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Mondal K, Majumdar D, Patel JC, Ragumani S, Sahrawat TR. Potential Determinants of Manual Lifting: Validation of Ergonomic Assessment by Scoping Review Applying Meta-analysis Approach. J Clin Diagn Res 2022. [DOI: 10.7860/jcdr/2022/53143.16422] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Introduction: Despite automation, manual load lifting is unavoidable in occupations like Industry, healthcare, defence, etc. Ergonomics studies on manual lifting conducted across the globe explored few aspects of biomechanical and physiological responses. It was hypothesised that, ‘holistic ergonomics approach’ involving simultaneous recording of these responses under single study, would elucidate potential injury causing factors more effectively and results could be validated by applying meta-analysis technique of literature review. Aim: To identify the potential determinants of manual lifting by applying multivariate statistics to existing data and correlate the results with determinants as per literature review applying meta-Analysis. Materials and Methods: Clustering and principal component analysis tools of factor analysis was applied on the data obtained under the pilot study (n=11) undertaken by same authors previously on manual lifting that assessed 26 dependent parameters simultaneously for load magnitudes (10 kg, 20 kg), lifting heights (floor-knuckle, knuckle-shoulder and floorshoulder) and lifting frequencies (1lift.min-1, 4lifts.min-1). Further, extensive scoping literature review on determinants of manual load lifting was done applying text mining tool of meta-analysis technique on R software platform using 921 pubmed abstracts published between 1991 and 2018. Results: Salient findings of factor analysis corroborated with that of scoping literature review. Accordingly, dependent variable ‘Vertical Ground Reaction Force (VGRF)’ and independent variable ‘vertical height of lift’ changed most significantly during manual lifting, showing significant positive correlations. Newton’s third law of motion states that while bipedal standing/walking/running on floor, two forces (with three vector components) are acting upon a person: the force of gravity (downward force, equivalent to body weight) and the Ground Reaction Force (GRF, an equal upward force exerted by floor). However, while standing still at one place for lifting load, only the largest vector component of GRF, i.e., VGRF acts on the body (=‘body weight’+‘load magnitude’) through the vertical height of lift. Conclusion: It may be concluded that ‘vertical height of lift’ and VGRF are possible indicators of injury potential of manual lifting. However, studies on larger sample size and meta-analysis of relevant full papers instead of abstracts need to be done in future.
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Patel JC, Singh A, Tulswani R, Sharma YK, Khurana P, Ragumani S. Identification of VEGFA-centric temporal hypoxia-responsive dynamic cardiopulmonary network biomarkers. Life Sci 2021; 281:119718. [PMID: 34147483 DOI: 10.1016/j.lfs.2021.119718] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/31/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
AIMS Hypoxia, a pathophysiological condition, is profound in several cardiopulmonary diseases (CPD). Every individual's lethality to a hypoxia state differs in terms of hypoxia exposure time, dosage units and dependent on the individual's genetic makeup. Most of the proposed markers for CPD were generally aim to distinguish disease samples from normal samples. Although, as per the 2018 GOLD guidelines, clinically useful biomarkers for several cardio pulmonary disease patients in stable condition have yet to be identified. We attempt to address these key issues through the identification of Dynamic Network Biomarkers (DNB) to detect hypoxia induced early warning signals of CPD before the catastrophic deterioration. MATERIALS AND METHODS The human microvascular endothelial tissues microarray datasets (GSE11341) of lung and cardiac expose to hypoxia (1% O2) for 3, 24 and 48 h were retrieved from the public repository. The time dependent differentially expressed genes were subjected to tissue specificity and promoter analysis to filtrate the noise levels in the networks and to dissect the tissue specific hypoxia induced genes. These filtered out genes were used to construct the dynamic segmentation networks. The hypoxia induced dynamic differentially expressed genes were validated in the lung and heart tissues of male rats. These rats were exposed to hypobaric hypoxia (simulated altitude of 25,000 or PO2 - 282 mm of Hg) progressively for 3, 24 and 48 h. KEY FINDINGS To identify the temporal key genes regulated in hypoxia, we ranked the dominant genes based on their consolidated topological features from tissue specific networks, time dependent networks and dynamic networks. Overall topological ranking described VEGFA as a single node dynamic hub and strongly communicated with tissue specific genes to carry forward their tissue specific information. We named this type of VEGFAcentric dynamic networks as "V-DNBs". As a proof of principle, our methodology helped us to identify the V-DNBs specific for lung and cardiac tissues namely V-DNBL and V-DNBC respectively. SIGNIFICANCE Our experimental studies identified VEGFA, SLC2A3, ADM and ENO2 as the minimum and sufficient candidates of V-DNBL. The dynamic expression patterns could be readily exploited to capture the pre disease state of hypoxia induced pulmonary vascular remodelling. Whereas in V-DNBC the minimum and sufficient candidates are VEGFA, SCL2A3, ADM, NDRG1, ENO2 and BHLHE40. The time dependent single node expansion indicates V-DNBC could also be the pre disease state pathological hallmark for hypoxia-associated cardiovascular remodelling. The network cross-talk and expression pattern between V-DNBL and V-DNBC are completely distinct. On the other hand, the great clinical advantage of V-DNBs for pre disease predictions, a set of samples during the healthy condition should suffice. Future clinical studies might further shed light on the predictive power of V-DNBs as prognostic and diagnostic biomarkers for CPD.
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Affiliation(s)
- Jai Chand Patel
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Ajeet Singh
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Rajkumar Tulswani
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Yogendra Kumar Sharma
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Pankaj Khurana
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India
| | - Sugadev Ragumani
- Defence Institute of Physiology and Allied Sciences, Defence Research and Development Organization, Lucknow Road, Timarpur, Delhi, India.
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Gupta A, Ragumani S, Sharma YK, Ahmad Y, Khurana P. Analysis of Hypoxiamir-Gene Regulatory Network Identifies Critical MiRNAs Influencing Cell-Cycle Regulation Under Hypoxic Conditions. Microrna 2019; 8:223-236. [PMID: 30806334 DOI: 10.2174/2211536608666190219094204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/14/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Hypoxia is a pathophysiological condition which arises due to low oxygen concentration in conditions like cardiovascular diseases, inflammation, ascent to higher altitude, malignancies, deep sea diving, prenatal birth, etc. A number of microRNAs (miRNAs), Transcription Factors (TFs) and genes have been studied separately for their role in hypoxic adaptation and controlling cell-cycle progression and apoptosis during this stress. OBJECTIVE We hypothesize that miRNAs and TFs may act in conjunction to regulate a multitude of genes and play a crucial and combinatorial role during hypoxia-stress-responses and associated cellcycle control mechanisms. METHOD We collected a comprehensive and non-redundant list of human hypoxia-responsive miRNAs (also known as hypoxiamiRs). Their experimentally validated gene-targets were retrieved from various databases and a comprehensive hypoxiamiR-gene regulatory network was built. RESULTS Functional characterization and pathway enrichment of genes identified phospho-proteins as enriched nodes. The phospho-proteins which were localized both in the nucleus and cytoplasm and could potentially play important role as signaling molecules were selected; and further pathway enrichment revealed that most of them were involved in NFkB signaling. Topological analysis identified several critical hypoxiamiRs and network perturbations confirmed their importance in the network. Feed Forward Loops (FFLs) were identified in the subnetwork of enriched genes, miRNAs and TFs. Statistically significant FFLs consisted of four miRNAs (hsa-miR-182-5p, hsa- miR-146b-5p, hsa-miR-96, hsa-miR-20a) and three TFs (SMAD4, FOXO1, HIF1A) both regulating two genes (NFkB1A and CDKN1A). CONCLUSION Detailed BioCarta pathway analysis identified that these miRNAs and TFs together play a critical and combinatorial role in regulating cell-cycle under hypoxia, by controlling mechanisms that activate cell-cycle checkpoint protein, CDKN1A. These modules work synergistically to regulate cell-proliferation, cell-growth, cell-differentiation and apoptosis during hypoxia. A detailed mechanistic molecular model of how these co-regulatory FFLs may regulate the cell-cycle transitions during hypoxic stress conditions is also put forth. These biomolecules may play a crucial and deterministic role in deciding the fate of the cell under hypoxic-stress.
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Affiliation(s)
- Apoorv Gupta
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Sugadev Ragumani
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Yogendra Kumar Sharma
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Yasmin Ahmad
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Pankaj Khurana
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
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Odokonyero D, Ragumani S, Lopez MS, Bonanno JB, Ozerova NDS, Woodard DR, Machala BW, Swaminathan S, Burley SK, Almo SC, Glasner ME. Divergent evolution of ligand binding in the o-succinylbenzoate synthase family. Biochemistry 2013; 52:7512-21. [PMID: 24060347 DOI: 10.1021/bi401176d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thermobifida fusca o-succinylbenzoate synthase (OSBS), a member of the enolase superfamily that catalyzes a step in menaquinone biosynthesis, has an amino acid sequence that is 22 and 28% identical with those of two previously characterized OSBS enzymes from Escherichia coli and Amycolatopsis sp. T-1-60, respectively. These values are considerably lower than typical levels of sequence identity among homologous proteins that have the same function. To determine how such divergent enzymes catalyze the same reaction, we determined the structure of T. fusca OSBS and identified amino acids that are important for ligand binding. We discovered significant differences in structure and conformational flexibility between T. fusca OSBS and other members of the enolase superfamily. In particular, the 20s loop, a flexible loop in the active site that permits ligand binding and release in most enolase superfamily proteins, has a four-amino acid deletion and is well-ordered in T. fusca OSBS. Instead, the flexibility of a different region allows the substrate to enter from the other side of the active site. T. fusca OSBS was more tolerant of mutations at residues that were critical for activity in E. coli OSBS. Also, replacing active site amino acids found in one protein with the amino acids that occur at the same place in the other protein reduces the catalytic efficiency. Thus, the extraordinary divergence between these proteins does not appear to reflect a higher tolerance of mutations. Instead, large deletions outside the active site were accompanied by alteration of active site size and electrostatic interactions, resulting in small but significant differences in ligand binding.
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Affiliation(s)
- Denis Odokonyero
- Department of Biochemistry and Biophysics, Texas A&M University , 2128 TAMU, College Station, Texas 77843-2128, United States
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Ornelas A, Korczynska M, Ragumani S, Kumaran D, Narindoshvili T, Shoichet BK, Swaminathan S, Raushel FM. Functional annotation and three-dimensional structure of an incorrectly annotated dihydroorotase from cog3964 in the amidohydrolase superfamily. Biochemistry 2012; 52:228-38. [PMID: 23214420 DOI: 10.1021/bi301483z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The substrate specificities of two incorrectly annotated enzymes belonging to cog3964 from the amidohydrolase superfamily were determined. This group of enzymes are currently misannotated as either dihydroorotases or adenine deaminases. Atu3266 from Agrobacterium tumefaciens C58 and Oant2987 from Ochrobactrum anthropi ATCC 49188 were found to catalyze the hydrolysis of acetyl-(R)-mandelate and similar esters with values of k(cat)/K(m) that exceed 10(5) M(-1) s(-1). These enzymes do not catalyze the deamination of adenine or the hydrolysis of dihydroorotate. Atu3266 was crystallized and the structure determined to a resolution of 2.62 Å. The protein folds as a distorted (β/α)(8) barrel and binds two zincs in the active site. The substrate profile was determined via a combination of computational docking to the three-dimensional structure of Atu3266 and screening of a highly focused library of potential substrates. The initial weak hit was the hydrolysis of N-acetyl-D-serine (k(cat)/K(m) = 4 M(-1) s(-1)). This was followed by the progressive identification of acetyl-(R)-glycerate (k(cat)/K(m) = 4 × 10(2) M(-1) s(-1)), acetyl glycolate (k(cat)/K(m) = 1.3 × 10(4) M(-1) s(-1)), and ultimately acetyl-(R)-mandelate (k(cat)/K(m) = 2.8 × 10(5) M(-1) s(-1)).
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Affiliation(s)
- Argentina Ornelas
- Department of Chemistry, P.O. Box 30012, Texas A&M University, College Station, TX 77842-3012, USA
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Ragumani S, Sauder JM, Burley SK, Swaminathan S. Structural studies on cytosolic domain of magnesium transporter MgtE from Enterococcus faecalis. Proteins 2010; 78:487-91. [PMID: 19787770 DOI: 10.1002/prot.22585] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Sugadev Ragumani
- Brookhaven National Laboratory, Biology Department, Upton, New York 11973, USA
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Affiliation(s)
- Sugadev Ragumani
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973
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Almo SC, Bonanno JB, Sauder JM, Emtage S, Dilorenzo TP, Malashkevich V, Wasserman SR, Swaminathan S, Eswaramoorthy S, Agarwal R, Kumaran D, Madegowda M, Ragumani S, Patskovsky Y, Alvarado J, Ramagopal UA, Faber-Barata J, Chance MR, Sali A, Fiser A, Zhang ZY, Lawrence DS, Burley SK. Structural genomics of protein phosphatases. ACTA ACUST UNITED AC 2007; 8:121-40. [PMID: 18058037 DOI: 10.1007/s10969-007-9036-1] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [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] [Received: 08/31/2007] [Accepted: 11/06/2007] [Indexed: 12/11/2022]
Abstract
The New York SGX Research Center for Structural Genomics (NYSGXRC) of the NIGMS Protein Structure Initiative (PSI) has applied its high-throughput X-ray crystallographic structure determination platform to systematic studies of all human protein phosphatases and protein phosphatases from biomedically-relevant pathogens. To date, the NYSGXRC has determined structures of 21 distinct protein phosphatases: 14 from human, 2 from mouse, 2 from the pathogen Toxoplasma gondii, 1 from Trypanosoma brucei, the parasite responsible for African sleeping sickness, and 2 from the principal mosquito vector of malaria in Africa, Anopheles gambiae. These structures provide insights into both normal and pathophysiologic processes, including transcriptional regulation, regulation of major signaling pathways, neural development, and type 1 diabetes. In conjunction with the contributions of other international structural genomics consortia, these efforts promise to provide an unprecedented database and materials repository for structure-guided experimental and computational discovery of inhibitors for all classes of protein phosphatases.
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Affiliation(s)
- Steven C Almo
- Albert Einstein College of Medicine, Bronx, NY, USA.
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