1
|
Matcham F, Simblett SK, Leightley D, Dalby M, Siddi S, Haro JM, Lamers F, Penninx BWHJ, Bruce S, Nica R, Zormpas S, Gilpin G, White KM, Oetzmann C, Annas P, Brasen JC, Narayan VA, Hotopf M, Wykes T. The association between persistent cognitive difficulties and depression and functional outcomes in people with major depressive disorder. Psychol Med 2023; 53:6334-6344. [PMID: 37743838 PMCID: PMC10520589 DOI: 10.1017/s0033291722003671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/24/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Cognitive symptoms are common during and following episodes of depression. Little is known about the persistence of self-reported and performance-based cognition with depression and functional outcomes. METHODS This is a secondary analysis of a prospective naturalistic observational clinical cohort study of individuals with recurrent major depressive disorder (MDD; N = 623). Participants completed app-based self-reported and performance-based cognitive function assessments alongside validated measures of depression, functional disability, and self-esteem every 3 months. Participants were followed-up for a maximum of 2-years. Multilevel hierarchically nested modelling was employed to explore between- and within-participant variation over time to identify whether persistent cognitive difficulties are related to levels of depression and functional impairment during follow-up. RESULTS 508 individuals (81.5%) provided data (mean age: 46.6, s.d.: 15.6; 76.2% female). Increasing persistence of self-reported cognitive difficulty was associated with higher levels of depression and functional impairment throughout the follow-up. In comparison to low persistence of objective cognitive difficulty (<25% of timepoints), those with high persistence (>75% of timepoints) reported significantly higher levels of depression (B = 5.17, s.e. = 2.21, p = 0.019) and functional impairment (B = 4.82, s.e. = 1.79, p = 0.002) over time. Examination of the individual cognitive modules shows that persistently impaired executive function is associated with worse functioning, and poor processing speed is particularly important for worsened depressive symptoms. CONCLUSIONS We replicated previous findings of greater persistence of cognitive difficulty with increasing severity of depression and further demonstrate that these cognitive difficulties are associated with pervasive functional disability. Difficulties with cognition may be an indicator and target for further treatment input.
Collapse
Affiliation(s)
- F. Matcham
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- School of Psychology, University of Sussex, Falmer, UK
| | - S. K. Simblett
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - D. Leightley
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - M. Dalby
- Muna Therapeutics, Copenhagen, Denmark
| | - S. Siddi
- Parc Sanitari Sant Joan de Déu, Fundació San Joan de Déu, Universitat de Barcelona, CIBERSAM, Barcelona, Spain
| | - J. M. Haro
- Parc Sanitari Sant Joan de Déu, Fundació San Joan de Déu, Universitat de Barcelona, CIBERSAM, Barcelona, Spain
| | - F. Lamers
- Department of Psychiatry, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Amsterdam Public Health, Mental Health Program, Amsterdam, The Netherlands
| | - B. W. H. J. Penninx
- Department of Psychiatry, Amsterdam UMC location Vrije Universiteit Amsterdam, Boelelaan 1117, Amsterdam, The Netherlands
- Amsterdam Public Health, Mental Health Program, Amsterdam, The Netherlands
| | - S. Bruce
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - R. Nica
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- The Romanian League for Mental Health, Bucharest, Romania
| | - S. Zormpas
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- EPIONI Greek Carers Network, Athens, Greece
| | - G. Gilpin
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - K. M. White
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - C. Oetzmann
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - P. Annas
- H. Lundbeck A/S, Copenhagen, Denmark
| | | | | | - M. Hotopf
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
| | - T. Wykes
- The Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
| | | |
Collapse
|
2
|
Siddi S, Bailon R, Giné-Vázquez I, Matcham F, Lamers F, Kontaxis S, Laporta E, Garcia E, Lombardini F, Annas P, Hotopf M, Penninx BWJH, Ivan A, White KM, Difrancesco S, Locatelli P, Aguiló J, Peñarrubia-Maria MT, Narayan VA, Folarin A, Leightley D, Cummins N, Vairavan S, Ranjan Y, Rintala A, de Girolamo G, Simblett SK, Wykes T, Myin-Germeys I, Dobson R, Haro JM. The usability of daytime and night-time heart rate dynamics as digital biomarkers of depression severity. Psychol Med 2023; 53:3249-3260. [PMID: 37184076 DOI: 10.1017/s0033291723001034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND Alterations in heart rate (HR) may provide new information about physiological signatures of depression severity. This 2-year study in individuals with a history of recurrent major depressive disorder (MDD) explored the intra-individual variations in HR parameters and their relationship with depression severity. METHODS Data from 510 participants (Number of observations of the HR parameters = 6666) were collected from three centres in the Netherlands, Spain, and the UK, as a part of the remote assessment of disease and relapse-MDD study. We analysed the relationship between depression severity, assessed every 2 weeks with the Patient Health Questionnaire-8, with HR parameters in the week before the assessment, such as HR features during all day, resting periods during the day and at night, and activity periods during the day evaluated with a wrist-worn Fitbit device. Linear mixed models were used with random intercepts for participants and countries. Covariates included in the models were age, sex, BMI, smoking and alcohol consumption, antidepressant use and co-morbidities with other medical health conditions. RESULTS Decreases in HR variation during resting periods during the day were related with an increased severity of depression both in univariate and multivariate analyses. Mean HR during resting at night was higher in participants with more severe depressive symptoms. CONCLUSIONS Our findings demonstrate that alterations in resting HR during all day and night are associated with depression severity. These findings may provide an early warning of worsening depression symptoms which could allow clinicians to take responsive treatment measures promptly.
Collapse
Affiliation(s)
- S Siddi
- Parc Sanitari Sant Joan de Déu, Fundació Sant Joan de Déu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain
| | - R Bailon
- Aragón Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain
- Centros de investigación biomédica en red en el área de bioingeniería, biomateriales y nanomedicina (CIBER-BBN), Madrid, Spain
| | - I Giné-Vázquez
- Parc Sanitari Sant Joan de Déu, Fundació Sant Joan de Déu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain
| | - F Matcham
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- School of Psychology, University of Sussex, Falmer, UK
| | - F Lamers
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - S Kontaxis
- Aragón Institute of Engineering Research (I3A), University of Zaragoza, Zaragoza, Spain
- Centros de investigación biomédica en red en el área de bioingeniería, biomateriales y nanomedicina (CIBER-BBN), Madrid, Spain
| | - E Laporta
- Centros de investigación biomédica en red en el área de bioingeniería, biomateriales y nanomedicina (CIBER-BBN), Madrid, Spain
| | - E Garcia
- Centros de investigación biomédica en red en el área de bioingeniería, biomateriales y nanomedicina (CIBER-BBN), Madrid, Spain
- Microelectrónica y Sistemas Electrónicos, Universidad Autónoma de Barcelona, CIBERBBN, Barcelona, Spain
| | - F Lombardini
- Parc Sanitari Sant Joan de Déu, Fundació Sant Joan de Déu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain
| | - P Annas
- H. Lundbeck A/S, Valby, Denmark
| | - M Hotopf
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
| | - B W J H Penninx
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - A Ivan
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - K M White
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - S Difrancesco
- Department of Psychiatry, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - P Locatelli
- Department of Engineering and Applied Science, University of Bergamo, Bergamo, Italy
| | - J Aguiló
- Centros de investigación biomédica en red en el área de bioingeniería, biomateriales y nanomedicina (CIBER-BBN), Madrid, Spain
- Microelectrónica y Sistemas Electrónicos, Universidad Autónoma de Barcelona, CIBERBBN, Barcelona, Spain
| | - M T Peñarrubia-Maria
- Catalan Institute of Health, Primary Care Research Institute (IDIAP Jordi Gol), CIBERESP, Barcelona, Spain
| | - V A Narayan
- Research and Development Information Technology, Janssen Research & Development, LLC, Titusville, NJ, USA
| | - A Folarin
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - D Leightley
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - N Cummins
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - S Vairavan
- Research and Development Information Technology, Janssen Research & Development, LLC, Titusville, NJ, USA
| | - Y Ranjan
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - A Rintala
- Department for Neurosciences, Center for Contextual Psychiatry, Katholieke Universiteit Leuven, Leuven, Belgium
- Faculty of Social Services and Health Care, LAB University of Applied Sciences, Lahti, Finland
| | - G de Girolamo
- IRCCS Instituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - S K Simblett
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - T Wykes
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
| | - I Myin-Germeys
- Department for Neurosciences, Center for Contextual Psychiatry, Katholieke Universiteit Leuven, Leuven, Belgium
| | - R Dobson
- King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, UK
| | - J M Haro
- Parc Sanitari Sant Joan de Déu, Fundació Sant Joan de Déu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain
| |
Collapse
|
3
|
Matcham F, Carr E, White KM, Leightley D, Lamers F, Siddi S, Annas P, de Girolamo G, Haro JM, Horsfall M, Ivan A, Lavelle G, Li Q, Lombardini F, Mohr DC, Narayan VA, Penninx BWHJ, Oetzmann C, Coromina M, Simblett SK, Weyer J, Wykes T, Zorbas S, Brasen JC, Myin-Germeys I, Conde P, Dobson RJB, Folarin AA, Ranjan Y, Rashid Z, Cummins N, Dineley J, Vairavan S, Hotopf M. Predictors of engagement with remote sensing technologies for symptom measurement in Major Depressive Disorder. J Affect Disord 2022; 310:106-115. [PMID: 35525507 DOI: 10.1016/j.jad.2022.05.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/28/2022] [Accepted: 05/02/2022] [Indexed: 01/10/2023]
Abstract
BACKGROUND Remote sensing for the measurement and management of long-term conditions such as Major Depressive Disorder (MDD) is becoming more prevalent. User-engagement is essential to yield any benefits. We tested three hypotheses examining associations between clinical characteristics, perceptions of remote sensing, and objective user engagement metrics. METHODS The Remote Assessment of Disease and Relapse - Major Depressive Disorder (RADAR-MDD) study is a multicentre longitudinal observational cohort study in people with recurrent MDD. Participants wore a FitBit and completed app-based assessments every two weeks for a median of 18 months. Multivariable random effects regression models pooling data across timepoints were used to examine associations between variables. RESULTS A total of 547 participants (87.8% of the total sample) were included in the current analysis. Higher levels of anxiety were associated with lower levels of perceived technology ease of use; increased functional disability was associated with small differences in perceptions of technology usefulness and usability. Participants who reported higher system ease of use, usefulness, and acceptability subsequently completed more app-based questionnaires and tended to wear their FitBit activity tracker for longer. All effect sizes were small and unlikely to be of practical significance. LIMITATIONS Symptoms of depression, anxiety, functional disability, and perceptions of system usability are measured at the same time. These therefore represent cross-sectional associations rather than predictions of future perceptions. CONCLUSIONS These findings suggest that perceived usability and actual use of remote measurement technologies in people with MDD are robust across differences in severity of depression, anxiety, and functional impairment.
Collapse
Affiliation(s)
- F Matcham
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK.
| | - E Carr
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - K M White
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - D Leightley
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - F Lamers
- Department of Psychiatry and Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - S Siddi
- Parc Sanitari Sant Joan de Déu, Fundació San Joan de Déu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain
| | - P Annas
- H. Lundbeck A/S, Valby, Denmark
| | - G de Girolamo
- IRCCS Instituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - J M Haro
- Parc Sanitari Sant Joan de Déu, Fundació San Joan de Déu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain
| | - M Horsfall
- Department of Psychiatry and Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - A Ivan
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - G Lavelle
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - Q Li
- Janssen Research and Development, LLC, Titusville, NJ, USA
| | - F Lombardini
- Parc Sanitari Sant Joan de Déu, Fundació San Joan de Déu, CIBERSAM, Universitat de Barcelona, Barcelona, Spain
| | - D C Mohr
- Center for Behavioral Intervention Technologies, Department of Preventative Medicine, Northwestern University, Chicago, IL, USA
| | - V A Narayan
- Janssen Research and Development, LLC, Titusville, NJ, USA
| | - B W H J Penninx
- Department of Psychiatry and Amsterdam Public Health Research Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - C Oetzmann
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - M Coromina
- Parc Sanitari Joan de Déu, Barcelona, Spain
| | - S K Simblett
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - J Weyer
- RADAR-CNS Patient Advisory Board
| | - T Wykes
- Department of Psychology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK; South London and Maudsley NHS Foundation Trust, London, UK
| | - S Zorbas
- RADAR-CNS Patient Advisory Board
| | | | - I Myin-Germeys
- Department for Neurosciences, Center for Contextual Psychiatry, KU Leuven, Leuven, Belgium
| | - P Conde
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - R J B Dobson
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - A A Folarin
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - Y Ranjan
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - Z Rashid
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - N Cummins
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - J Dineley
- Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK; EIHW - Chair of Embedded Intelligence for Health Care and Wellbeing, University of Augsburg, Augsburg, Germany
| | - S Vairavan
- Janssen Research and Development, LLC, Titusville, NJ, USA
| | - M Hotopf
- Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK; South London and Maudsley NHS Foundation Trust, London, UK
| | | |
Collapse
|
4
|
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, Yao A, Ye J, Zhan M, Zhang W, Zhang H, Zhao Q, Zheng L, Zhong F, Zhong W, Zhu S, Zhao S, Gilbert D, Baumhueter S, Spier G, Carter C, Cravchik A, Woodage T, Ali F, An H, Awe A, Baldwin D, Baden H, Barnstead M, Barrow I, Beeson K, Busam D, Carver A, Center A, Cheng ML, Curry L, Danaher S, Davenport L, Desilets R, Dietz S, Dodson K, Doup L, Ferriera S, Garg N, Gluecksmann A, Hart B, Haynes J, Haynes C, Heiner C, Hladun S, Hostin D, Houck J, Howland T, Ibegwam C, Johnson J, Kalush F, Kline L, Koduru S, Love A, Mann F, May D, McCawley S, McIntosh T, McMullen I, Moy M, Moy L, Murphy B, Nelson K, Pfannkoch C, Pratts E, Puri V, Qureshi H, Reardon M, Rodriguez R, Rogers YH, Romblad D, Ruhfel B, Scott R, Sitter C, Smallwood M, Stewart E, Strong R, Suh E, Thomas R, Tint NN, Tse S, Vech C, Wang G, Wetter J, Williams S, Williams M, Windsor S, Winn-Deen E, Wolfe K, Zaveri J, Zaveri K, Abril JF, Guigó R, Campbell MJ, Sjolander KV, Karlak B, Kejariwal A, Mi H, Lazareva B, Hatton T, Narechania A, Diemer K, Muruganujan A, Guo N, Sato S, Bafna V, Istrail S, Lippert R, Schwartz R, Walenz B, Yooseph S, Allen D, Basu A, Baxendale J, Blick L, Caminha M, Carnes-Stine J, Caulk P, Chiang YH, Coyne M, Dahlke C, Deslattes Mays A, Dombroski M, Donnelly M, Ely D, Esparham S, Fosler C, Gire H, Glanowski S, Glasser K, Glodek A, Gorokhov M, Graham K, Gropman B, Harris M, Heil J, Henderson S, Hoover J, Jennings D, Jordan C, Jordan J, Kasha J, Kagan L, Kraft C, Levitsky A, Lewis M, Liu X, Lopez J, Ma D, Majoros W, McDaniel J, Murphy S, Newman M, Nguyen T, Nguyen N, Nodell M, Pan S, Peck J, Peterson M, Rowe W, Sanders R, Scott J, Simpson M, Smith T, Sprague A, Stockwell T, Turner R, Venter E, Wang M, Wen M, Wu D, Wu M, Xia A, Zandieh A, Zhu X. The sequence of the human genome. Science 2001; 291:1304-51. [PMID: 11181995 DOI: 10.1126/science.1058040] [Citation(s) in RCA: 7678] [Impact Index Per Article: 333.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.
Collapse
Affiliation(s)
- J C Venter
- Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
5
|
Narayan VA, Kriwacki RW, Caradonna JP. Structures of zinc finger domains from transcription factor Sp1. Insights into sequence-specific protein-DNA recognition. J Biol Chem 1997; 272:7801-9. [PMID: 9065444 DOI: 10.1074/jbc.272.12.7801] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The carboxyl terminus of transcription factor Sp1 contains three contiguous Cys2-His2 zinc finger domains with the consensus sequence Cys-X2-4-Cys-X12-His-X3-His. We have used standard homonuclear two-dimensional NMR techniques to solve the solution structures of synthetic peptides corresponding to the last two zinc finger domains (Sp1f2 and Sp1f3, respectively) of Sp1. Our studies indicate a classical Cys2-His2 type fold for both the domains differing from each other primarily in the conformation of Cys-X2-Cys (beta-type I turn) and Cys-X4-Cys (beta-type II turn) elements. There are, however, no significant differences in the metal binding properties between the Cys-X4-Cys (Sp1f2) and Cys-X2-Cys (Sp1f3) subclasses of zinc fingers. The free solution structures of Sp1f2 and Sp1f3 are very similar to those of the analogous fingers of Zif268 bound to DNA. There is NMR spectral evidence suggesting that the Arg-Asp buttressing interaction observed in the Zif-268.DNA complex is also preserved in unbound Sp1f2 and Sp1f3. Modeling Sp1-DNA complex by overlaying the Sp1f2 and Sp1f3 structures on Zif268 fingers 1 and 2, respectively, predicts the role of key amino acid residues, the interference/protection data, and supports the model of Sp1-DNA interaction proposed earlier.
Collapse
Affiliation(s)
- V A Narayan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
| | | | | |
Collapse
|
6
|
Abstract
Transition metal complexes of a number of 1-substituted tetrazoline-5-thiones have been prepared and their infrared spectra examined in the 3 600 – 500 cm−1 region. The analytical applications of 1-substituted tetrazoline-5-thiones for the gravimetric determination of cadmium and palladium have been studied.
Collapse
|
7
|
|