1
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Zhang P, Abudukelimu N, Sali A, Chen JX, Li M, Mao YY, Zhu Y, Zhu QX. Sociodemographic features associated with the MoCA, SPPB, and GDS scores in a community-dwelling elderly population. BMC Geriatr 2023; 23:557. [PMID: 37704972 PMCID: PMC10500811 DOI: 10.1186/s12877-023-04162-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 07/11/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND An accurate evaluation of cognitive function, physical health, and psychological health is fundamental for assessing health problems in the elderly population, and it is important to identify the necessity of early therapeutic intervention. The objective of this study was to evaluate the states of mental and physical functions and to investigate the relationships between sociodemographic features and these functions in a community-dwelling elderly population. METHODS This community-based cross-sectional study was conducted in a suburban district of Shanghai, China. A total of 1025 participants aged 60-89 years underwent investigations of demographic and lifestyle features and a multidimensional geriatric evaluation comprising the Montreal Cognitive Assessment (MoCA), Short Physical Performance Battery (SPPB), and Geriatric Depression Scale (GDS). RESULTS The results of the multivariate linear regression models demonstrated that the MoCA and SPPB scores decreased with advancing age (all P < 0.01). However, the GDS score did not exhibit an age-related decrease (P = 0.09). Both sex and living alone influenced the MoCA score (P < 0.01 and P = 0.04, respectively), SPPB score (P < 0.01 and P = 0.04, respectively), and GDS score (P < 0.01 and P < 0.01, respectively). A higher education level was related to better MoCA and SPPB scores (all P < 0.01). Furthermore, age and sex had interactive effects on the MoCA score (P = 0.03) and SPPB score (P < 0.01). The kernel-weighted local polynomial smoothing curves exhibited similar trends. CONCLUSIONS It is imperative to develop a more sensitive evaluation of physical function, and to encourage various intellectually and emotionally stimulating social activity strategies to promote healthy aging, especially in elderly women and those living alone who have a low education level.
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Affiliation(s)
- Peng Zhang
- School of Management, Hainan Medical University, Haikou, Hainan, 571199, China
| | - Nazhakaiti Abudukelimu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Ayijiamal Sali
- Department of Medicine, Kashgar Vocational and Technical College, Kashgar, Xinjiang Uygur Autonomous Region, 844099, China
| | - Jin-Xia Chen
- Emergency Department, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212000, China
| | - Min Li
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yan-Yan Mao
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yi Zhu
- Emergency Department, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, 212000, China.
- School of Clinical Medicine, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.
| | - Qian-Xi Zhu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China.
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2
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Ed-Dahmouny A, Zeiri N, Fakkahi A, Arraoui R, Jaouane M, Sali A, Es-Sbai N, El-Bakkari K, Duque C. Impurity photo-ionization cross section and stark shift of ground and two low-lying excited electron-states in a core/shell ellipsoidal quantum dot. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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3
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Menon S, Shah A, Sali A, Prakash G, Bakshi G, Pal M, Joshi A, Murthy V, Maitre P, Arora A, Desai S. Concordance of histological grade between pre-operative biopsy and resection specimen in penile squamous cell carcinoma. EUR UROL SUPPL 2022. [DOI: 10.1016/s2666-1683(22)02457-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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4
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Ballas L, Aron M, Xiong Y, McCarthy S, Phuong C, Sali A, Chen M, Clark E, Tsao-Wei D, Dorff T, Bhanvadia S, Magliocco A, Daneshmand S. Can Bladder Cancer Biomarkers from Patients Undergoing Cystectomy Predict the Need for Adjuvant Radiotherapy? Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.1941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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5
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Raja Abdullah R, Salah A, Alnaeb A, Sali A, Abd Rashid N, Ibrahim I. Micro‐Doppler detection in forward scattering radar: theoretical analysis and experiment. Electron lett 2017; 53:426-428. [DOI: 10.1049/el.2016.4163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Affiliation(s)
- R.S.A. Raja Abdullah
- Wireless and Photonic Network Research Center, Faculty of EngineeringUniversiti Putra MalaysiaSerdang43400SelangorMalaysia
| | - A.A. Salah
- Wireless and Photonic Network Research Center, Faculty of EngineeringUniversiti Putra MalaysiaSerdang43400SelangorMalaysia
| | - A.A. Alnaeb
- Wireless and Photonic Network Research Center, Faculty of EngineeringUniversiti Putra MalaysiaSerdang43400SelangorMalaysia
| | - A. Sali
- Wireless and Photonic Network Research Center, Faculty of EngineeringUniversiti Putra MalaysiaSerdang43400SelangorMalaysia
| | - N.E. Abd Rashid
- Faculty of Electrical EngineeringUniversiti Teknologi MARA (UiTM)40450Shah AlamSelangorMalaysia
| | - I.P. Ibrahim
- Faculty of Electrical EngineeringUniversiti Teknologi MARA (UiTM)40450Shah AlamSelangorMalaysia
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6
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Umar IA, Mohd Hanapi Z, Sali A, Zulkarnain ZA. FuGeF: A Resource Bound Secure Forwarding Protocol for Wireless Sensor Networks. Sensors (Basel) 2016; 16:s16060943. [PMID: 27338411 PMCID: PMC4934368 DOI: 10.3390/s16060943] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/04/2016] [Accepted: 05/23/2016] [Indexed: 11/16/2022]
Abstract
Resource bound security solutions have facilitated the mitigation of spatio-temporal attacks by altering protocol semantics to provide minimal security while maintaining an acceptable level of performance. The Dynamic Window Secured Implicit Geographic Forwarding (DWSIGF) routing protocol for Wireless Sensor Network (WSN) has been proposed to achieve a minimal selection of malicious nodes by introducing a dynamic collection window period to the protocol’s semantics. However, its selection scheme suffers substantial packet losses due to the utilization of a single distance based parameter for node selection. In this paper, we propose a Fuzzy-based Geographic Forwarding protocol (FuGeF) to minimize packet loss, while maintaining performance. The FuGeF utilizes a new form of dynamism and introduces three selection parameters: remaining energy, connectivity cost, and progressive distance, as well as a Fuzzy Logic System (FLS) for node selection. These introduced mechanisms ensure the appropriate selection of a non-malicious node. Extensive simulation experiments have been conducted to evaluate the performance of the proposed FuGeF protocol as compared to DWSIGF variants. The simulation results show that the proposed FuGeF outperforms the two DWSIGF variants (DWSIGF-P and DWSIGF-R) in terms of packet delivery.
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Affiliation(s)
- Idris Abubakar Umar
- Department of Wireless and Communication Technology, Faculty of Computer Science and Information Technolog, University Putra Malaysia, Serdang 43400, Malaysia.
| | - Zurina Mohd Hanapi
- Department of Wireless and Communication Technology, Faculty of Computer Science and Information Technolog, University Putra Malaysia, Serdang 43400, Malaysia.
| | - A Sali
- Research Centre of Excellence for Wireless and Photonic Network (WIPNET), Department of Computer and Communication Systems Engineering, Faculty of Engineering, University Putra Malaysia, Serdang 43400, Malaysia.
| | - Zuriati A Zulkarnain
- Department of Wireless and Communication Technology, Faculty of Computer Science and Information Technolog, University Putra Malaysia, Serdang 43400, Malaysia.
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7
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Al-omari M, Ramli AR, Sali A, Azmir RS. A Femtocell Cross-Tier Interference Mitigation Technique in OFDMA-LTE System: A Cuckoo Search based Approach. Indian Journal of Science and Technology 2016; 9. [DOI: 10.17485/ijst/2016/v9i2/80490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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8
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Lasater EA, Massi ES, Stecula A, Politi J, Tan SK, Smith CC, Gunthorpe M, Holmes JP, Chehab F, Sali A, Shah NP. Novel TKI-resistant BCR-ABL1 gatekeeper residue mutations retain in vitro sensitivity to axitinib. Leukemia 2015; 30:1405-9. [PMID: 26511402 DOI: 10.1038/leu.2015.303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- E A Lasater
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - E S Massi
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - A Stecula
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - J Politi
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - S K Tan
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - C C Smith
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - M Gunthorpe
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - J P Holmes
- Annadel Medical Group, Santa Rosa, CA, USA
| | - F Chehab
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - A Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA
| | - N P Shah
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA.,Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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9
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Smith CC, Lin K, Stecula A, Sali A, Shah NP. FLT3 D835 mutations confer differential resistance to type II FLT3 inhibitors. Leukemia 2015; 29:2390-2. [PMID: 26108694 PMCID: PMC4675689 DOI: 10.1038/leu.2015.165] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 12/04/2022]
Affiliation(s)
- C C Smith
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - K Lin
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA
| | - A Stecula
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - A Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
| | - N P Shah
- Division of Hematology/Oncology, University of California, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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10
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Marx W, Ried K, Sali A, Vitetta L, McKavanagh D, McCarthy A, Isenring E. Ginger – Mechanism of action in chemotherapy-induced nausea and vomiting: A review. Journal of Nutrition & Intermediary Metabolism 2014. [DOI: 10.1016/j.jnim.2014.10.168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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11
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Zaidan A, Ahmad N, Abdul Karim H, Larbani M, Zaidan B, Sali A. On the multi-agent learning neural and Bayesian methods in skin detector and pornography classifier: An automated anti-pornography system. Neurocomputing 2014. [DOI: 10.1016/j.neucom.2013.10.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Webb B, Eswar N, Fan H, Khuri N, Pieper U, Dong G, Sali A. Comparative Modeling of Drug Target Proteins☆. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering 2014. [PMCID: PMC7157477 DOI: 10.1016/b978-0-12-409547-2.11133-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this perspective, we begin by describing the comparative protein structure modeling technique and the accuracy of the corresponding models. We then discuss the significant role that comparative prediction plays in drug discovery. We focus on virtual ligand screening against comparative models and illustrate the state-of-the-art by a number of specific examples.
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13
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Abstract
The 386 human SLC superfamily members are diverse in sequence, structure, and function. Using sequence similarity, we previously classified the SLC superfamily members and identified relationships among families. With the recent determination of new SLC structures and identification of previously unknown human SLC families, an update of our previous classification is timely. Here, we comprehensively compare the SLC sequences and structures and discuss the applicability of structure-based ligand discovery to key SLC members.
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Affiliation(s)
- A Schlessinger
- Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine, New York, New York, USA.
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14
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Pipingas A, Camfield DA, Stough C, Cox KHM, Fogg E, Tiplady B, Sarris J, White DJ, Sali A, Wetherell MA, Scholey AB. The effects of multivitamin supplementation on mood and general well-being in healthy young adults. A laboratory and at-home mobile phone assessment. Appetite 2013; 69:123-36. [PMID: 23727255 DOI: 10.1016/j.appet.2013.05.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 05/13/2013] [Accepted: 05/21/2013] [Indexed: 10/26/2022]
Abstract
Previous research has suggested that multivitamin (MV) supplementation may be associated with beneficial effects for mood and general well-being, although treatment durations have typically been less than 90 days, samples have often been restricted to males only and acute effects have not been adequately differentiated from chronic effects. In the current study a MV supplement containing high levels of B-vitamins was administered daily to 138 healthy young adult participants between the ages of 20 and 50 years over a 16-week period. Chronic mood measures (GHQ-28, POMS, Chalder fatigue, PILL, Bond-Lader and custom visual analogue scales) were administered pre-dose at baseline, 8- and 16-weeks. Changes in Bond-Lader and VAS in response to a multi-tasking framework (MTF) were also assessed at 8- and 16-weeks. For a subset of participants, at-home mobile-phone assessments of mood were assessed on a weekly basis using Bond-Lader and VAS. No significant treatment effects were found for any chronic laboratory mood measures. In response to the MTF, a significant treatment x time interaction was found for STAI-S, with a trend towards a greater increase in stress ratings for male participants in the MV group at 16 weeks. However, this finding may have been attributable to a larger proportion of students in the male MV group. In contrast, at-home mobile-phone assessments, where assessments were conducted post-dose, revealed significantly reduced stress, physical fatigue and anxiety in the MV group in comparison to placebo across a number of time points. Further research using both acute and chronic dosing regimens are required in order to properly differentiate these effects.
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Affiliation(s)
- A Pipingas
- Centre for Human Psychopharmacology, Swinburne University, Mail H24, PO Box 218, Hawthorn, Victoria 3122, Australia.
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15
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Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JDB. Strategic protein target analysis for developing drugs to stop dental caries. Adv Dent Res 2013; 24:86-93. [PMID: 22899687 DOI: 10.1177/0022034512449837] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Dental caries is the most common disease to cause irreversible damage in humans. Several therapeutic agents are available to treat or prevent dental caries, but none besides fluoride has significantly influenced the disease burden globally. Etiologic mechanisms of the mutans group streptococci and specific Lactobacillus species have been characterized to various degrees of detail, from identification of physiologic processes to specific proteins. Here, we analyze the entire Streptococcus mutans proteome for potential drug targets by investigating their uniqueness with respect to non-cariogenic dental plaque bacteria, quality of protein structure models, and the likelihood of finding a drug for the active site. Our results suggest specific targets for rational drug discovery, including 15 known virulence factors, 16 proteins for which crystallographic structures are available, and 84 previously uncharacterized proteins, with various levels of similarity to homologs in dental plaque bacteria. This analysis provides a map to streamline the process of clinical development of effective multispecies pharmacologic interventions for dental caries.
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Affiliation(s)
- J A Horst
- Division of Pediatric Dentistry, Department of Orofacial Sciences, University of California, San Francisco, CA, USA.
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16
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Abstract
Funders, publishers, and research institutions must act to ensure that research computer code is made widely available.
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Affiliation(s)
- A. Morin
- Harvard Medical School, Boston, MA 02115, USA
| | - J. Urban
- School of Law, University of California, Berkeley, Berkeley, CA 94720, USA
| | - P. D. Adams
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - I. Foster
- Argonne National Laboratory and University of Chicago, Argonne, IL 60439, USA
| | - A. Sali
- University of California, San Francisco, San Francisco, CA 94158, USA
| | - D. Baker
- University of Washington and Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - P. Sliz
- Harvard Medical School, Boston, MA 02115, USA
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17
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Pipigas A, Silberstein R, Sali A, Vitetta L. Homocysteine modifies event related steady state potential coherence in a recognition memory task. Int J Psychophysiol 2008. [DOI: 10.1016/j.ijpsycho.2008.05.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Abstract
In this perspective, we begin by describing the comparative protein structure modeling technique and the accuracy of the corresponding models. We then discuss the significant role that comparative prediction plays in drug discovery. We focus on virtual ligand screening against comparative models and illustrate the state of the art by a number of specific examples.
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Abstract
Long before the fountain of youth, mankind has had an interest in staying young. As we move into the 21st century, that interest has not only continued, but it has become an obsession. While no one can really prevent normal, chronological aging, there are things we can do to slow down "pathological aging." After all, aging is about accelerated inflammation, depletion, and wear and tear. With the marked increase in life expectancy and life span, clinicians need to be aware of the effects of aging on the provision of treatment modalities. Appropriate interventions individualized to the patient can help to "compress morbidity" by shortening the period of functional decline common in old age. Therefore, the "health span" will come closer to matching the life span. Disease and disuse are far more likely explanations for functional decline and the onset of common chronic conditions in older persons than is "true" natural or normal aging. Regardless of your genetic inheritance, you can accelerate aging by lifestyle choices and environmental conditions to which you expose your genes. There are even ways to reverse the problems associated with aging. Getting older does not have to mean growing older. Welcome to the world of preventative gerontology, better known as anti-aging medicine!
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Affiliation(s)
- B Anton
- Path Lab, Melbourne, Australia.
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20
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Thomsen M, Schmidt M, Vitetta L, Sali A. Do herbs increase the risk of herb-drug interactions for patients with arthritis? Ann Rheum Dis 2005; 64:1527; author reply 1528. [PMID: 16162912 PMCID: PMC1755246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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21
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Sali A, Topf M, Baker ML, Chiu W. Structure of protein assemblies by comparative modeling and electron microscopy. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305099897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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22
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Abstract
During evolution, DNA viruses have captured a broad array of cellular genes involved in immune recognition and growth control that are nonessential for viral replication. The encoded virokines and viroceptors may act as mimetics or antagonists of their cellular homologues, altering signal transduction and cell communication towards survival of virus-infected cells. Human herpesvirus type 8 (HHV8) is the most recently identified human oncogenic herpesvirus. It is associated with Kaposi's sarcoma and lymphoproliferative diseases, such as pleural effusion lymphomas and multicentric Castleman's disease. HHV8 has captured a unique number of cellular regulatory genes, which redirect gene expression and cell growth, prevent apoptosis and immune recognition, and interfere with tumor suppressor gene function. HHV8 encodes a unique virokine, viral interleukin-6, which is particularly relevant for the pathogenesis of HHV8-associated tumors, since it participates in transformation and mediates autocrine and paracrine mitogenic and proinflammatory effects. Viral IL-6 differs fundamentally from human IL-6 in receptor engagement for signal transduction and thus constitutes a singular model to understand the facets of human and viral cytokine biology. We provide an overview of the role of virokines in cancer, with a particular focus on the differences of human and viral IL-6 in the pathophysiology of HHV8-associated tumors.
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Affiliation(s)
- L Vitetta
- Centre for Molecular Biology and Medicine, Epworth Medical Centre, 185-187 Hoddle St. Richmond, Melbourne, Victoria, Australia 3121.
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23
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Abstract
Automated functional annotation of nsSNPs requires that amino-acid residue changes are represented by a set of descriptive features, such as evolutionary conservation, side-chain volume change, effect on ligand-binding, and residue structural rigidity. Identifying the most informative combinations of features is critical to the success of a computational prediction method. We rank 32 features according to their mutual information with functional effects of amino-acid substitutions, as measured by in vivo assays. In addition, we use a greedy algorithm to identify a subset of highly informative features. The method is simple to implement and provides a quantitative measure for selecting the best predictive features given a set of features that a human expert believes to be informative. We demonstrate the usefulness of the selected highly informative features by cross-validated tests of a computational classifier, a support vector machine (SVM). The SVM's classification accuracy is highly correlated with the ranking of the input features by their mutual information. Two features describing the solvent accessibility of "wild-type" and "mutant" amino-acid residues and one evolutionary feature based on superfamily-level multiple alignments produce comparable overall accuracy and 6% fewer false positives than a 32-feature set that considers physiochemical properties of amino acids, protein electrostatics, amino-acid residue flexibility, and binding interactions.
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Affiliation(s)
- R Karchin
- Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94143-2240, USA
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24
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Sali A, Eswar N, Pieper U, Marti-Renom MA, Madhusudhan M, Fiser A, Ilyin V. Comparative protein structure modeling of genes and genomes. Acta Crystallogr A 2002. [DOI: 10.1107/s0108767302087068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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25
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Banakh I, Sali A, Dubljevic V, Grobben B, Slegers H, Goding JW. Structural basis of allotypes of ecto-nucleotide pyrophosphatase/phosphodiesterase (plasma cell membrane glycoprotein PC-1) in the mouse and rat, and analysis of allele-specific xenogeneic antibodies. Eur J Immunogenet 2002; 29:307-13. [PMID: 12121276 DOI: 10.1046/j.1365-2370.2002.00330.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ecto-nucleotide pyrophosphatase/phosphodiesterases (E-NPPs) have been implicated in bone calcification, type II diabetes, control of purinergic signalling and tumour invasion. The gene for the plasma cell membrane glycoprotein PC-1 in the mouse (Enpp1) has been known since 1970 to exist in two allelic forms, but their structural basis was heretofore unknown. We show that the Enpp1a and Enpp1b alleles differ by only two amino acids, at positions 650 and 679 in the C-terminal nuclease-like domain. Histidine 650 but not arginine 679 forms an essential part of the Enpp1a epitope recognized by monoclonal antibody IR-518. Sequences of LEW and LOU rats and the rat glioma cell line C6 differ from that of the mouse by about 60 amino acids. The LOU and C6 cell line sequences differ by only three amino acids, but differ from the LEW sequence by 10 amino acids. All three rat strains possess the mouse Enpp1b allele at positions 650 and 679. Despite numerous other differences from the mouse, rats immunized with Enpp1a mouse cells have generated monoclonal antibodies specific for the Enpp1a allele, suggesting that amino acids 650 and 679 may be particularly immunogenic. The cytoplasmic tails of the mouse and rat are highly conserved, but are significantly different from human cytoplasmic tails.
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Affiliation(s)
- I Banakh
- Deparment of Pathology and Immunology, Manash Medical School, Manash University, Prahran, Victoria, Australia
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Wong GW, Yasuda S, Madhusudhan MS, Li L, Yang Y, Krilis SA, Sali A, Stevens RL. Human tryptase epsilon (PRSS22), a new member of the chromosome 16p13.3 family of human serine proteases expressed in airway epithelial cells. J Biol Chem 2001; 276:49169-82. [PMID: 11602603 DOI: 10.1074/jbc.m108677200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [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: 11/06/2022] Open
Abstract
Probing of the GenBank expressed sequence tag (EST) data base with varied human tryptase cDNAs identified two truncated ESTs that subsequently were found to encode overlapping portions of a novel human serine protease (designated tryptase epsilon or protease, serine S1 family member 22 (PRSS22)). The tryptase epsilon gene resides on chromosome 16p13.3 within a 2.5-Mb complex of serine protease genes. Although at least 7 of the 14 genes in this complex encode enzymatically active proteases, only one tryptase epsilon-like gene was identified. The trachea and esophagus were found to contain the highest steady-state levels of the tryptase epsilon transcript in adult humans. Although the tryptase epsilon transcript was scarce in adult human lung, it was present in abundance in fetal lung. Thus, the tryptase epsilon gene is expressed in the airways in a developmentally regulated manner that is different from that of other human tryptase genes. At the cellular level, tryptase epsilon is a major product of normal pulmonary epithelial cells, as well as varied transformed epithelial cell lines. Enzymatically active tryptase epsilon is also constitutively secreted from these cells. The amino acid sequence of human tryptase epsilon is 38-44% identical to those of human tryptase alpha, tryptase beta I, tryptase beta II, tryptase beta III, transmembrane tryptase/tryptase gamma, marapsin, and Esp-1/testisin. Nevertheless, comparative protein structure modeling and functional studies using recombinant material revealed that tryptase epsilon has a substrate preference distinct from that of its other family members. These data indicate that the products of the chromosome 16p13.3 complex of tryptase genes evolved to carry out varied functions in humans.
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Affiliation(s)
- G W Wong
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
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27
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Eyrich VA, Martí-Renom MA, Przybylski D, Madhusudhan MS, Fiser A, Pazos F, Valencia A, Sali A, Rost B. EVA: continuous automatic evaluation of protein structure prediction servers. Bioinformatics 2001; 17:1242-3. [PMID: 11751240 DOI: 10.1093/bioinformatics/17.12.1242] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.5] [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: 11/14/2022] Open
Abstract
UNLABELLED Evaluation of protein structure prediction methods is difficult and time-consuming. Here, we describe EVA, a web server for assessing protein structure prediction methods, in an automated, continuous and large-scale fashion. Currently, EVA evaluates the performance of a variety of prediction methods available through the internet. Every week, the sequences of the latest experimentally determined protein structures are sent to prediction servers, results are collected, performance is evaluated, and a summary is published on the web. EVA has so far collected data for more than 3000 protein chains. These results may provide valuable insight to both developers and users of prediction methods. AVAILABILITY http://cubic.bioc.columbia.edu/eva. CONTACT eva@cubic.bioc.columbia.edu
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Affiliation(s)
- V A Eyrich
- Department of Chemistry, Columbia University, 3000 Broadway MC 3136, New York, NY 10027, USA.
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28
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Bonanno JB, Edo C, Eswar N, Pieper U, Romanowski MJ, Ilyin V, Gerchman SE, Kycia H, Studier FW, Sali A, Burley SK. Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis. Proc Natl Acad Sci U S A 2001; 98:12896-901. [PMID: 11698677 PMCID: PMC60796 DOI: 10.1073/pnas.181466998] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [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: 11/18/2022] Open
Abstract
X-ray structures of two enzymes in the sterol/isoprenoid biosynthesis pathway have been determined in a structural genomics pilot study. Mevalonate-5-diphosphate decarboxylase (MDD) is a single-domain alpha/beta protein that catalyzes the last of three sequential ATP-dependent reactions which convert mevalonate to isopentenyl diphosphate. Isopentenyl disphosphate isomerase (IDI) is an alpha/beta metalloenzyme that catalyzes interconversion of isopentenyl diphosphate and dimethylallyl diphosphate, which condense in the next step toward synthesis of sterols and a host of natural products. Homology modeling of related proteins and comparisons of the MDD and IDI structures with two other experimentally determined structures have shown that MDD is a member of the GHMP superfamily of small-molecule kinases and IDI is similar to the nudix hydrolases, which act on nucleotide diphosphatecontaining substrates. Structural models were produced for 379 proteins, encompassing a substantial fraction of both protein superfamilies. All three enzymes responsible for synthesis of isopentenyl diphosphate from mevalonate (mevalonate kinase, phosphomevalonate kinase, and MDD) share the same fold, catalyze phosphorylation of chemically similar substrates (MDD decarboxylation involves phosphorylation of mevalonate diphosphate), and seem to have evolved from a common ancestor. These structures and the structural models derived from them provide a framework for interpreting biochemical function and evolutionary relationships.
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Affiliation(s)
- J B Bonanno
- Laboratories of Molecular Biophysics, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
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29
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Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, Blobel G, Frank J. Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA-ribosome and subunit-subunit interactions. Cell 2001; 107:373-86. [PMID: 11701127 DOI: 10.1016/s0092-8674(01)00539-6] [Citation(s) in RCA: 382] [Impact Index Per Article: 16.6] [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: 02/05/2023]
Abstract
A cryo-EM reconstruction of the translating yeast 80S ribosome was analyzed. Computationally separated rRNA and protein densities were used for docking of appropriately modified rRNA models and homology models of yeast ribosomal proteins. The core of the ribosome shows a remarkable degree of conservation. However, some significant differences in functionally important regions and dramatic changes in the periphery due to expansion segments and additional ribosomal proteins are evident. As in the bacterial ribosome, bridges between the subunits are mainly formed by RNA contacts. Four new bridges are present at the periphery. The position of the P site tRNA coincides precisely with its prokaryotic counterpart, with mainly rRNA contributing to its molecular environment. This analysis presents an exhaustive inventory of an eukaryotic ribosome at the molecular level.
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MESH Headings
- Base Sequence
- Binding Sites
- Cryoelectron Microscopy/methods
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- RNA
- RNA, Fungal/chemistry
- RNA, Fungal/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 5.8S/chemistry
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Ribosomes/metabolism
- Ribosomes/ultrastructure
- Saccharomyces cerevisiae/genetics
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Affiliation(s)
- C M Spahn
- Howard Hughes Medical Institute, Health Research Inc., Albany, NY 12201, USA
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30
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Beckmann R, Spahn CM, Eswar N, Helmers J, Penczek PA, Sali A, Frank J, Blobel G. Architecture of the protein-conducting channel associated with the translating 80S ribosome. Cell 2001; 107:361-72. [PMID: 11701126 DOI: 10.1016/s0092-8674(01)00541-4] [Citation(s) in RCA: 311] [Impact Index Per Article: 13.5] [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: 11/25/2022]
Abstract
In vitro assembled yeast ribosome-nascent chain complexes (RNCs) containing a signal sequence in the nascent chain were immunopurified and reconstituted with the purified protein-conducting channel (PCC) of yeast endoplasmic reticulum, the Sec61 complex. A cryo-EM reconstruction of the RNC-Sec61 complex at 15.4 A resolution shows a tRNA in the P site. Distinct rRNA elements and proteins of the large ribosomal subunit form four connections with the PCC across a gap of about 10-20 A. Binding of the PCC influences the position of the highly dynamic rRNA expansion segment 27. The RNC-bound Sec61 complex has a compact appearance and was estimated to be a trimer. We propose a binary model of cotranslational translocation entailing only two basic functional states of the translating ribosome-channel complex.
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Affiliation(s)
- R Beckmann
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.
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31
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Vitetta L, Sali A, Reavley NJ. Is coenzyme Q10 helpful for patients with idiopathic cardiomyopathy? Med J Aust 2001; 175:447; author reply 447-8. [PMID: 11700847 DOI: 10.5694/j.1326-5377.2001.tb143668.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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32
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Abstract
Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their structure and function. Although experimental structure determination methods are providing high-resolution structure information about a subset of the proteins, computational structure prediction methods will provide valuable information for the large fraction of sequences whose structures will not be determined experimentally. The first class of protein structure prediction methods, including threading and comparative modeling, rely on detectable similarity spanning most of the modeled sequence and at least one known structure. The second class of methods, de novo or ab initio methods, predict the structure from sequence alone, without relying on similarity at the fold level between the modeled sequence and any of the known structures. In this Viewpoint, we begin by describing the essential features of the methods, the accuracy of the models, and their application to the prediction and understanding of protein function, both for single proteins and on the scale of whole genomes. We then discuss the important role that protein structure prediction methods play in the growing worldwide effort in structural genomics.
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Affiliation(s)
- D Baker
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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33
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Borodovsky M, Koonin E, Burge C, Fickett J, Logsdon J, Sali A, Stormo G, Zhulin I. THE THIRD GEORGIA TECH-EMORY INTERNATIONAL CONFERENCE ON BIOINFORMATICS: IN SILICO BIOLOGY; BIOINFORMATICS AFTER HUMAN GENOME (NOVEMBER 15-18, 2001, ATLANTA, GEORGIA, USA). Bioinformatics 2001. [DOI: 10.1093/bioinformatics/17.10.859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Bello V, Goding JW, Greengrass V, Sali A, Dubljevic V, Lenoir C, Trugnan G, Maurice M. Characterization of a di-leucine-based signal in the cytoplasmic tail of the nucleotide-pyrophosphatase NPP1 that mediates basolateral targeting but not endocytosis. Mol Biol Cell 2001; 12:3004-15. [PMID: 11598187 PMCID: PMC60151 DOI: 10.1091/mbc.12.10.3004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [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: 12/23/2022] Open
Abstract
Enzymes of the nucleotide pyrophosphatase/phosphodiesterase (NPPase) family are expressed at opposite surfaces in polarized epithelial cells. We investigated the targeting signal of NPP1, which is exclusively expressed at the basolateral surface. Full-length NPP1 and different constructs and mutants were transfected into the polarized MDCK cell line. Expression of the proteins was analyzed by confocal microscopy and surface biotinylation. The basolateral signal of NPP1 was identified as a di-leucine motif located in the cytoplasmic tail. Mutation of either or both leucines largely redirected NPP1 to the apical surface. Furthermore, addition of the conserved sequence AAASLLAP redirected the apical nucleotide pyrophosphatase/phosphodiesterase NPP3 to the basolateral surface. Full-length NPP1 was not significantly internalized. However, when the cytoplasmic tail was deleted upstream the di-leucine motif or when the six upstream flanking amino acids were deleted, the protein was mainly found intracellularly. Endocytosis experiments indicated that these mutants were endocytosed from the basolateral surface. These results identify the basolateral signal of NPP1 as a short sequence including a di-leucine motif that is dominant over apical determinants and point to the importance of surrounding amino acids in determining whether the signal will function as a basolateral signal only or as an endocytotic signal as well.
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Affiliation(s)
- V Bello
- U538 INSERM, CHU St-Antoine, 75571 Paris Cedex 12, France
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35
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Vitetta L, Kenner D, Kissane D, Sali A. Clinical outcomes in terminally ill patients admitted to hospice care: diagnostic and therapeutic interventions. J Palliat Care 2001; 17:69-77. [PMID: 11477988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
This study's aim was to determine the impact of medical technologies on patient comfort and survival time, through retrospective review of the clinical course, symptom profile, and illness trajectory in 102 consecutive patients (50 males and 52 females), and of diagnostic and therapeutic interventions delivered to them. The average age of males was 72.3 years and of females 73.1 years. Ninety-four patients were admitted for palliation of symptoms due to malignant disease and eight other patients for non-malignant diseases. The median survival time was 12 days. On admission, higher univariate hazard risks for survival were significantly associated with male gender, metastatic disease, and dyspnea. Higher adjusted Charlson comorbidity scores were associated with significantly decreased survival time, while de novo symptoms and diagnostic interventions were associated with lower univariate risk rates and increased survival times. Palliative therapeutic interventions were not significantly associated with increased patient survival. A multivariate analysis showed that pain, dyspnea, immobility, and adjusted Charlson comorbidity scores were independent risks for shorter patient survival times. Diagnostic interventions were significant for increased patient survival. No requests for euthanasia had been recorded, which may, in part, reflect the significant family support most of these patients had received.
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Affiliation(s)
- L Vitetta
- Graduate School of Integrative Medicine, Swinburne University, Melbourne, Australia
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36
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Abstract
SUMMARY The DBAli database includes approximately 35000 alignments of pairs of protein structures from SCOP (Lo Conte et al., Nucleic Acids Res., 28, 257-259, 2000) and CE (Shindyalov and Bourne, Protein Eng., 11, 739-747, 1998). DBAli is linked to several resources, including Compare3D (Shindyalov and Bourne, http://www.sdsc.edu/pb/software.htm, 1999) and ModView (Ilyin and Sali, http://guitar.rockefeller.edu/ModView/, 2001) for visualizing sequence alignments and structure superpositions. A flexible search of DBAli by protein sequence and structure properties allows construction of subsets of alignments suitable for a number of applications, such as benchmarking of sequence-sequence and sequence-structure alignment methods under a variety of conditions. AVAILABILITY http://guitar.rockefeller.edu/DBAli/
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Affiliation(s)
- M A Martí-Renom
- Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Ave, New York, NY 10021, USA
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37
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38
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39
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Wong GW, Li L, Madhusudhan MS, Krilis SA, Gurish MF, Rothenberg ME, Sali A, Stevens RL. Tryptase 4, a new member of the chromosome 17 family of mouse serine proteases. J Biol Chem 2001; 276:20648-58. [PMID: 11259427 DOI: 10.1074/jbc.m010422200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [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: 11/06/2022] Open
Abstract
Genomic blot analysis raised the possibility that uncharacterized tryptase genes reside on chromosome 17 at the complex containing the three genes that encode mouse mast cell protease (mMCP) 6, mMCP-7, and transmembrane tryptase (mTMT). Probing of GenBank's expressed sequence tag data base with these three tryptase cDNAs resulted in the identification of an expressed sequence tag that encodes a portion of a novel mouse serine protease (now designated mouse tryptase 4 (mT4) because it is the fourth member of this family). 5'- and 3'-rapid amplification of cDNA ends approaches were carried out to deduce the nucleotide sequence of the full-length mT4 transcript. This information was then used to clone its approximately 5.0-kilobase pair gene. Chromosome mapping analysis of its gene, sequence analysis of its transcript, and comparative protein structure modeling of its translated product revealed that mT4 is a new member of the chromosome 17 family of mouse tryptases. mT4 is 40-44% identical to mMCP-6, mMCP-7, and mTMT, and this new serine protease has all of the structural features of a functional tryptase. Moreover, mT4 is enzymatically active when expressed in insect cells. Due to its 17-mer hydrophobic domain at its C terminus, mT4 is a membrane-anchored tryptase more analogous to mTMT than the other members of its family. As assessed by RNA blot, reverse transcriptase-polymerase chain reaction, and/or in situ hybridization analysis, mT4 is expressed in interleukin-5-dependent mouse eosinophils, as well as in ovaries and testes. The observation that recombinant mT4 is preferentially retained in the endoplasmic reticulum of transiently transfected COS-7 cells suggests a convertase-like role for this integral membrane serine protease.
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Affiliation(s)
- G W Wong
- Department of Medicine, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA
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40
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Glas R, Reavley N, Mrazek L, Vitetta L, Sali A. Psychosocial interventions and cancer patients: psychological and immune responses may depend on cancer type. Med Hypotheses 2001; 56:480-2. [PMID: 11339851 DOI: 10.1054/mehy.2000.1205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [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: 11/18/2022]
Abstract
Psychological and immunological responses of cancer patients to a psychosocial intervention program will be assessed over time. Previously it has been proposed that there are two large divisions in cancer histology (type I and II) and that the psychobiology of patients will vary accordingly.
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Affiliation(s)
- R Glas
- Graduate School of Medicine, Swinburne University, Melbourne, Victoria, Australia
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41
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Affiliation(s)
- R Sánchez
- Laboratories of Molecular Biophysics, Rockefeller University, New York, NY, USA
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42
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Gopal S, Schroeder M, Pieper U, Sczyrba A, Aytekin-Kurban G, Bekiranov S, Fajardo JE, Eswar N, Sanchez R, Sali A, Gaasterland T. Homology-based annotation yields 1,042 new candidate genes in the Drosophila melanogaster genome. Nat Genet 2001; 27:337-40. [PMID: 11242120 DOI: 10.1038/85922] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [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: 11/09/2022]
Abstract
The approach to annotating a genome critically affects the number and accuracy of genes identified in the genome sequence. Genome annotation based on stringent gene identification is prone to underestimate the complement of genes encoded in a genome. In contrast, over-prediction of putative genes followed by exhaustive computational sequence, motif and structural homology search will find rarely expressed, possibly unique, new genes at the risk of including non-functional genes. We developed a two-stage approach that combines the merits of stringent genome annotation with the benefits of over-prediction. First we identify plausible genes regardless of matches with EST, cDNA or protein sequences from the organism (stage 1). In the second stage, proteins predicted from the plausible genes are compared at the protein level with EST, cDNA and protein sequences, and protein structures from other organisms (stage 2). Remote but biologically meaningful protein sequence or structure homologies provide supporting evidence for genuine genes. The method, applied to the Drosophila melanogaster genome, validated 1,042 novel candidate genes after filtering 19,410 plausible genes, of which 12,124 matched the original 13,601 annotated genes. This annotation strategy is applicable to genomes of all organisms, including human.
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Affiliation(s)
- S Gopal
- Laboratories of Computational Genomics, The Rockefeller University, New York, New York, USA
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43
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Barrientos LG, Campos-Olivas R, Louis JM, Fiser A, Sali A, Gronenborn AM. 1H, 13C, 15N resonance assignments and fold verification of a circular permuted variant of the potent HIV-inactivating protein cyanovirin-N. J Biomol NMR 2001; 19:289-290. [PMID: 11330821 DOI: 10.1023/a:1011292919947] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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44
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Abstract
Comparative modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. The number of protein sequences that can be modeled and the accuracy of the predictions are increasing steadily because of the growth in the number of known protein structures and because of the improvements in the modeling software. Further advances are necessary in recognizing weak sequence-structure similarities, aligning sequences with structures, modeling of rigid body shifts, distortions, loops and side chains, as well as detecting errors in a model. Despite these problems, it is currently possible to model with useful accuracy significant parts of approximately one third of all known protein sequences. The use of individual comparative models in biology is already rewarding and increasingly widespread. A major new challenge for comparative modeling is the integration of it with the torrents of data from genome sequencing projects as well as from functional and structural genomics. In particular, there is a need to develop an automated, rapid, robust, sensitive, and accurate comparative modeling pipeline applicable to whole genomes. Such large-scale modeling is likely to encourage new kinds of applications for the many resulting models, based on their large number and completeness at the level of the family, organism, or functional network.
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Affiliation(s)
- M A Martí-Renom
- Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, Rockefeller University, New York, NY 10021, USA
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45
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Abstract
Ribosome anti-association factor eIF6 (originally named according to translation initiation terminology as eukaryotic initiation factor 6) binds to the large ribosomal subunit, thereby preventing inappropriate interactions with the small subunit during initiation of protein synthesis. We have determined the X-ray structures of two IF6 homologs, Methanococcus jannaschii archaeal aIF6 and Sacchromyces cerevisiae eIF6, revealing a phylogenetically conserved 25 kDa protein consisting of five quasi identical alpha/beta subdomains arrayed about a five-fold axis of pseudosymmetry. Yeast eIF6 prevents ribosomal subunit association. Comparative protein structure modeling with other known archaeal and eukaryotic homologs demonstrated the presence of two conserved surface regions, one or both of which may bind the large ribosomal subunit.
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Affiliation(s)
- C M Groft
- Laboratories of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
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46
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Abstract
Single and multiple cholesterol gallstones constitute at least 80% of the gallstone population observed at cholecystectomy in Western countries. While supersaturation of bile with cholesterol is necessary for gallstone growth, the kinetic determinant of crystal nucleation is perhaps the critical factor leading to the incidence of gallstones. Nucleation involves aggregation of nidus-forming materials like pigment precipitates and mucus proteins. In combination with cholesterol precipitates and crystal formation, gallstone propagation is enhanced. Bacterial species may augment the process of nucleation and gallstone growth by contributing specific enzyme activities resulting in the formation of insoluble precipitates in bile, or by acting as a nidus upon which the deposition of cholesterol crystals may initiate gallstone formation. The utilization of Raman microscopic techniques permits detailed mapping of the distribution of the gallstone components leading to identification and characterization of the site of nucleation. This, when coupled to molecular genetic tools such as PCR DNA amplification, would permit elucidation of the role of bacteria in vivo gallstone propagation mechanisms.
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Affiliation(s)
- L Vitetta
- Graduate School of Integrative Medicine, Swinburne University, Hawthorn, Victoria, Australia.
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47
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Nathan PJ, Sitaram G, Stough C, Silberstein RB, Sali A. Serotonin, noradrenaline and cognitive function: a preliminary investigation of the acute pharmacodynamic effects of a serotonin versus a serotonin and noradrenaline reuptake inhibitor. Behav Pharmacol 2000; 11:639-42. [PMID: 11198135 DOI: 10.1097/00008877-200011000-00011] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [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: 11/26/2022]
Abstract
Comparisons of the behavioural side-effect profiles of antidepressants that inhibit either serotonin or both serotonin and noradrenaline reuptake, may reveal differences in cognitive and psychomotor functions, which may be attributed to their relative pharmacological selectivity for potentiating monoamine neurotransmission in the central nervous system. The aim of the present study was to determine the acute pharmacodynamic effects of citalopram and venlafaxine, on cognitive and psychomotor performance. Nine healthy male volunteers received a single clinical dose of citalopram, venlafaxine or amitriptyline (positive control) in a double-blind placebo-controlled design. Cognitive and psychomotor tests and a subjective measure of sedation were examined before and 1, 2 and 4 hours after drug administration. Citalopram improved psychomotor responses to sensory stimuli and sustained attention, with significant decreases in movement times of the choice reaction time test and an increase in critical flicker fusion threshold. Venlafaxine did not affect performances on any of the cognitive or psychomotor tests examined. Differences may be related to relative potencies of the compounds for monoamine reuptake inhibition.
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Affiliation(s)
- P J Nathan
- Brain Sciences Institute, Swinburne University of Technology, Hawthorn, Australia.
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48
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Sánchez R, Pieper U, Melo F, Eswar N, Martí-Renom MA, Madhusudhan MS, Mirković N, Sali A. Protein structure modeling for structural genomics. Nat Struct Biol 2000; 7 Suppl:986-90. [PMID: 11104007 DOI: 10.1038/80776] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The shapes of most protein sequences will be modeled based on their similarity to experimentally determined protein structures. The current role, limitations, challenges and prospects for protein structure modeling (using information about genes and genomes) are discussed in the context of structural genomics.
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Affiliation(s)
- R Sánchez
- Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, New York 10021, USA
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49
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Abstract
Terminally ill patients are very susceptible to infections, which are the result of disease-related processes and/or therapy-induced mechanisms. These patients are already subject to multiple severe symptoms and associated comorbid conditions, with much resultant distress. Infection increases this symptom burden and further reduces quality of life. We have retrospectively investigated the prevalence of infection and clinical course in 102 consecutive patients who died after admission to a tertiary palliative care unit and assessed the site-specific frequency of infection, pathogenic organisms involved, and the pattern of antibiotic agents used. The prevalence of symptoms and comorbid conditions on admission and during the progress phase of care were noted. Median overall survival of the total cohort was 12 days. The median survival of patients with infections was 22 days. Thirty-seven patients (36.3%) were diagnosed with 42 separate infections. The sites of infections were the urinary tract (42.5%), the respiratory tract (22.9%), blood (12.5%), skin and subcutaneous tissues (12.5%), and the eyes (10.0%). There were 20 separate positive cultures isolated from specimens obtained from 13 individual patients. Three isolates were obtained from 1 patient, 2 isolates obtained from 5 patients, and 1 isolate was obtained from each of the 7 remaining patients. Escherichia coli was the most common pathogen isolated. Eleven patients with infections (31.4%) were diagnosed on admission, and antibiotic treatment was commenced within 48 hours of admission in 21 patients (60%). Overall antibiotic response and symptom control of infections was observed to be a minimum of 40%. Psychological distress was common in this group of patients (P = 0.001) as were disabling symptoms on admission, such as pain, immobility, and weakness. Symptoms indicating poor survival, such as severe pain and dyspnea, were not significantly associated with infection. Decreased patient survival in this cohort was not significantly associated with the presence of bacterial infection (P = 0.07), irrespective of whether or not a positive culture isolate was obtained. We conclude that appropriate management of infection resulted in enhanced palliative symptom control.
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Affiliation(s)
- L Vitetta
- Graduate School of Medicine, Swinburne University, Hawthorn, Victoria, Australia
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50
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Abstract
Comparative protein structure prediction is limited mostly by the errors in alignment and loop modeling. We describe here a new automated modeling technique that significantly improves the accuracy of loop predictions in protein structures. The positions of all nonhydrogen atoms of the loop are optimized in a fixed environment with respect to a pseudo energy function. The energy is a sum of many spatial restraints that include the bond length, bond angle, and improper dihedral angle terms from the CHARMM-22 force field, statistical preferences for the main-chain and side-chain dihedral angles, and statistical preferences for nonbonded atomic contacts that depend on the two atom types, their distance through space, and separation in sequence. The energy function is optimized with the method of conjugate gradients combined with molecular dynamics and simulated annealing. Typically, the predicted loop conformation corresponds to the lowest energy conformation among 500 independent optimizations. Predictions were made for 40 loops of known structure at each length from 1 to 14 residues. The accuracy of loop predictions is evaluated as a function of thoroughness of conformational sampling, loop length, and structural properties of native loops. When accuracy is measured by local superposition of the model on the native loop, 100, 90, and 30% of 4-, 8-, and 12-residue loop predictions, respectively, had <2 A RMSD error for the mainchain N, C(alpha), C, and O atoms; the average accuracies were 0.59 +/- 0.05, 1.16 +/- 0.10, and 2.61 +/- 0.16 A, respectively. To simulate real comparative modeling problems, the method was also evaluated by predicting loops of known structure in only approximately correct environments with errors typical of comparative modeling without misalignment. When the RMSD distortion of the main-chain stem atoms is 2.5 A, the average loop prediction error increased by 180, 25, and 3% for 4-, 8-, and 12-residue loops, respectively. The accuracy of the lowest energy prediction for a given loop can be estimated from the structural variability among a number of low energy predictions. The relative value of the present method is gauged by (1) comparing it with one of the most successful previously described methods, and (2) describing its accuracy in recent blind predictions of protein structure. Finally, it is shown that the average accuracy of prediction is limited primarily by the accuracy of the energy function rather than by the extent of conformational sampling.
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Affiliation(s)
- A Fiser
- Laboratory of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, New York, New York 10021, USA.
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