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Yu HM, Malhotra K, Butler JS, Patel A, Sewell MD, Li YZ, Molloy S. The relationship between spinopelvic measurements and patient-reported outcome scores in patients with multiple myeloma of the spine. Bone Joint J 2016; 98-B:1234-9. [DOI: 10.1302/0301-620x.98b9.37786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 05/06/2016] [Indexed: 11/05/2022]
Abstract
Aims Patients with multiple myeloma (MM) develop deposits in the spine which may lead to vertebral compression fractures (VCFs). Our aim was to establish which spinopelvic parameters are associated with the greatest disability in patients with spinal myeloma and VCFs. Patients and Methods We performed a retrospective cross-sectional review of 148 consecutive patients (87 male, 61 female) with spinal myeloma and analysed correlations between spinopelvic parameters and patient-reported outcome scores. The mean age of the patients was 65.5 years (37 to 91) and the mean number of vertebrae involved was 3.7 (1 to 15). Results The thoracolumbar region was most commonly affected (109 patients, 73.6%), and was the site of most posterior vertebral wall defects (47 patients, 31.8%). Poorer Oswestry Disability Index scores correlated with an increased sagittal vertical axis (p = 0.006), an increased number of VCFs (p = 0.035) and sternal involvement (p = 0.012). Poorer EuroQol visual analogue scale scores correlated with posterior vertebral wall defects in the thoracolumbar region (p = 0.012). The sagittal vertical axis increased with the number of fractures and kyphosis in the thoracolumbar (p = 0.009) and lumbar (p < 0.001) regions. Conclusions In MM, patients with VCFs have poorer clinical scores at presentation in the presence of sagittal imbalance. Outcome is particularly affected by multiple fractures in the thoracolumbar and lumbar regions and by failure to prevent kyphosis. Patients with MM should be screened for spinal lesions early. Cite this article: Bone Joint J 2016;98-B:1234–9.
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Malhotra K, Navathe SB, Chau DH, Hadjipanayis C, Sun J. Constraint based temporal event sequence mining for Glioblastoma survival prediction. J Biomed Inform 2016; 61:267-75. [PMID: 27064059 DOI: 10.1016/j.jbi.2016.03.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/05/2016] [Accepted: 03/25/2016] [Indexed: 10/22/2022]
Abstract
OBJECTIVE A significant challenge in treating rare forms of cancer such as Glioblastoma (GBM) is to find optimal personalized treatment plans for patients. The goals of our study is to predict which patients survive longer than the median survival time for GBM based on clinical and genomic factors, and to assess the predictive power of treatment patterns. METHOD We developed a predictive model based on the clinical and genomic data from approximately 300 newly diagnosed GBM patients for a period of 2years. We proposed sequential mining algorithms with novel clinical constraints, namely, 'exact-order' and 'temporal overlap' constraints, to extract treatment patterns as features used in predictive modeling. With diverse features from clinical, genomic information and treatment patterns, we applied both logistic regression model and Cox regression to model patient survival outcome. RESULTS The most predictive features influencing the survival period of GBM patients included mRNA expression levels of certain genes, some clinical characteristics such as age, Karnofsky performance score, and therapeutic agents prescribed in treatment patterns. Our models achieved c-statistic of 0.85 for logistic regression and 0.84 for Cox regression. CONCLUSIONS We demonstrated the importance of diverse sources of features in predicting GBM patient survival outcome. The predictive model presented in this study is a preliminary step in a long-term plan of developing personalized treatment plans for GBM patients that can later be extended to other types of cancers.
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Malhotra K, Kulshreshtha D, Shukla S, Husain N. ENL developing 10 years after leprosy treatment masquerading as atypical-mycobacterial infection. QJM 2015; 108:905-6. [PMID: 25660606 DOI: 10.1093/qjmed/hcv042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Hackett C, Ramanathan R, Malhotra K, Quigley M, Kelly K, Tian M, Protetch J, Wong C, Wright D, Tayal A. Safety of venous thromboembolism prophylaxis with fondaparinux in ischemic stroke. Thromb Res 2015; 135:249-54. [DOI: 10.1016/j.thromres.2014.11.041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/11/2014] [Accepted: 11/04/2014] [Indexed: 11/27/2022]
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Fisher JO, Wright G, Herman AN, Malhotra K, Serrano EL, Foster GD, Whitaker RC. "Snacks are not food". Low-income, urban mothers' perceptions of feeding snacks to their preschool-aged children. Appetite 2014; 84:61-7. [PMID: 25240637 DOI: 10.1016/j.appet.2014.09.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 09/12/2014] [Accepted: 09/13/2014] [Indexed: 11/19/2022]
Abstract
Snacking has become more frequent among US preschool-aged children in recent decades and represents a significant proportion of daily energy intake. Social influences on snacking among children, however, are not well understood. This qualitative research described low-income, urban mothers' perceptions of feeding snacks to their preschool-aged children using data from 7 focus groups with 32 participants. Focus group transcripts were analyzed using a constant comparative method to identify themes. Mothers described snacks as involving less preparation, balance, and sustenance than meals (Theme 1). Mothers also made reference to some snacks as not being "real food" (Theme 2). At the same time, snacks had significant hedonic value as reflected in mothers' enjoyment of those foods (Theme 3), the effectiveness of snacks to manage children's behavior (Theme 4), and the variety of restrictions that mothers placed on children's access to snacks, such as locking cabinets, offering small servings, and reducing the number of snacks in sight (Theme 5). Two overarching themes highlighted distinctions mothers made in feeding children snacks vs. meals as well as the powerful hedonic appeal of snacks for both mother and child. These observations suggest that low-income, urban mothers of preschool-aged children may perceive snacks as serving a more important role in managing children's behavior than in providing nutrition. Child feeding interventions should address non-food related ways of managing children's behavior as well as encouraging caregivers to see snacks as structured opportunities for nutrition and connecting with their children.
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Chaudhary K, Malhotra K, Sowers J, Aroor A. Uric Acid - key ingredient in the recipe for cardiorenal metabolic syndrome. Cardiorenal Med 2014; 3:208-220. [PMID: 24454316 DOI: 10.1159/000355405] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Elevated serum uric acid levels are a frequent finding in persons with obesity, hypertension, cardiovascular and kidney disease as well as in those with the cardiorenal metabolic syndrome (CRS). The increased consumption of a fructose-rich Western diet has contributed to the increasing incidence of the CRS, obesity and diabetes especially in industrialized populations. There is also increasing evidence that supports a causal role of high dietary fructose driving elevations in uric acid in association with the CRS. Animal and epidemiological studies support the notion that elevated serum uric acid levels play an important role in promoting insulin resistance and hypertension and suggest potential pathophysiological mechanisms that contribute to the development of the CRS and associated cardiovascular disease and chronic kidney disease. To this point, elevated serum levels of uric acid appear to contribute to impaired nitric oxide production/endothelial dysfunction, increased vascular stiffness, inappropriate activation of the renin-angiotensin-aldosterone system, enhanced oxidative stress, and maladaptive immune and inflammatory responses. These abnormalities, in turn, promote vascular, cardiac and renal fibrosis as well as associated functional abnormalities. Small clinical trials have suggested that uric acid-lowering therapies may be beneficial in such patients; however, a consensus on the treatment of asymptomatic hyperuricemia is lacking. Larger randomized controlled trials need to be performed in order to critically evaluate the beneficial effect of lowering serum uric acid in patients with the CRS and those with diabetes and/or hypertension.
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Deodhar A, Mease P, Reveille J, Curtis J, Karunaratne P, Malhotra K, Pangan A. THU0065 Prevalence of Axial Spondyloarthritis among Undiagnosed Chronic Back Pain Patients in the United States: Table 1. Ann Rheum Dis 2014. [DOI: 10.1136/annrheumdis-2014-eular.1135] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ramanathan RS, Malhotra K, Scott T. Teaching NeuroImages: Diffuse cerebral neurosarcoidosis mimicking gliomatosis cerebri. Neurology 2013; 81:e46. [DOI: 10.1212/wnl.0b013e3182a08d47] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Malhotra K, Schramke C, Ku A. E-057 Risk factors influencing duration of Cerebral Angiography: A single centre study. J Neurointerv Surg 2013. [DOI: 10.1136/neurintsurg-2013-010870.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Dhawan V, Ariyamuthu V, Malhotra K, Dalal P, Bichu P, Dorairajan S. Isolated pleural effusion as a presentation of high cardiac output heart failure in a hemodialysis patient. Hemodial Int 2013; 16 Suppl 1:S54-7. [PMID: 23036038 DOI: 10.1111/j.1542-4758.2012.00746.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Congestive heart failure is a well-recognized complication of hemodialysis arteriovenous fistula. Symptoms of dyspnea are usually associated with signs of congestive heart failure including pulmonary edema, pleural effusions, lower extremity edema, and liver enlargement, to name a few. We present a case of a gentleman with end-stage renal disease on chronic hemodialysis, which developed acute bilateral transudative pleural effusions in the absence of other signs of systemic venous congestion, associated with pulmonary venous congestion. We also discuss the pathogenesis and role of hemodialysis in management of this patient.
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Malhotra K, Dhawan V, Dalal P, Ariyamuthu V, Bichu P, Botdorf J, Khanna R. Decompensated high-output congestive heart failure in a patient with AVF and the role of right heart catheterization: a case study. Hemodial Int 2013; 16 Suppl 1:S58-61. [PMID: 23036039 DOI: 10.1111/j.1542-4758.2012.00749.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
A 70-year-old Caucasian male presented 8 months postcadaveric renal transplant with slowly progressive shortness of breath, abdominal distention, and cough for a duration of a few days. Thorough evaluation found him to have severe pulmonary hypertension (PH) on echocardiogram with decompensated high-output congestive heart failure. A right heart catheterization was done, which confirmed elevated right-sided pressures and high cardiac output. The mean pulmonary artery pressure, on a Swan-Ganz catheter, improved from 37 to 30 mmHg on partial manual occlusion of his still functioning hemodialysis arteriovenous fistula. Subsequently, the patient underwent ligation of the fistula and this led to gradual improvement in his symptoms. Follow-up right heart catheterization and echocardiogram showed marked improvement and normalization of right heart pressures. We recommend that patients with arteriovenous fistula should undergo close monitoring for development of early signs and symptoms of congestive heart failure and screening for PH by echocardiography post-kidney transplant. Right heart catheterization should be considered if screening is positive. Risk and benefit of fistula closure should be weighed in face of reduced survival from PH in dialysis patients and closure should be considered in post-transplant patients.
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Camille B, Christophe B, Yvon B, Henri VC, Pierre M, Dominique T, Bataille S, Chondolu S, An T, Khan S, Rayamajhi S, Kim GH, Roh YW, Lee CH, Kang CM, Bansal R, Singh KN, Saxena S, Malhotra K, Van Laecke S, Nagler E, Van Biesen W, Jadoul M, Vanholder R, Cucchiari D, Cucchiari D, Angelini C, Mirani M, Arosio P, Graziani G, Badalamenti S, Girfoglio D, Allen D, Kirkham A, Johri N, Wheeler DC, Choong S, Moochhala S, Unwin R, Fabris A, Lupo A, Fantin F, Ferraro PM, Caletti C, Comellato G, Messa M, Gambaro G, Tanaka H, Tatsumoto N, Tsuneyoshi S, Daijo Y, Bacallao Mendez RA, Bacallao R, Crombet T, Davalos JM, Llerena B, Leyva C, Manalich R, Beltrami P, Ruggera L, Iannetti A, Iafrate M, Guttilla A, Zattoni F, Arancio M, Zattoni F, Beltrami P, Ruggera L, Guttilla A, Iannetti A, Zattoni F, Gigli F, Zattoni F. Electrolyte disorders / Nephrolithiasis. Nephrol Dial Transplant 2012. [DOI: 10.1093/ndt/gfs222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Dalal P, Bichu P, Dhawan V, Ariyamuthu V, Malhotra K, Misra M, Khanna R. Post-transplant Lymphoproliferative Disorder--a case of late-onset T-cell lymphoma after failed renal transplant. ADVANCES IN PERITONEAL DIALYSIS. CONFERENCE ON PERITONEAL DIALYSIS 2012; 28:94-96. [PMID: 23311222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Post-transplant lymphoproliferative disease (PTLD) is a rare but life-threatening complication after solid organ transplantation. The risk of PTLD varies with recipient age, serostatus of the donor and the recipient for Epstein-Barr virus, type of organ transplanted, and intensity of immunosuppression. The risk of PTLD is highest in the early post-transplant period, but the cumulative risk increases with time. We report a case of PTLD occurring 17 years after renal transplantation in a 59-year-old woman.
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Haygood T, Malhotra K, Ng C, Chasen B, McEnery K, Chasen M. Migration of central lines from the superior vena cava to the azygous vein. Clin Radiol 2012; 67:49-54. [DOI: 10.1016/j.crad.2011.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 05/10/2011] [Accepted: 05/31/2011] [Indexed: 10/15/2022]
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Malhotra K, Georgiades IB, Davies J. Functional colonic obstruction in an adult as a presenting feature of thymoma. Ann R Coll Surg Engl 2011; 93:e61-3. [PMID: 21929885 DOI: 10.1308/147870811x589588] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Functional colonic obstruction is a colonic motility disorder with a number of causes. One cause is myenteric ganglionitis, which may result from paraneoplastic processes. We present the case of a previously healthy 53-year-old man who presented with a week's history of functional colonic obstruction. A transverse loop colostomy failed to resolve his symptoms and he subsequently underwent an extended right hemicolectomy. Histology demonstrated lymphocytic myenteric ganglionitis that was felt to be of paraneoplastic origin. The patient later developed bilateral ptosis and was diagnosed with ocular myasthenia gravis. Further investigation revealed the presence of a thymoma that was resected, resulting in an improvement to his symptoms. We present this case and a review of the literature to illustrate the importance of seeking out a paraneoplastic cause for functional colonic obstruction in adults as early resection of the tumour may help alleviate symptoms and avoid bowel surgery.
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Rao RN, Krishnani N, Malhotra K, Suresh B, Mehrotra R. Dilemmas in cytodiagnosis of subcutaneous swellings: mimics and look-alikes of cysticercosis. J Clin Pathol 2010; 63:926-9. [DOI: 10.1136/jcp.2010.076976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Malhotra K, Schwartz T, Hameed U. Presence of suicidality as a prognostic indicator. J Postgrad Med 2004; 50:185-7; discussion 187-8. [PMID: 15377802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
BACKGROUND Suicidal symptoms in depression are often thought to predict a higher severity of illness and a worse prognosis. AIMS To determine if suicidal ideation at the time of treatment for major depression can predict response to antidepressant medication in primary care. SETTINGS AND DESIGN A retrospective analysis of subjects receiving anti-depressant drugs in a primary care setting METHODS AND MATERIAL Nine depressed patients (14%) who acknowledged suicidality on the PHQ-9 depression scale were followed up for and compared to a group of 54 (86%) depressed patients (controls) who did not have suicidal thoughts for four months. All were given treatment with antidepressants and followed with a disease management protocol where the PHQ-9 was used as a systematic outcome measure. STATISTICAL ANALYSIS Descriptive measures and t-tests were utilized to show statistical significance. RESULTS There were no statistical differences in remission from depressive symptoms based on the PHQ-9 scale after antidepressant treatment, between patients with suicidal thoughts (56%) and those without (44%). CONCLUSION The presence of suicidality as a depressive symptom did not predict poorer clinical outcome when treating depression in the primary care setting in the patients studied.
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Alao AO, Malhotra K, Pies R, Dewan MJ. Pharmacological strategies in treatment-resistant depression. West Afr J Med 2004; 22:211-8. [PMID: 14696943 DOI: 10.4314/wajm.v22i3.27952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Treatment-resistant depression may be due to factors such as co-morbid psychiatric or medical illnesses, chronic psychosocial stresses, and medication nonadherence. Alternative treatment strategies such as optimization, switching to a different antidepressant, augmentation or combination with another antidepressant are strategies useful in such patients. The first strategy in treating resistant depression is to optimize monotherapy. A switch should be made to another agent if there is no response to treatment after an adequate duration. Augmentation and combination strategies are useful if there is sub-optimal response to the initial antidepressant. With several antidepressants (selective serotonin reuptake inhibitors, tricyclic antidepressants, monoamine oxidase inhibitors and the newer antidepresssants) and various antidepressant augmentation and combination strategies available to clinicians, the outcome of treating patients with depression should improve.
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Martin KJ, González E, Lindberg JS, Taccetta C, Amdahl M, Malhotra K, Llach F. Paricalcitol dosing according to body weight or severity of hyperparathyroidism: a double-blind, multicenter, randomized study. Am J Kidney Dis 2001; 38:S57-63. [PMID: 11689389 DOI: 10.1053/ajkd.2001.28112] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Vitamin D therapy for patients with end-stage renal disease (ESRD) on hemodialysis therapy has relied on patient dry weight to determine the initial dose of medication. Obtaining a patient's dry weight can be difficult, and no correlation has been established between a patient's body weight and severity of secondary hyperparathyroidism. We conducted a double-blind, double-dummy, randomized, 12-week, multicenter trial to compare the incidence of hypercalcemia (single occurrence) between two dosing regimens: one regimen based on baseline intact parathyroid hormone (iPTH; PTH/80) level, and the other regimen based on patient body weight (0.04 microgram/kg). One hundred twenty-five adult patients with ESRD on maintenance hemodialysis therapy were enrolled at multiple sites. Before treatment, all patients were required to have PTH levels of 300 pg/mL or greater, calcium levels of 8.0 mg/dL or greater and 10.5 mg/dL or less, and a calcium x phosphorus (Ca x P) product of 70 or less. Patients were randomized to one of two regimens: the nonrandomized treatment was also administered as a placebo dummy. No incidence of hypercalcemia occurred in either treatment group during the study. Patients treated according to the formula iPTH/80 required fewer dose adjustments and achieved the first of four consecutive reductions from baseline PTH level of 30% or greater more rapidly than patients treated based on body weight (P = 0.0306). Incidences of elevated Ca x P product levels were similar between treatment groups. Treatment with paricalcitol injection based on degree of secondary hyperparathyroidism incurred no greater risk for hypercalcemia and achieved meaningful therapeutic results with fewer dose adjustments than dosing based on patient body weight.
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Malhotra KT, Malhotra K, Lubin BH, Kuypers FA. Identification and molecular characterization of acyl-CoA synthetase in human erythrocytes and erythroid precursors. Biochem J 1999; 344 Pt 1:135-43. [PMID: 10548543 PMCID: PMC1220623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Full-length cDNA species encoding two forms of acyl-CoA synthetase from a K-562 human erythroleukaemic cell line were cloned, sequenced and expressed. The first form, named long-chain acyl-CoA synthetase 5 (LACS5), was found to be a novel, unreported, human acyl-CoA synthetase with high similarity to rat brain ACS2 (91% identical). The second form (66% identical with LACS5) was 97% identical with human liver LACS1. The LACS5 gene encodes a highly expressed 2.9 kb mRNA transcript in human haemopoietic stem cells from cord blood, bone marrow, reticulocytes and fetal blood cells derived from fetal liver. An additional 6.3 kb transcript is also found in these erythrocyte precursors; 2.9 and 9.6 kb transcripts of LACS5 are found in human brain, but transcripts are virtually absent from human heart, kidney, liver, lung, pancreas, spleen and skeletal muscle. The 78 kDa expressed LACS5 protein used the long-chain fatty acids palmitic acid, oleic acid and arachidonic acid as substrates. Antibodies directed against LACS5 cross-reacted with erythrocyte membranes. We conclude that early erythrocyte precursors express at least two different forms of acyl-CoA synthetase and that LACS5 is present in mature erythrocyte plasma membranes.
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Malhotra K, Luehrsen KR, Costello LL, Raich TJ, Sim K, Foltz L, Davidson S, Xu H, Chen A, Yamanishi DT, Lindemann GW, Cain CA, Madlansacay MR, Hashima SM, Pham TL, Mahoney W, Schueler PA. Identification of differentially expressed mRNAs in human fetal liver across gestation. Nucleic Acids Res 1999; 27:839-47. [PMID: 9889281 PMCID: PMC148255 DOI: 10.1093/nar/27.3.839] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Differential gene expression, with its precise start and stop times, is believed to be critical for the programmed development of new cells and tissues. Within the developing fetus, one tissue of particular interest is fetal liver. This organ undergoes rapid changes in the pathway toward liver development in utero since it is also the major site of hematopoiesis, until bone marrow hematopoiesis predominates. Believing that patterns would emerge from the bi-weekly large-scale inspection of expressed genes in the fetal liver, we employed differential display reverse transcription-polymerase chain reaction (DDRT-PCR) as ourprimary inspection tool. Using DDRT-PCR, we isolated cDNAs differentially expressed throughout fetal liver development and in adult liver. We displayed approximately 25 000 cDNAs from 10 and 24 week fetal liver and adult liver. From this initial screen, we determined that approximately 0.1-1% of the mRNA population undergoes expression changes. We extracted, purified and sequenced 25 differentially displayed cDNA bands. Fourteen cDNAs had similarities to known genes, while 11 cDNAs were not similar to any characterized gene. The differentially expressed cDNAs from known genes present in fetal liver include alpha-fetoprotein, stem cell factor, erythroid alpha-spectrin, 2,3-bisphosphoglycerate mutase, insulin-like growth factor-2, porphobilinogen deaminase and Mac30. The differentially expressed cDNAs present in adult liver but not in 10 week fetal liver were nicotinamide deaminase, human fibrinogen-related protein and alpha-acid glycoprotein. The majority of differentially expressed genes found during this effort appear to be turned on during organogenesis, however, some genes were found that are apparently turned off completely.
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Malhotra K, Foltz L, Mahoney WC, Schueler PA. Interaction and effect of annealing temperature on primers used in differential display RT-PCR. Nucleic Acids Res 1998; 26:854-6. [PMID: 9443980 PMCID: PMC147309 DOI: 10.1093/nar/26.3.854] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Differential display of mRNA is a simple, sensitive and powerful method to identify differentially expressed gene fragments. The main drawback of differential display is the lack of reproducibility and the inability to read and compare complex gels. This issue results from employing unoptimized primer combinations and non-specific amplification, most likely due to unavoidable low annealing temperatures. In order to display most of the expressed transcripts (80-120 bands/lane), 26 different 5' primers were used in conjunction with nine different 3' poly (dT) primers. These primer combinations, used with the optimized annealing temperature for each set of primers, produced highly reproducible bands. BSA has a direct effect on the number of bands resolved. Variations in ramping time (9-40 s) had little or no effect on the resolution and reproducibility of differential display.
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Kim ST, Malhotra K, Ryo H, Sancar A, Todo T. Purification and characterization of Drosophila melanogaster photolyase. Mutat Res 1996; 363:97-104. [PMID: 8676930 DOI: 10.1016/0921-8777(96)00003-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Animal-type photolyases have very limited sequence homology to microbial-type photolyases. We wanted to find out whether the two types of enzymes have different or similar biochemical and photochemical properties. In particular, the chromophore/cofactor composition of animal photolyases is of special interest since the presence and nature of a second chromophore in these enzymes are not known in contrast to the microbial photolyases which contain FAD cofactor, and folate or deazaflavin as second chromophores. We overproduced the Drosophila melanogaster photolyase in Escherichia coli using the cloned gene. The enzyme contains FAD and folate and thus belongs in the folate class of enzymes but with an action spectrum peak at 420 nm.
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Kim ST, Malhotra K, Taylor JS, Sancar A. Purification and partial characterization of (6-4) photoproduct DNA photolyase from Xenopus laevis. Photochem Photobiol 1996; 63:292-5. [PMID: 8881333 DOI: 10.1111/j.1751-1097.1996.tb03028.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The (6-4) photoproduct DNA photolyase was detected in two vertebrate animals Crotalus atrox (rattlesnake) and Xenopus laevis (South African clawed toad). The enzyme was extensively purified from X. laevis and characterized. The highly purified enzyme is fluorescent with an excitation maximum at 420-440 nm and emission maximum at 460-480 nm. The photorepair action spectrum matches the fluorescence excitation spectrum with a 430 nm maximum.
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