion to mica is notable for its dependence on Dopa, which is most stable under reducing conditions and acidic pH. Mefp-5 also exhibits strong protein-protein interactions with itself as well as with Mefp-3 from M. edulis.
doi:10.1021/bi3002538
PMCID: PMC3428132  PMID: 22873939

Results 1-25 (238)