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Schalkwijk HH, Shewakramani NR, Das K, Andrei G, Snoeck R. Combination of ganciclovir and trifluridine prevents drug-resistance emergence in HSV-1. Antimicrob Agents Chemother 2024; 68:e0011024. [PMID: 38619252 DOI: 10.1128/aac.00110-24] [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: 01/19/2024] [Accepted: 03/15/2024] [Indexed: 04/16/2024] Open
Abstract
Ocular herpes simplex virus 1 (HSV-1) infections can lead to visual impairment. Long-term acyclovir (ACV) prophylaxis reduces the frequency of recurrences but is associated with drug resistance. Novel therapies are needed to treat drug-resistant HSV-1 infections. Here, we describe the effects of trifluridine (TFT) in combination with ACV or ganciclovir (GCV) on HSV-1 replication and drug-resistance emergence. Wild-type HSV-1 was grown under increasing doses of one antiviral (ACV, GCV, or TFT) or combinations thereof (ACV + TFT or GCV + TFT). Virus cultures were analyzed by Sanger sequencing and deep sequencing of the UL23 [thymidine kinase (TK)] and UL30 [DNA polymerase (DP)] genes. The phenotypes of novel mutations were determined by cytopathic effect reduction assays. TFT showed overall additive anti-HSV-1 activity with ACV and GCV. Five passages under ACV, GCV, or TFT drug pressure gave rise to resistance mutations, primarily in the TK. ACV + TFT and GCV + TFT combinatory pressure induced mutations in the TK and DP. The DP mutations were mainly located in terminal regions, outside segments that typically carry resistance mutations. TK mutations (R163H, A167T, and M231I) conferring resistance to all three nucleoside analogs (ACV, TFT, and GCV) emerged under ACV, TFT, ACV + TFT pressure and under GCV + TFT pressure initiated from suboptimal drug concentrations. However, higher doses of GCV and TFT prevented drug resistance in the resistance selection experiments. In summary, we identified novel mutations conferring resistance to nucleoside analogs, including TFT, and proposed that GCV + TFT combination therapy may be an effective strategy to prevent the development of drug resistance.
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Affiliation(s)
- Hanna Helena Schalkwijk
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Neesha Rajesh Shewakramani
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Graciela Andrei
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | - Robert Snoeck
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
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2
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Padilha JAG, Santos S, Willems T, Souza-Kasprzyk J, Leite A, Cunha LST, Costa ES, Pessôa AR, Eens M, E P, Torres JPM, Das K, Lepoint G, Dorneles PR, Bervoets L, Groffen T. Assessing the trophic ecology and migration on the exposure of cape petrels and Wilson's storm petrels from Antarctica to perfluoroalkylated substances, trace and major elements. Environ Res 2024; 244:117827. [PMID: 38072112 DOI: 10.1016/j.envres.2023.117827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/19/2023]
Abstract
Chemical pollution is a global concern as contaminants are transported and reach even the remote regions of Antarctica. Seabirds serve as important sentinels of pollution due to their high trophic position and wide distribution. This study examines the influence of migration and trophic ecology on the exposure of two Antarctic seabirds, Wilson's storm petrel (Oceanites oceanicus - Ooc), and Cape petrel (Daption capense - Dca), to chemical elements and perfluoroalkyl substances (PFAS). Our methodology involved assessing the concentration of these pollutants in feather samples obtained from carcasses, offering a practical means for monitoring contamination. Trace and major element concentrations were comparable in both species, suggesting that migratory patterns have a minimal impact on exposure levels. However, Ooc had higher concentration of PFAS compared to Dca (mean, ng g-1dry weight, PFOA: Ooc:0.710, Dca:0.170; PFTrDA: Ooc:0.550, Dca:0.360, and PFTeDA: Ooc:1.01, Dca:0.190), indicating that migration to the more polluted Northern Hemisphere significantly affects PFAS exposure. Furthermore, while no strong associations were found between either trace elements or PFAS and the three stable isotopes (δ13C, δ15N, and δ34S), a negative association was observed between PFUnDA and δ15N, hinting at potential biodilution. The research concludes that the migratory patterns of these seabird species affect their PFAS exposure, underscoring the critical need for further exploration and understanding of these relationships to better inform conservation strategies.
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Affiliation(s)
- J A G Padilha
- Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; CBMA - Centre for Molecular and Environmental Biology/ARNET-Aquatic Research Network, Portugal; IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal.
| | - S Santos
- CBMA - Centre for Molecular and Environmental Biology/ARNET-Aquatic Research Network, Portugal; IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal
| | - T Willems
- ECOSPHERE, Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - J Souza-Kasprzyk
- Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Ul. Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - A Leite
- CBMA - Centre for Molecular and Environmental Biology/ARNET-Aquatic Research Network, Portugal; IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal
| | - L S T Cunha
- Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - E S Costa
- Environment and Sustainability, State University of Rio Grande do Sul, Assis Brasil Street, 842, Downtown, São Francisco de Paula, Rio Grande do Sul, Brazil
| | - A R Pessôa
- Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - M Eens
- Behavioural Ecology and Ecophysiology Group (BECO), Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Prinsen E
- Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - J P M Torres
- Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - K Das
- Freshwater and Oceanic ScienCes Unit of ReSearch (FOCUS), Laboratory of Oceanology, University of Liège, 4000, Liège, Belgium
| | - G Lepoint
- Freshwater and Oceanic ScienCes Unit of ReSearch (FOCUS), Laboratory of Trophic and Isotope Ecology, University of Liège, 4000, Liège, Belgium
| | - P R Dorneles
- Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Freshwater and Oceanic ScienCes Unit of ReSearch (FOCUS), Laboratory of Oceanology, University of Liège, 4000, Liège, Belgium
| | - Lieven Bervoets
- ECOSPHERE, Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - T Groffen
- ECOSPHERE, Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium; Behavioural Ecology and Ecophysiology Group (BECO), Department of Biology, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
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3
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Aguirre CG, Woo JH, Romero-Sosa JL, Rivera ZM, Tejada AN, Munier JJ, Perez J, Goldfarb M, Das K, Gomez M, Ye T, Pannu J, Evans K, O'Neill PR, Spigelman I, Soltani A, Izquierdo A. Dissociable Contributions of Basolateral Amygdala and Ventrolateral Orbitofrontal Cortex to Flexible Learning Under Uncertainty. J Neurosci 2024; 44:e0622232023. [PMID: 37968116 PMCID: PMC10860573 DOI: 10.1523/jneurosci.0622-23.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 04/02/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/17/2023] Open
Abstract
Reversal learning measures the ability to form flexible associations between choice outcomes with stimuli and actions that precede them. This type of learning is thought to rely on several cortical and subcortical areas, including the highly interconnected orbitofrontal cortex (OFC) and basolateral amygdala (BLA), and is often impaired in various neuropsychiatric and substance use disorders. However, the unique contributions of these regions to stimulus- and action-based reversal learning have not been systematically compared using a chemogenetic approach particularly before and after the first reversal that introduces new uncertainty. Here, we examined the roles of ventrolateral OFC (vlOFC) and BLA during reversal learning. Male and female rats were prepared with inhibitory designer receptors exclusively activated by designer drugs targeting projection neurons in these regions and tested on a series of deterministic and probabilistic reversals during which they learned about stimulus identity or side (left or right) associated with different reward probabilities. Using a counterbalanced within-subject design, we inhibited these regions prior to reversal sessions. We assessed initial and pre-/post-reversal changes in performance to measure learning and adjustments to reversals, respectively. We found that inhibition of the ventrolateral orbitofrontal cortex (vlOFC), but not BLA, eliminated adjustments to stimulus-based reversals. Inhibition of BLA, but not vlOFC, selectively impaired action-based probabilistic reversal learning, leaving deterministic reversal learning intact. vlOFC exhibited a sex-dependent role in early adjustment to action-based reversals, but not in overall learning. These results reveal dissociable roles for BLA and vlOFC in flexible learning and highlight a more crucial role for BLA in learning meaningful changes in the reward environment.
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Affiliation(s)
- C G Aguirre
- Department of Psychology, University of California, Los Angeles, California 90095
| | - J H Woo
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - J L Romero-Sosa
- Department of Psychology, University of California, Los Angeles, California 90095
| | - Z M Rivera
- Department of Psychology, University of California, Los Angeles, California 90095
| | - A N Tejada
- Department of Psychology, University of California, Los Angeles, California 90095
| | - J J Munier
- Section of Biosystems and Function, School of Dentistry, University of California, Los Angeles, California 90095
| | - J Perez
- Department of Psychology, University of California, Los Angeles, California 90095
| | - M Goldfarb
- Department of Psychology, University of California, Los Angeles, California 90095
| | - K Das
- Department of Psychology, University of California, Los Angeles, California 90095
| | - M Gomez
- Department of Psychology, University of California, Los Angeles, California 90095
| | - T Ye
- Department of Psychology, University of California, Los Angeles, California 90095
| | - J Pannu
- Section of Biosystems and Function, School of Dentistry, University of California, Los Angeles, California 90095
| | - K Evans
- Department of Psychology, University of California, Los Angeles, California 90095
| | - P R O'Neill
- Shirley and Stefan Hatos Center for Neuropharmacology, Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, California 90095
| | - I Spigelman
- Section of Biosystems and Function, School of Dentistry, University of California, Los Angeles, California 90095
| | - A Soltani
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire 03755
| | - A Izquierdo
- Department of Psychology, University of California, Los Angeles, California 90095
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Rahman M, Jahan N, Hoque MM, Hossain MM, Ghosh K, Nupur NR, Zerin IJ, Badal MFA, Ali MA, Das K. Initial Six Month's Study of Neonatal Covid-19 in a Tertiary Care Hospital of Bangladesh. Mymensingh Med J 2024; 33:206-213. [PMID: 38163794] [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: 01/03/2024]
Abstract
The pandemic Covid-19 affects mainly adult causing fatal illness specially who have co-morbidities. But as days pass by with increasing surveillances it's gradually obvious that this devastating disease also affects the children as well as neonates with greater number. The aim of study was to determine the Covid-19 in neonates. So, we can give proper emphasis on neonatal Covid-19. This cross-sectional study was conducted from April 2020 to September 2020 at Dhaka Shishu (Children) Hospital in Bangladesh. Neonates with suspected Covid-19 were tested for SARS-CoV-2 by RT- PCR. Newborn who had suspected or confirmed COVID-19 mother, exposed to relatives infected with Covid-19, related with cluster outbreak or with abnormal clinical courses such as respiratory distress, not responded to conventional treatment and also abnormal chest x-ray was selected for Covid-19 test. Data regarding gestational age, birth weight, gender, positive cases and other findings were collected and analyzed. Statistics analysis was done by SPSS version 26.0. Forty three cases were Covid-19 positive. Among them 28(65.1%) cases were male and 15(34.9%) female. Term was 39(90.6%) cases and preterm 4(9.4%). Twenty nine (67.5%) cases were belonged to medicine and 14(32.6%) surgical cases. Fourteen (32.5%) cases with Covid-19 lived in Dhaka and 29(67.5%) cases in outside of Dhaka. Eleven (25.5%) cases were positive for SARS -CoV-2 by RT- PCR within 3 days, among them 5 (11.6%) cases were within 24 hours of age. Nine (20.9%) and 23(53.5%) cases were test positive at day 4-7 and 8-28 days respectively. The main symptoms at admission were respiratory difficulty (12/43, 27.9%), fever (8/43, 18.6%), convulsion (8/43, 18.6%) and reluctance to feed (7/43, 16.6%). In neonate two or more diseases coexist in same cases. Sepsis was present in 20 (46.5%) cases with COVID-19. Perinatal asphyxia was present in 10(23.3%) and pneumonia in 8 (18.6%) cases. In laboratory findings low Hb% was present in 2/43(4.7%) cases, leukopenia in 4/43(9.3%), leukocytosis in 2/43(4.7%) and thrombocytopenia in 5/43(11.6%). Elevated CRP was present in 14/29 (32.6%) cases, hypernatremia in 10/33 (30.3%), hyponatremia in 1/33(3%), increased serum creatinine in 10/18(55.6%), and prolonged PT, aPTT in 2/2(100%). Hyperglycaemia was found in 1/15(6.7%) cases and hypoglycaemia in 2/15(13.3%). No organism was found in blood C/S. In chest X-ray, one showed patchy opacities in right lower lobe, another showed bilateral ground-glass opacity and third one revealed few patchy opacities in the right perihilar region. Among 43 cases 21(48.9%) were discharged with advice, 12(27.9%) cases referred to Covid-19 designated hospital, 2(4.7%) cases LAMA (Leave against medical advice) and 8(18.6%) cases died including one surgical case. A good number (43) of Covid-19 cases were found in this study. In neonates the clinical features could not be differentiated properly between Covid-19 or associated diseases unlike children and adult. The neonate may be a source of transmission of this disease. So, we should give proper emphasis on test, tracing and management of neonatal Covid-19.
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Affiliation(s)
- M Rahman
- Dr Maksudur Rahman, Associate Professor, Neonatology, Bangladesh Institute of Child Health (BICH), Dhaka Shishu (Children) Hospital, Bangladesh; E-mail:
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5
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Afroz L, Nessa A, Tanvir IA, Noshin N, Sharmin A, Yeasmin F, Sharmin T, Das K. Status of Hemoglobin Concentration and Serum Total Iron Binding Capacity among Iron Deficiency Anemic Adolescent Girls. Mymensingh Med J 2024; 33:68-71. [PMID: 38163775] [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: 01/03/2024]
Abstract
Adolescence may be defined as the period from 10 to 19 years of age. Adolescence is a significant period of human growth and maturation when various changes occur and requirement of nutrients is increased in girls due to increase demands for growth. This prospective type of analytical cross-sectional study was carried out to observe the status of Hb concentration and serum total iron binding capacity (TIBC) levels among iron deficiency anemic adolescent girl. This study was conducted in the Department of Physiology, Mymensingh Medical College, Bangladesh from July 2019 to December 2020. For this purpose, 140 adolescent girl's age ranged from 10-19 years were selected in this study, among them, 70 healthy adolescent girls as control group (Group I) and 70 girls selected as study group (Group II) and they are iron deficiency anemic adolescent girls. Estimation of hemoglobin by cyanmethaemoglobin method and estimation of serum total iron binding capacity (TIBC) was determined by Ferrozine method using Globals iron and TIBC kit, UK. All data were expressed as mean ±SD and statistical significance of difference among the Group I and Group II were calculated by unpaired students''t' test. Hemoglobin (Hb) concentration significantly lowers in study group (Group II) in comparison with control group (Group I), Result is highly significant (p<0.001). Total iron binding capacity (TIBC) significantly higher in study group (Group II) in comparison with control group (Group I), Result is highly significant p<0.001). Immediate, long term and sustainable public health intervention would require for overcome the situation.
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Affiliation(s)
- L Afroz
- Dr Lily Afroz, Lecturer, Department of Physiology, Mymensingh Medical College (MMC), Mymensingh, Bangladesh; E-mail:
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Haque SMA, Mehataz T, Afros F, Jahan S, Islam S, Latif MS, Debnath D, Ahmed M, Das K, Avik AD. Anatomical Study of Number, Location and Position of Nutrient Foramina of Fully Ossified Dry Human Humerus. Mymensingh Med J 2024; 33:91-96. [PMID: 38163778] [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: 01/03/2024]
Abstract
The nutrient foramen is the natural opening present in the shaft of the humerus. It passes the nutrient artery to the medullary cavity. The nutrient artery is the chief artery that enters the bone through a nutrient foramen to provide nutrition for its growth. It plays an important role in healing during fracture and trauma and is also important for bone grafting. This study aimed to determine the common location, position and number of nutrient foramina of fully ossified dry human humerus. One hundred samples (right- 43 and left- 57) were selected through the purposive sampling technique for this cross-sectional descriptive study carried out in the Department of Anatomy, Mymensingh Medical College, Bangladesh from July 2021 to June 2022. Any damaged, unossified bones or fractured bones were excluded. Data were tabulated and statistically analyzed using Microsoft Excel and SPSS software. Among 43 right humeri, 37(75.51%) have single-nutrient foramen and 06(24.49%) have double-nutrient foramina. Among 57 left humeri, 53(92.98%) have single nutrient foramen, 03(5.27%) have double nutrient foramina and 01(1.75%) has triple nutrient foramina. In case of location of nutrient foramina, among 49 right nutrient foramina, 45(91.84%) were found on the anteromedial surface, 02(4.08%) were found on the anterolateral surface and 02(4.08%) were on the posterior surface of the shaft of the humerus. In case of 62 left nutrient foramina, 57(91.94%) were found on the anteromedial surface and 05(8.06%) were found on the posterior surface of the shaft of the humerus. Among 49 right nutrient foramina, 01(2.04%) was found on the upper third, 46(93.88%) on the middle third and 02(4.08%) on the lower third of the shaft of the humerus. In case of 62 left nutrient foramina, 01(1.60%) was on the upper third, 57(91.95%) were on the middle third and 04(6.45%) were on the lower third of the shaft of the humerus.
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Affiliation(s)
- S M A Haque
- Dr Shah Md Atiqul Haque, Lecturer, Department of Anatomy, Mymensingh Medical College (MMC), Mymensingh, Bangladesh; E-mail:
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Padilha JAG, Souza-Kasprzyk J, Pinzoni M, Prohaska G, Espejo W, Leite A, Santos S, Cunha LST, Costa ES, Pessôa AR, Torres JPM, Lepoint G, Das K, Dorneles PR. Mercury exposure in Antarctic seabirds: Assessing the influence of trophic position and migration patterns. Chemosphere 2023; 340:139871. [PMID: 37611760 DOI: 10.1016/j.chemosphere.2023.139871] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 08/25/2023]
Abstract
Although naturally present in the environment, mercury (Hg) input is significantly amplified by anthropogenic activities on a global scale, leading to a growing concern about the recent increase in Hg levels observed in Antarctica. This study investigated total mercury (THg) concentrations in feathers and eggs of resident and migratory Antarctic seabirds. Stable isotope data (δ15N, δ13C, and δ34S) were employed to ascertain the key factors influencing the exposure of these species to Hg. We gathered feathers and eggs from three resident species - Adélie, Gentoo, and Chinstrap penguins, as well as five migratory species - Snowy Sheathbill, Antarctic Tern, Southern Giant Petrel, Kelp Gull, and South Polar Skua. These samples were collected from Admiralty Bay, King George Island, in the Antarctica Peninsula. For all species, THg concentrations were higher in feathers (mean ± SD: 2267 ± 2480 ng g-1 dw) than in eggs (906 ± 1461 ng g-1 dw). Species occupying higher trophic positions, such as the Southern Giant Petrel (5667 ± 1500 ng g-1 dw) and South Polar Skua (4216 ± 1101 ng. g-1 dw), exhibited higher THg levels in their feathers than those at lower positions, like Antarctic Tern (1254 ± 400 ng g-1 dw) and Chinstrap Penguin (910 ± 364 ng g-1 dw). The δ15N values, which serve as a proxy for the trophic position, significantly correlated with THg concentrations. These findings reveal that trophic position influences THg concentrations in Antarctic seabirds. Migration did not appear to significantly affect the exposure of seabirds to THg, contrary to initial expectations. This research highlights the importance of evaluating the impacts of THg contamination on the Antarctic ecosystem by considering a variety of species. This multi-species approach offers critical insights into the factors that may potentially influence the exposure of these species to contaminants.
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Affiliation(s)
- J A G Padilha
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; CBMA - Centre for Molecular and Environmental Biology/ARNET-Aquatic Research Network & IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal; IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal.
| | - J Souza-Kasprzyk
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Ul. Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - M Pinzoni
- Freshwater and Oceanic ScienCes Unit of ReSearch (FOCUS), Laboratory of Oceanology, University of Liège, 4000, Liège, Belgium
| | - G Prohaska
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - W Espejo
- Department of Animal Science, Facultad de Ciencias Veterinarias, Universidad de Concepción, P.O. Box 537, Chillán, Chile
| | - A Leite
- CBMA - Centre for Molecular and Environmental Biology/ARNET-Aquatic Research Network & IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal; IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal
| | - S Santos
- CBMA - Centre for Molecular and Environmental Biology/ARNET-Aquatic Research Network & IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal; IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal
| | - L S T Cunha
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - E S Costa
- Mestrado Profissional Em Ambiente e Sustentabilidade. Universidade Estadual Do Rio Grande Do Sul, Rua Assis Brasil, 842, Centro, São Francisco de Paula, Rio Grande do Sul, Brazil
| | - A R Pessôa
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - J P M Torres
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - G Lepoint
- Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Ul. Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - K Das
- Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Ul. Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
| | - P R Dorneles
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Ul. Uniwersytetu Poznańskiego 8, 61-614, Poznan, Poland
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Paul A, Sarker S, Banik BC, Paul A, Paul SK, Nasreen SA, Haque N, Ahmed S, Khanam J, Arafa P, Nila SS, Chowdhury CS, Das AK, Das K. Detection of Oncogenic Human Papillomavirus (HPV-16 and HPV-18) from Bacterial Vaginosis Positive Patient Attending at Tertiary Care Hospital in Mymensingh. Mymensingh Med J 2023; 32:959-967. [PMID: 37777887] [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: 10/02/2023]
Abstract
Cervical cancer is the fourth most common cancer in women in the world and is the second leading malignancy among Bangladeshi women. Persistent infection with high risk human papillomavirus (HPV) is an important cause of development of cervical intraepithelial neoplasia (CIN) followed by cancer. Bacterial vaginosis (BV), a common treatable vaginal infection which can disrupt the balanced vaginal ecosystem and its innate protective mechanisms against infection, can play an essential role in the acquisition and persistence of high risk human papillomavirus (HR-HPV) infection. This cross sectional study was conducted to detect the HR-HPV (HPV-16 and HPV-18) infection among bacterial vaginosis positive patient in the Department of Microbiology, Mymensingh Medical College (MMC), Bangladesh, from March 2018 to February 2019. A total of 300 endocervical swabs and high vaginal swabs were collected from the VIA (Visual inspection with acetic acid) outdoor clinic of Obstetrics and Gynaecology Department of Mymensingh Medical college Hospital. HPV DNA was tested among all 300 cases by nested PCR. Typing of HPV 16 and HPV 18 was done among HPV DNA positive cases with BV and intermediate flora by multiplex PCR. BV was diagnosed according to Nugent criteria by using the gram stained smear of high vaginal swab. A total of 57/300 (19.0%) samples were positive for HPV DNA by nested PCR. Of the total 300 cases 78(26.0%) had BV, 38(13.0%) had intermediate flora and 184(61.0%) had normal vaginal flora. HPV DNA was more positive in patients having intermediate flora 08/38 (21.05%) followed by the patients having normal vaginal flora 37/184 (20.11%) and BV 12/78 (15.38%). Among the 12 BV patients who were also HPV DNA positive (83.33%) were belong to high risk HPV (type 16 and 18) group and among them 08(66.67%) were HPV-16 and 02(16.67%) were HPV-18. But among 08 HPV DNA positive intermediate flora containing patients only 01(12.5%) were belong to HR-HPV (type 16 and no type 18 was detected).
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Affiliation(s)
- A Paul
- Dr Anindita Paul, Medical Officer, Department of Microbiology, Mymensingh Medical College (MMC), Mymensingh, Bangladesh; E-mail:
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Goovaerts Q, Shen J, De Wijngaert B, Basu U, Patel SS, Das K. Structures illustrate step-by-step mitochondrial transcription initiation. Nature 2023; 622:872-879. [PMID: 37821701 PMCID: PMC10600007 DOI: 10.1038/s41586-023-06643-y] [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: 09/19/2022] [Accepted: 09/13/2023] [Indexed: 10/13/2023]
Abstract
Transcription initiation is a key regulatory step in gene expression during which RNA polymerase (RNAP) initiates RNA synthesis de novo, and the synthesized RNA at a specific length triggers the transition to the elongation phase. Mitochondria recruit a single-subunit RNAP and one or two auxiliary factors to initiate transcription. Previous studies have revealed the molecular architectures of yeast1 and human2 mitochondrial RNAP initiation complexes (ICs). Here we provide a comprehensive, stepwise mechanism of transcription initiation by solving high-resolution cryogenic electron microscopy (cryo-EM) structures of yeast mitochondrial RNAP and the transcription factor Mtf1 catalysing two- to eight-nucleotide RNA synthesis at single-nucleotide addition steps. The growing RNA-DNA is accommodated in the polymerase cleft by template scrunching and non-template reorganization, creating stressed intermediates. During early initiation, non-template strand scrunching and unscrunching destabilize the short two- and three-nucleotide RNAs, triggering abortive synthesis. Subsequently, the non-template reorganizes into a base-stacked staircase-like structure supporting processive five- to eight-nucleotide RNA synthesis. The expanded non-template staircase and highly scrunched template in IC8 destabilize the promoter interactions with Mtf1 to facilitate initiation bubble collapse and promoter escape for the transition from initiation to the elongation complex (EC). The series of transcription initiation steps, each guided by the interplay of multiple structural components, reveal a finely tuned mechanism for potential regulatory control.
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Affiliation(s)
- Quinten Goovaerts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Brent De Wijngaert
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA.
| | - Kalyan Das
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium.
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium.
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Das K, Ali MA, Akter MM, Kabir MR, Sadika S, Momo FR, Dipu MR, Avik AD, Paul A, Noshin N. Thyroid Hormone Level in Children with Nephrotic Syndrome. Mymensingh Med J 2023; 32:1005-1008. [PMID: 37777893] [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: 10/02/2023]
Abstract
Nephrotic syndrome is the most common glomerular disease affecting children. Hypothyroidism is one of the most important complications which occur due to urinary loss of protein bound thyroid hormones, such as thyroxin binding globulin, transthyretin and albumin. This cross sectional study was conducted in the Department of Pediatric, Mymensingh Medical College Hospital (MMCH), Bangladesh from February 2018 to October 2019. This study was carried out to find out the thyroid profile in children with nephrotic syndrome and compared with thyroid profile of other acute illness in children. Total 122 children aged 2-12 years, further subdivided into Group A (n=61) suffering from nephrotic syndrome (1st attack, infrequent relapse) and Group B (n=61) other disease like viral fever, pneumonia, bronchiolitis, diarrhoea, UTI. Demographic details of patients and their relevant clinical details were obtained by an interviewer administered questionnaire. Blood for free T4, TSH were taken and compared between both groups. The mean FT4 values in Group A and Group B were 16.09±22.32fmol/ml and 68.22±11.65fmol/ml respectively, whereas the TSH level was significantly higher in Group A than controls (5.42±1.04 vs. 3.53±1.44). The T4 levels in nephrotic syndrome (Group A) patients were low. Analysis was done by using SPSS 22.0 version for windows software. Continuous and catagorical parameters were compared by unpaired 't' test and Chi-Square test. A p-value of 0.05 was considered significant. Hypothyroidism was found more in younger children i.e. age less than 6 years. This study concluded that children with nephrotic syndrome have a state of hypothyroidism.
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Affiliation(s)
- K Das
- Dr Kakoli Das, Senior Consultant Paediatrics, Mymensingh Medical College Hospital, Bangladesh; E-mail:
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Pauwels E, Shewakramani NR, De Wijngaert B, Camps A, Provinciael B, Stroobants J, Kalies KU, Hartmann E, Maes P, Vermeire K, Das K. Structural insights into TRAP association with ribosome-Sec61 complex and translocon inhibition by a CADA derivative. Sci Adv 2023; 9:eadf0797. [PMID: 36867692 PMCID: PMC9984176 DOI: 10.1126/sciadv.adf0797] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/31/2023] [Indexed: 05/26/2023]
Abstract
During cotranslational translocation, the signal peptide of a nascent chain binds Sec61 translocon to initiate protein transport through the endoplasmic reticulum (ER) membrane. Our cryo-electron microscopy structure of ribosome-Sec61 shows binding of an ordered heterotetrameric translocon-associated protein (TRAP) complex, in which TRAP-γ is anchored at two adjacent positions of 28S ribosomal RNA and interacts with ribosomal protein L38 and Sec61α/γ. Four transmembrane helices (TMHs) of TRAP-γ cluster with one C-terminal helix of each α, β, and δ subunits. The seven TMH bundle helps position a crescent-shaped trimeric TRAP-α/β/δ core in the ER lumen, facing the Sec61 channel. Further, our in vitro assay establishes the cyclotriazadisulfonamide derivative CK147 as a translocon inhibitor. A structure of ribosome-Sec61-CK147 reveals CK147 binding the channel and interacting with the plug helix from the lumenal side. The CK147 resistance mutations surround the inhibitor. These structures help in understanding the TRAP functions and provide a new Sec61 site for designing translocon inhibitors.
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Affiliation(s)
- Eva Pauwels
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Neesha R. Shewakramani
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Brent De Wijngaert
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Anita Camps
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Becky Provinciael
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Joren Stroobants
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Kai-Uwe Kalies
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck 23562, Germany
| | - Enno Hartmann
- Centre for Structural and Cell Biology in Medicine, Institute of Biology, University of Lübeck, Lübeck 23562, Germany
| | - Piet Maes
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Kurt Vermeire
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
| | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Leuven 3000, Belgium
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Padilha JA, Carvalho GO, Espejo W, Pessôa ARL, Cunha LST, Costa ES, Torres JPM, Lepoint G, Das K, Dorneles PR. Trace elements in migratory species arriving to Antarctica according to their migration range. Mar Pollut Bull 2023; 188:114693. [PMID: 36773589 DOI: 10.1016/j.marpolbul.2023.114693] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The levels of eighteen trace elements (TEs) were evaluated in association with stable isotopes (δ15N, δ34S, and δ13C) in feathers and eggs of five migratory species breeding on the Antarctic Peninsula to test the factors that influence their exposure to contaminants. The feathers of seabirds migrating to the Northern Hemisphere (South polar skua) have concentrations (mean ± SD, μg. g-1) of Li (1.71 ± 2.08) and Mg (1169.5 ± 366.8) one order of magnitude higher than southern migrants, such as Snowy sheathbill Li (0.01 ± 0.005) and Mg (499.6 ± 111.9). Feathers had significantly higher concentrations for 11 of a total of 18 metals measured compared to eggs. South polar skua have higher concentrations of all TEs in eggs compared to antarctic tern. Therefore, the present study showed that migration and trophic ecology (δ15N, δ13C, and δ34S) influence Fe, Mn, Cu, and Se concentrations in feathers of Antarctic seabirds. The concentrations of Cu, Mn, Rb, Zn, Pb, Cd, Cr are higher than previously reported, which may be due to increased local and global human activities.
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Affiliation(s)
- J A Padilha
- Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; CBMA - Centre for Molecular and Environmental Biology/ARNET-Aquatic Research Network & IB-S, Institute of Science and Innovation for Bio-Sustainability, Department of Biology, University of Minho, Campus Gualtar, 4710-057 Braga, Portugal.
| | - G O Carvalho
- Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - W Espejo
- Department of Soils and Natural Resources, Facultad de Agronomía, Universidad de Concepción, P.O. Box 537, Chillán, Chile
| | - A R L Pessôa
- Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - L S T Cunha
- Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - E S Costa
- Mestrado Profissional em Ambiente e Sustentabilidade, Universidade Estadual do Rio Grande do Sul, Rua Assis Brasil, 842, Centro, São Francisco de Paula, Rio Grande do Sul, Brazil
| | - J P M Torres
- Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - G Lepoint
- Freshwater and Oceanic Sciences Unit of research (FOCUS), Laboratory of Oceanology, University of Liege, Belgium
| | - K Das
- Freshwater and Oceanic Sciences Unit of research (FOCUS), Laboratory of Oceanology, University of Liege, Belgium
| | - P R Dorneles
- Biophysics Institute, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Freshwater and Oceanic Sciences Unit of research (FOCUS), Laboratory of Oceanology, University of Liege, Belgium
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Chaturvedi K, Basu S, Singha S, Das K. Predictive microbial growth modelling for an effective shelf-life extension strategy of Chhana (Indian cottage cheese). Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109697] [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: 02/25/2023]
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Dibyachintan S, Nandy P, Das K, Vinjanampathy S, Mitra M. Unequal lives: a sociodemographic analysis of COVID-19 transmission and mortality in India. Public Health 2023; 214:133-139. [PMID: 36549022 PMCID: PMC9666378 DOI: 10.1016/j.puhe.2022.11.009] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022]
Abstract
OBJECTIVES Existing socio-economic inequalities shape, in very particular and measurable ways, the differential impact that a disease has on different sections of the same society. This is particularly true of COVID-19, which has rapidly exhausted the public health system in India, and magnified the gradient of vulnerability in an underserved populace. Using publicly available data, we have aimed to deconstruct this gradient into individual variables of inequality and quantify their impact on the transmission and mortality outcomes of COVID-19 in India. STUDY DESIGN Sociodemographic analysis. METHODS We quantify doubling times and case fatality ratios for all districts in India, then correlate them to 20 variables of socio-economic vulnerability and demographic structure. Variables that exhibit persistent correlation are then analysed using multivariate beta regression models to validate their impact on COVID-19 outcomes in India. RESULTS The transmission of COVID-19 in India is enhanced by the lack of access to indoor latrines, drainage facilities, electricity, and proximate sources of drinking water. Transmission is slowed by the presence of an elderly population. Fatality rates relate negatively to an area's medical infrastructure and the presence of a college-educated populace. CONCLUSIONS An interactive matrix of social inequalities, cultural practices, and behavioural patterns determines the path of COVID-19 through a community. Specific variables exhibit patterns of persistent vulnerability; others indicate a resistance to infection and mortality. This body of evidence, when incorporated into policy design, may lead to localised, need-sensitive models of intervention, both for preventive measures and medical care.
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Affiliation(s)
- S. Dibyachintan
- Department of Chemical Engineering, IIT Bombay, Mumbai, India,Département de Biochimie, de Microbiologie et de Bio-Informatique, Université Laval, Québec, QC, Canada
| | - P. Nandy
- Department of Chemical Engineering, IIT Bombay, Mumbai, India,Laureate Centre for History and Population, UNSW Sydney, Australia,Corresponding author. Postal Address: Laureate Centre for History and Population, University of New South Wales Sydney, Kensington 2052, NSW, Australia
| | - K. Das
- Department of Mathematics, IIT Bombay, Mumbai, India
| | | | - M.K. Mitra
- Department of Physics, IIT Bombay, Mumbai, India,Corresponding author. Postal Address: Department of Physics, IIT Bombay, Powai, Mumbai – 400076, India. Tel.: +91 22 2576-7565 (O), +91-7506187565 (M); Fax: +91 22 2576-7552
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Sethy PK, Geetha Devi A, Padhan B, Behera SK, Sreedhar S, Das K. Lung cancer histopathological image classification using wavelets and AlexNet. J Xray Sci Technol 2023; 31:211-221. [PMID: 36463485 DOI: 10.3233/xst-221301] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Among malignant tumors, lung cancer has the highest morbidity and fatality rates worldwide. Screening for lung cancer has been investigated for decades in order to reduce mortality rates of lung cancer patients, and treatment options have improved dramatically in recent years. Pathologists utilize various techniques to determine the stage, type, and subtype of lung cancers, but one of the most common is a visual assessment of histopathology slides. The most common subtypes of lung cancer are adenocarcinoma and squamous cell carcinoma, lung benign, and distinguishing between them requires visual inspection by a skilled pathologist. The purpose of this article was to develop a hybrid network for the categorization of lung histopathology images, and it did so by combining AlexNet, wavelet, and support vector machines. In this study, we feed the integrated discrete wavelet transform (DWT) coefficients and AlexNet deep features into linear support vector machines (SVMs) for lung nodule sample classification. The LC25000 Lung and colon histopathology image dataset, which contains 5,000 digital histopathology images in three categories of benign (normal cells), adenocarcinoma, and squamous carcinoma cells (both are cancerous cells) is used in this study to train and test SVM classifiers. The study results of using a 10-fold cross-validation method achieve an accuracy of 99.3% and an area under the curve (AUC) of 0.99 in classifying these digital histopathology images of lung nodule samples.
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Affiliation(s)
| | - A Geetha Devi
- Department of Electronics and Communication Engineering, PVP Siddhartha Institute of Technology, Vijayawada, AP, India
| | - Bikash Padhan
- Department of Electronics, Sambalpur University, Jyoti Vihar, Burla, India
| | | | | | - Kalyan Das
- Department Computer Science Engineering and Application, Sambalpur University Institute of Information Technology, Burla, India
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Das S, Majumder M, Das D, Chowdhury N, Das A, Das K, Fardous J, Hasan MJ. Prevalence and Risk Factors of Secondary Hyperparathyroidism among CKD Patients and Correlation with Different Laboratory Parameters. Mymensingh Med J 2022; 31:1084-1092. [PMID: 36189556] [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: 06/16/2023]
Abstract
Hyperthyroidism is one of the major complications in CKD patients who results in a number of metabolic disorders and contributes to morbidity and mortality. The objective of the study was to investigate the prevalence and risk factors for secondary hyperparathyroidism among CKD patients as well as its correlation with different laboratory parameters. This was a cross-sectional study conducted among the admitted CKD patients of Sylhet MAG Osmani Medical College Hospital, Sylhet, Bangladesh from January 2019 to December 2019. Following recruitment, clinical parameters were extracted from the patients' medical records. Afterward, blood sample blood was collected to measure the biochemical parameters and serum parathyroid hormone levels. A binary logistic regression model was used to assess the factors associated with hyperparathyroidism. The mean±SD serum PTH in all CKD patients was 215.04±168.15 pg/ml. The overall prevalence of secondary hyperparathyroidism among CKD patients was 75.0% (32.0% in stage 3, 88.0% in stage 4 and 93.0% in stage 5 CKD). Serum PTH levels had a significant positive correlation with serum creatinine and serum phosphate levels and a significant negative correlation with serum albumin and serum calcium levels. However, only female sex was revealed as a significant risk factor in the adjusted regression model (aOR 0.26, 95% CI 0.07-0.98 for male sex compared to female sex). As the prevalence of secondary hyperparathyroidism increases in advanced stages of CKD, early detection and management of CKD are crucial to prevent metabolic disorders that could trigger the development of this complication.
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Affiliation(s)
- S Das
- Dr Supti Das, Assistant Professor, Department of Biochemistry, Sylhet MAG Osmani Medical College, Sylhet, Bangladesh; E-mail:
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Olivet J, Maseko SB, Volkov AN, Salehi-Ashtiani K, Das K, Calderwood MA, Twizere JC, Gorgulla C. A systematic approach to identify host targets and rapidly deliver broad-spectrum antivirals. Mol Ther 2022; 30:1797-1800. [PMID: 35231394 PMCID: PMC8884476 DOI: 10.1016/j.ymthe.2022.02.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/10/2021] [Accepted: 02/11/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Julien Olivet
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven (KU Leuven), Leuven, Belgium; Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium
| | - Sibusiso B Maseko
- Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium
| | - Alexander N Volkov
- VIB-VUB Center for Structural Biology, Flemish Institute of Biotechnology (VIB), Brussels, Belgium; Jean Jeener NMR Centre, Free University of Brussels (VUB), Brussels, Belgium
| | | | - Kalyan Das
- Structural Biology Unit, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research and Department of Microbiology, Immunology and Transplantation, Catholic University of Leuven (KU Leuven), Leuven, Belgium
| | - Michael A Calderwood
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes Networks, Unit of Molecular Biology of Diseases, Interdisciplinary Cluster for Applied Genoproteomics (GIGA Institute), University of Liège, Liège, Belgium; Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; TERRA Research and Teaching Centre, Microbial Processes and Interactions (MiPI), Gembloux Agro Bio-tech, University of Liège, Gembloux, Belgium.
| | - Christoph Gorgulla
- Department of Cancer Biology, Dana-Farber Cancer Institute (DFCI), Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School (HMS), Boston, MA, USA; Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA.
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Bhattacharyya A, Sarma P, Kaur H, Hafezi F, Bhattacharyya J, Kirubakaran R, Prajapat M, Medhi B, Das K, Prakash A, Singh A, Kumar S, Singh R, Reddy D, Kaur G, Sharma S. Short- and long-term safety and efficacy of corneal collagen cross-linking in progressive keratoconus: A systematic review and meta-analysis of randomized controlled trials. Taiwan J Ophthalmol 2022. [PMID: 37484615 PMCID: PMC10361434 DOI: 10.4103/2211-5056.361974] [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: 11/27/2022] Open
Abstract
PURPOSE The purpose of the study is to evaluate the safety and outcomes of corneal collagen cross-linking (CXL) and different CXL protocols in progressive keratoconus (PK) population at short and long-term. MATERIALS AND METHODS A systematic review and meta-analysis was conducted. A total of eight literature databases were searched (up to February 15, 2022). Randomized controlled trials (RCTs) comparing CXL versus placebo/control or comparing different CXL protocols in the PK population were included. The primary objective was assessment of outcomes of CXL versus placebo and comparison of different CXL protocols in terms of maximum keratometry (Kmax) or Kmax change from baseline (Δ), spherical equivalent, best corrected visual acuity (BCVA), and central corneal thickness (CCT) in both at short term (6 months) and long term (1st, 2nd, and 3rd year or more). The secondary objective was comparative evaluation of safety. For the meta-analysis, the RevMan5.3 software was used. RESULTS A total of 48 RCTs were included. Compared to control, CXL was associated with improvement in Δ Kmax at 1 year (4 RCTs, mean difference [MD], -1.78 [-2.71, -0.86], P = 0.0002) and 2 and 3 years (1 RCT); ΔBCVA at 1 year (7 RCTs, -0.10 [-0.14, -0.06], P < 0.00001); and Δ CCT at 1 year (2 RCTs) and 3 years (1 RCT). Compared to conventional CXL (C-CXL), deterioration in Δ Kmax, ΔBCVA and endothelial cell density was seen at long term in the transepithelial CXL (TE-CXL, chemical enhancer). Up to 2 years, there was no difference between TE-CXL using iontophoresis (T-ionto) and C-CXL. At 2 and 4 years, C-CXL performed better compared to accelerated CXL (A-CXL) in terms of improving Kmax. Although CCT was higher in the A-CXL arm at 2 years, there was no difference at 4 years. While exploring heterogeneity among studies, selection of control eye (fellow eye of the same patient vs. eye of different patient) and baseline difference in Kmax were important sources of heterogeneity. CONCLUSION CXL outperforms placebo/control in terms of enhancing Kmax and CCT, as well as slowing disease progression over time (till 3 years). T-ionto protocol, on the other hand, performed similarly to C-CXL protocol up to 2 years.
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Das K, Das S. Energy-Efficient Cloud-Integrated Sensor Network Model Based on Data Forecasting Through ARIMA. International Journal of e-Collaboration 2022. [DOI: 10.4018/ijec.290292] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An energy-efficient Model for Sensor-cloud is proposed based on data forecasting through an autoregressive integrated moving average (ARIMA). Generally, all the user requests are redirected to the wireless sensor network (WSN) through the cloud. In the traditional approach, user requests are generated every fifteen minutes, so the sensor must send data to the cloud every fifteen minutes. In the current approach, the sensors within the WSN communicate with the cloud every two hours. The data forecasting technique addresses most of the user requests using the ARIMA one-step ahead forecasting model in the cloud. This results in less frequency of data communication, thereby increasing the battery life of the sensor. The ARIMA-based forecasting model provides better accuracy because of fewer temperature data changes with respect to the current temperature, for the next two hours. The proposed method for the simulation in the sensor cloud system consumes significantly less energy than the traditional approach, and the error in forecasting becomes highly negligible.
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Affiliation(s)
- Kalyan Das
- Department of Computer Science and Engineering, Veer Surendra Sai University of Technology, Burla, India
| | - Satyabrata Das
- Department of Computer Science and Engineering, Veer Surendra Sai University of Technology, Burla, India
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Losada N, Ruiz FX, Curreli F, Gruber K, Pilch A, Altieri A, Kurkin AV, Das K, Debnath AK, Arnold E. Correction to "HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites". J Med Chem 2021; 65:885. [PMID: 34915707 DOI: 10.1021/acs.jmedchem.1c02061] [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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Singh AK, Martinez SE, Gu W, Nguyen H, Schols D, Herdewijn P, De Jonghe S, Das K. Sliding of HIV-1 reverse transcriptase over DNA creates a transient P pocket - targeting P-pocket by fragment screening. Nat Commun 2021; 12:7127. [PMID: 34880240 PMCID: PMC8654897 DOI: 10.1038/s41467-021-27409-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 11/17/2021] [Indexed: 11/09/2022] Open
Abstract
HIV-1 reverse transcriptase (RT) slides over an RNA/DNA or dsDNA substrate while copying the viral RNA to a proviral DNA. We report a crystal structure of RT/dsDNA complex in which RT overstepped the primer 3'-end of a dsDNA substrate and created a transient P-pocket at the priming site. We performed a high-throughput screening of 300 drug-like fragments by X-ray crystallography that identifies two leads that bind the P-pocket, which is composed of structural elements from polymerase active site, primer grip, and template-primer that are resilient to drug-resistance mutations. Analogs of a fragment were synthesized, two of which show noticeable RT inhibition. An engineered RT/DNA aptamer complex could trap the transient P-pocket in solution, and structures of the RT/DNA complex were determined in the presence of an inhibitory fragment. A synthesized analog bound at P-pocket is further analyzed by single-particle cryo-EM. Identification of the P-pocket within HIV RT and the developed structure-based platform provide an opportunity for the design new types of polymerase inhibitors.
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Affiliation(s)
- Abhimanyu K Singh
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Sergio E Martinez
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Weijie Gu
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.,Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Hoai Nguyen
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Dominique Schols
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Piet Herdewijn
- Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Steven De Jonghe
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium
| | - Kalyan Das
- Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000, Leuven, Belgium.
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Gu W, Martinez S, Singh AK, Nguyen H, Rozenski J, Schols D, Herdewijn P, Das K, De Jonghe S. Exploring the dNTP -binding site of HIV-1 reverse transcriptase for inhibitor design. Eur J Med Chem 2021; 225:113785. [PMID: 34425311 DOI: 10.1016/j.ejmech.2021.113785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/29/2021] [Revised: 08/13/2021] [Accepted: 08/14/2021] [Indexed: 11/17/2022]
Abstract
HIV-1 reverse transcriptase (RT) plays a central role in the viral life cycle, and roughly half of the FDA-approved anti-HIV drugs are targeting RT. Nucleoside analogs (NRTIs) require cellular phosphorylation for binding to RT, and to bypass this rate-limiting path, we designed a new series of acyclic nucleoside phosphonate analogs as nucleoside triphosphate mimics, aiming at the chelation of the catalytic Mg2+ ions via a phosphonate and/or a carboxylic acid group. Novel synthetic procedures were developed to access these nucleoside phosphonate analogs. X-ray structures in complex with HIV-1 RT/dsDNA demonstrated that their binding modes are distinct from that of our previously reported compound series. The impact of chain length, chirality and linker atom have been discussed. The detailed structural understanding of these new compounds provides opportunities for designing new class of HIV-1 RT inhibitors.
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Affiliation(s)
- Weijie Gu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium; KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, 3000, Leuven, Belgium
| | - Sergio Martinez
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Abhimanyu K Singh
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Hoai Nguyen
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, 3000, Leuven, Belgium
| | - Jef Rozenski
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, 3000, Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Laboratory of Medicinal Chemistry, Herestraat 49, 3000, Leuven, Belgium
| | - Kalyan Das
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium.
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, 3000, Leuven, Belgium.
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Borthakur D, Rani M, Das K, Shah MP, Sharma BK, Kumar A. Bioremediation: an alternative approach for detoxification of polymers from the contaminated environment. Lett Appl Microbiol 2021; 75:744-758. [PMID: 34825392 DOI: 10.1111/lam.13616] [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: 08/06/2021] [Revised: 10/04/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022]
Abstract
The industries and metropolitan wastes produced by anthropogenic activities are of great concern for nature as it causes soil contamination and deteriorate the environment. Plastic utilization is rapidly enhancing globally with passing days that last for a more extended period in the environment due to slow decomposition and natural degradation. Excessive use of polymer has risked the life of both marine, freshwater and terrestrial organisms. Lack of proper waste management and inappropriate disposal leads to environmental threats. Bioremediation processes involve microbes such as fungi, bacteria, etc. which contribute a crucial role in the breakdown of plastics. Extremophiles secrete extremozymes that are functionally active in extreme conditions and are highly crucial for polymer disaggregation in those conditions.
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Affiliation(s)
- D Borthakur
- Department of Microbiology, Tripura University (A Central University), Agartala, Tripura, India.,Department of Life Sciences, Assam Don Bosco University, Tepesia, Assam, India
| | - M Rani
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - K Das
- Department of Microbiology, Tripura University (A Central University), Agartala, Tripura, India
| | - M P Shah
- Enviro Technology Ltd., Ankleshwar, Gujarat, India
| | - B K Sharma
- Department of Microbiology, Tripura University (A Central University), Agartala, Tripura, India
| | - A Kumar
- Department of Microbiology, Tripura University (A Central University), Agartala, Tripura, India
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Losada N, Ruiz FX, Curreli F, Gruber K, Pilch A, Das K, Debnath AK, Arnold E. HIV-1 gp120 Antagonists Also Inhibit HIV-1 Reverse Transcriptase by Bridging the NNRTI and NRTI Sites. J Med Chem 2021; 64:16530-16540. [PMID: 34735153 PMCID: PMC10655131 DOI: 10.1021/acs.jmedchem.1c01104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/28/2022]
Abstract
HIV-1 infection is typically treated using ≥2 drugs, including at least one HIV-1 reverse transcriptase (RT) inhibitor. Drugs targeting RT comprise nucleos(t)ide RT inhibitors (NRTIs) and non-nucleoside RT inhibitors (NNRTIs). NRTI-triphosphates bind at the polymerase active site and, following incorporation, inhibit DNA elongation. NNRTIs bind at an allosteric pocket ∼10 Å away from the polymerase active site. This study focuses on compounds ("NBD derivatives") originally developed to bind to HIV-1 gp120, some of which inhibit RT. We have determined crystal structures of three NBD compounds in complex with HIV-1 RT, correlating with RT enzyme inhibition and antiviral activity, to develop structure-activity relationships. Intriguingly, these compounds bridge the dNTP and NNRTI-binding sites and inhibit the polymerase activity of RT in the enzymatic assays (IC50 < 5 μM). Two of the lead compounds, NBD-14189 and NBD-14270, show potent antiviral activity (EC50 < 200 nM), and NBD-14270 shows low cytotoxicity (CC50 > 100 μM).
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Affiliation(s)
- Natalie Losada
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Francesca Curreli
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065, USA
| | - Kevin Gruber
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Alyssa Pilch
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
| | - Asim K. Debnath
- Laboratory of Molecular Modeling & Drug Design, Lindsley F. Kimball Research Institute, New York Blood Center, New York, 10065, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08854, USA
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Prabhakar PK, Srivastav PP, Pathak SS, Das K. Mathematical Modeling of Total Volatile Basic Nitrogen and Microbial Biomass in Stored Rohu (Labeo rohita) Fish. Front Sustain Food Syst 2021. [DOI: 10.3389/fsufs.2021.669473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The paper deals with the dynamical behavior of fish volatiles and microbial growth in stored Rohu fish through mathematical modeling. Total volatile basic nitrogen (TVB-N) is formed in stored Rohu (Labeo rohita) fish due to some complicated biochemical activities. It considered the biomass populace of volatiles (TVB-N) and microorganisms in fish stored at two different temperatures, separately. The different models may be used to forecast TVB-N, microbial populace (total viable count; TVC), and various properties change during nourishment stockpiling coordination and diverse preparing tasks. Models might be dynamic, exact, hypothetical, and stochastic in nature. Various parameters are required to build up a model which can be utilized to foresee the freshness and timeframe of realistic usability of storage duration. The ecosystem is represented by algebraic equations involving volatile compounds and microbial populations separately. TVB-N and TVC of stored rohu fish was determined at an interval of 4 days for 24 days. The initial and final biomass of TVB-N was 4.57 (fresh sample), 19.88 (24 days at 5°C), and 7.10 mg/100 g (24th day at 0°C), respectively. The TVC values were found to be 2.29 (fresh sample), 9.5 (24 days at 5°C) and 8.1 log (cfu/g) (24 days at 0°C). Exponential, modified exponential, Howgate, and adapted Howgate models were considered for modeling the TVB-N formation, whereas logistic, modified logistic, Gompertz, and modified Gompertz model were taken forward for modeling the microbial biomass developed in stored rohu fish. The exponential model found be the best fit model fit model for TVB-N prediction in rohu fish stored at 0 and 5°C as it showed the highest R2 (0.9796, 0.9887) the lowest χ2 (0.2782, 0.3976), RMSE (0.52741, 0.6306) AIC (−7.3122, −4.8106), AICc (−0.5122, 1.9894) and BIC (−7.4204, −4.9188), respectively. The Gompertz model was found to be the best fit model for microbial biomass prediction in rohu fish stored at 5°C (R2 = 0.9947, χ2 = 0.0537, AIC = −18.379, AICc = −6.3792 and BIC = −18.542), in contrast, both of the logistic and modified logistic models were the best suited at 0°C storage condition (R2 = 0.9919, χ2 = 0.0823).
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Padilha JA, Carvalho GO, Espejo W, Souza JS, Pizzochero AC, Cunha LST, Costa ES, Pessôa ARL, Almeida AP, Torres JPM, Lepoint G, Michel LN, Das K, Dorneles PR. Factors that influence trace element levels in blood and feathers of Pygoscelis penguins from South Shetland Islands, Antarctica. Environ Pollut 2021; 284:117209. [PMID: 33932832 DOI: 10.1016/j.envpol.2021.117209] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/08/2021] [Accepted: 04/19/2021] [Indexed: 06/12/2023]
Abstract
Contaminant levels are lower in Antarctica than elsewhere in the world because of its low anthropogenic activities. However, the northern region of the Antarctic Peninsula, is close to South America and experiences the greatest anthropogenic pressure in Antarctica. Here, we investigated, in two Antarctic Peninsula islands, intra and interspecific factors that influence the concentrations of 17 trace elements (TEs) in blood and feathers of three penguin species breeding sympatrically in relation to their trophic ecology assessed via a stable isotopic approach (C, N and S). Geographical location, foraging zone (δ13C and δ34S) and diet influences the interspecific difference, and sex and maturity stage diet influence the intraspecific difference of Pygoscelis penguins. Penguins from Livingston showed higher values (mean, ng. g-1, dry weight - dw) of Zn (103), Mn (0.3), and Fe (95) than those from King George Island (Zn: 80, Mn: 1.9, and Fe: 11). Gender-related differences were observed, as males showed significantly higher values (mean, ng. g-1, dw) of Rb (3.4) and δ15N in blood of gentoo, and Ca (1344) in Adélie feathers. Chicks of gentoo and Adélie presented higher Zn, Mg, Ca, and Sr and lower 13C values in blood than adults. The highest concentrations (mean, ng. g-1, dw) of Cd (0.2) and Cu (26), and the lowest δ15N values were found in chinstrap. Geographical, intraspecific (i.e., ontogenetic and gender-related) and interspecific differences in feeding seemed to have influenced TE and stable isotope values in these animals. The TE bioaccumulation by penguins may have also been influenced by natural enrichment in environmental levels of these elements, which seems to be the case for Fe, Zn, and Mn. However, the high level of some of the TEs (Mn, Cd, and Cr) may reflect the increase of local and global human activities.
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Affiliation(s)
- J A Padilha
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - G O Carvalho
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - W Espejo
- Department of Animal Science, Facultad de Ciencias Veterinarias, Universidad de Concepción, P.O. Box 537, Chillán, Chile
| | - J S Souza
- Department of Analytical Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Ul. Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - A C Pizzochero
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - L S T Cunha
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - E S Costa
- Mestrado Profissional Em Ambiente e Sustentabilidade, Universidade Estadual Do Rio Grande Do Sul, Rua Assis Brasil, 842, Centro, São Francisco de Paula, Rio Grande do Sul, Brazil
| | - A R L Pessôa
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - A P Almeida
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - J P M Torres
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - G Lepoint
- Freshwater and Oceanic Sciences Unit of Research (FOCUS), Laboratory of Oceanology, University of Liege, Belgium
| | - L N Michel
- Freshwater and Oceanic Sciences Unit of Research (FOCUS), Laboratory of Oceanology, University of Liege, Belgium
| | - K Das
- Freshwater and Oceanic Sciences Unit of Research (FOCUS), Laboratory of Oceanology, University of Liege, Belgium
| | - P R Dorneles
- Radioisotope Laboratory, Biophysics Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil; Freshwater and Oceanic Sciences Unit of Research (FOCUS), Laboratory of Oceanology, University of Liege, Belgium
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Harrison JJEK, Tuske S, Das K, Ruiz FX, Bauman JD, Boyer PL, DeStefano JJ, Hughes SH, Arnold E. Crystal Structure of a Retroviral Polyprotein: Prototype Foamy Virus Protease-Reverse Transcriptase (PR-RT). Viruses 2021; 13:v13081495. [PMID: 34452360 PMCID: PMC8402755 DOI: 10.3390/v13081495] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/23/2022] Open
Abstract
In most cases, proteolytic processing of the retroviral Pol portion of the Gag-Pol polyprotein precursor produces protease (PR), reverse transcriptase (RT), and integrase (IN). However, foamy viruses (FVs) express Pol separately from Gag and, when Pol is processed, only the IN domain is released. Here, we report a 2.9 Å resolution crystal structure of the mature PR-RT from prototype FV (PFV) that can carry out both proteolytic processing and reverse transcription but is in a configuration not competent for proteolytic or polymerase activity. PFV PR-RT is monomeric and the architecture of PFV PR is similar to one of the subunits of HIV-1 PR, which is a dimer. There is a C-terminal extension of PFV PR (101-145) that consists of two helices which are adjacent to the base of the RT palm subdomain, and anchors PR to RT. The polymerase domain of PFV RT consists of fingers, palm, thumb, and connection subdomains whose spatial arrangements are similar to the p51 subunit of HIV-1 RT. The RNase H and polymerase domains of PFV RT are connected by flexible linkers. Significant spatial and conformational (sub)domain rearrangements are therefore required for nucleic acid binding. The structure of PFV PR-RT provides insights into the conformational maturation of retroviral Pol polyproteins.
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Affiliation(s)
- Jerry Joe E. K. Harrison
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry, University of Ghana, Legon P.O. Box LG 56, Ghana
| | - Steve Tuske
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
| | - Paul L. Boyer
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA; (P.L.B.); (S.H.H.)
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD 20742, USA;
| | - Stephen H. Hughes
- HIV Dynamics and Replication Program, National Cancer Institute, Frederick, MD 21702, USA; (P.L.B.); (S.H.H.)
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ 08854, USA; (J.J.E.K.H.); (S.T.); (K.D.); (F.X.R.); (J.D.B.)
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers University, Piscataway, NJ 08854, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
- Correspondence:
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Martinez SE, Singh A, De Wijngaert B, Sultana S, Dharia C, Vanbuel H, Shen J, Vasilchuk D, Patel SS, Das K. Assembly and Cryo-EM structure determination of yeast mitochondrial RNA polymerase initiation complex intermediates. STAR Protoc 2021; 2:100431. [PMID: 33870232 PMCID: PMC8044712 DOI: 10.1016/j.xpro.2021.100431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
In yeast mitochondria, transcription initiation requires assembly of mitochondrial RNA polymerase and transcription initiation factor MTF1 at the DNA promoter initiation site. This protocol describes the purification of the component proteins and assembly of partially melted and fully melted initiation complex states. Both states co-exist in equilibrium in the same sample as seen by cryoelectron microscopy (cryo-EM) and allow elucidation of MTF1's structural roles in controlling the transition into elongation. We further outline how analysis of the complex by light scattering, thermal shift assay, and ultrafiltration assay exhibits reproducible results. For complete details on the use and execution of this protocol, please refer to De Wijngaert et al. (2021).
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Affiliation(s)
- Sergio E. Martinez
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Anupam Singh
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Brent De Wijngaert
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Shemaila Sultana
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Chhaya Dharia
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Hans Vanbuel
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Daniel Vasilchuk
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Smita S. Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Kalyan Das
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
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Affiliation(s)
- Nitamani Choudhury
- Department of Basic & Applied Sciences National Institute of Food Technology Entrepreneurship and Management Kundli India
| | - Murlidhar Meghwal
- Department of Food Science and Technology National Institute of Food Technology Entrepreneurship and Management Kundli India
| | - Kalyan Das
- Department of Basic & Applied Sciences National Institute of Food Technology Entrepreneurship and Management Kundli India
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Das K, Ranjith Kumar G, Madhusudhan Reddy K, Lakshminarayan K. Sensitivity and elasticity analysis of novel corona virus transmission model: A mathematical approach. Sens Int 2021; 2:100088. [PMID: 34766050 PMCID: PMC7943394 DOI: 10.1016/j.sintl.2021.100088] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 11/28/2022] Open
Abstract
The deadly corona virus continues to pound the globe mercilessly compelling mathematical models and computational simulations which might prove effective tools to enable global efforts to estimate key transmission parameters involved in the system. We propose a mathematical model using a set of non-linear differential equations to account for the spread of the COVID-19 infection with special compartment class isolation or quarantine and estimate the model parameters by fitting the model with reported data of the ongoing pandemic situation in India. The basic reproduction number is defined and local stability analysis is carried out at each equilibrium point in terms of the reproduction numberR 0 . The model is fitted mathematically and makes the data India specific. Additionally, we examined sensitivity analysis of the model. These outcomes recommend how to control the spread of corona, keeping in mind contact and recovery rate. Also we have investigated the elasticity of the basic reproduction number as a measure of control parameters of the dynamical system. Numerical simulations were also done to show that the proposed model is valid for the type and spread of the outbreak which happened in India.
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Affiliation(s)
- Kalyan Das
- Department of Basic and Applied Sciences, National Institute of Food Technology Entrepreneurship and Management, HSIIDC Industrial Estate, Kundli, Haryana, India
| | - G Ranjith Kumar
- Department of Mathematics, Anurag University, Hyderabad, Telangana, India
| | - K Madhusudhan Reddy
- Department of Mathematics, Vardhaman College of Engineering, Hyderabad, Telangana, India
| | - K Lakshminarayan
- Department of Mathematics, Vidya Jyothi Institute of Technology, Hyderabad, Telangana, India
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Dietz R, Sonne C, Jenssen BM, Das K, de Wit CA, Harding KC, Siebert U, Olsen MT. The Baltic Sea: An ecosystem with multiple stressors. Environ Int 2021; 147:106324. [PMID: 33326905 DOI: 10.1016/j.envint.2020.106324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
This introductory chapter to our Environment International VSI does not need an abstract and therefore we just include our recommendations below in order to proceed with the resubmission. Future work should examine waterbirds as food web sentinels of multiple stressors as well as Baltic Sea food web dynamics of hazardous substances and how climate change may modify it. Also, future work should aim at further extending the new frameworks developed within BALTHEALTH for energy and contaminant transfer at the population level (Desforges et al., 2018, Cervin et al., 2020/this issue Silva et al., 2020/this issue) and their long term effects on Baltic Sea top predators, such as harbour porpoises, grey seals ringed seals, and white-tailed eagles. Likewise, the risk evaluation conducted for PCB in connection with mercury on Arctic wildlife (Dietz et al., 2019, not a BONUS BALTHEALTH product) could be planned for Baltic Sea molluscs, fish, bird and marine mammals in the future. Finally, future efforts could include stressors not covered by the BONUS BALTHEALTH project, such as food web fluxes, overexploitation, bycatches, eutrophication and underwater noise.
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Affiliation(s)
- R Dietz
- Department of Bioscience, Arctic Research Centre (ARC), Aarhus University, Faculty of Science and Technology, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark.
| | - C Sonne
- Department of Bioscience, Arctic Research Centre (ARC), Aarhus University, Faculty of Science and Technology, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - B M Jenssen
- Department of Bioscience, Arctic Research Centre (ARC), Aarhus University, Faculty of Science and Technology, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark; Department of Biology, Norwegian University of Science and Technology, Høgskoleringen 5, 7491 Trondheim, Norway
| | - K Das
- Freshwater and Oceanic sciences Unit of reSearch (FOCUS), Laboratory of Oceanology, University of Liege, Allée du six Août 11, Bât. B6C, 4000 Liège, Belgium
| | - C A de Wit
- Department of Environmental Science, Stockholm University, Svante Arrheniusvägen 8, SE-10691 Stockholm, Sweden
| | - K C Harding
- Department of Biological and Environmental Sciences, Gothenburg University, Box 461, SE-40530 Gothenburg, Sweden
| | - U Siebert
- Institute for Terrestrial and Aquatic Wildlife Research, University of Veterinary Medicine Hannover, Foundation, Büsum, Germany
| | - M T Olsen
- Evolutionary Genomics, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, DK-1353 Copenhagen K, Denmark
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Mallik S, Prasad R, Das K, Sen P. Alcohol functionality in the fatty acid backbone of sphingomyelin guides the inhibition of blood coagulation. RSC Adv 2021; 11:3390-3398. [PMID: 35424312 PMCID: PMC8694017 DOI: 10.1039/d0ra09218e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022] Open
Abstract
Cell-surface sphingomyelin (SM) inhibits binary and ternary complex activity of blood coagulation by an unknown mechanism. Here we show the OH functionality of SM contributes in forming the close assembly through intermolecular H-bond and through Ca2+ chelation, which restricts the protein–lipid/protein–protein interactions and thus inhibits the coagulation procedure. Cell-surface sphingomyelin (SM) inhibits binary and ternary complex activity of blood coagulation.![]()
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Affiliation(s)
- S Mallik
- Department of Biological Chemistry, Indian Association for the Cultivation of Science 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata-700032 India
| | - R Prasad
- Department of Biological Chemistry, Indian Association for the Cultivation of Science 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata-700032 India
| | - K Das
- Department of Biological Chemistry, Indian Association for the Cultivation of Science 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata-700032 India
| | - P Sen
- Department of Biological Chemistry, Indian Association for the Cultivation of Science 2A & 2B Raja S. C. Mullick Road, Jadavpur Kolkata-700032 India
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Das K, Raturi M, Agrawal N, Kala M, Kusum A. Indian blood donor selection guidelines: Review in the context of the ongoing COVID-19 pandemic. Transfus Clin Biol 2021; 28:213-216. [PMID: 33453376 DOI: 10.1016/j.tracli.2020.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/12/2020] [Revised: 12/18/2020] [Accepted: 12/29/2020] [Indexed: 01/28/2023]
Abstract
The National Blood Transfusion Services under the aegis of the ministry of health and family welfare, India has recently issued guidelines regarding the blood donor selection criteria and the processing of blood. Care has been taken to make the blood transfusions safer. However, COVID-19 has disrupted the organization of the voluntary blood donation drives, whole blood donations [WBD] and restricted the donors' movement to the blood transfusion centres all across the world. While sickness and the need for transfusions are very much in place, the gap of demand against blood collection has widened. Additionally, with the monsoon season at hand, and the categorical challenges of a dengue outbreak, the subsequent need for blood components especially the platelet concentrates is going to rise. Some of the criteria laid for deferring a blood donor from his or her WBD need a categorical revision, considering these unprecedented times. We, therefore, critically analyzed the blood donor selection criteria and hereby, suggest an updating regarding the pre-donation haemoglobin, sexually transmitted diseases, lactation, pregnancy and many such subheadings. We also suggest collecting smaller blood volumes in the blood bags for the optimal benefit of the recipients both for now and also as a measure of pandemic preparedness for future use.
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Affiliation(s)
- K Das
- Department of Pediatrics, Division of Pediatric Oncology and BMT, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, 248016 Dehradun, Uttarakhand, India
| | - M Raturi
- Department of Immunohematology and Blood Transfusion, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Swami Ram Nagar, 248016 Jolly Grant Dehradun, Uttarakhand, India.
| | - N Agrawal
- Department of Pediatrics, Division of Pediatric Critical Care, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, 248016 Dehradun, Uttarakhand, India
| | - M Kala
- Department of Pathology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Swami Ram Nagar, 248016 Jolly Grant Dehradun, Uttarakhand, India
| | - A Kusum
- Department of Pathology, Himalayan Institute of Medical Sciences, Swami Rama Himalayan University, Swami Ram Nagar, 248016 Jolly Grant Dehradun, Uttarakhand, India
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Basu U, Bostwick AM, Das K, Dittenhafer-Reed KE, Patel SS. Structure, mechanism, and regulation of mitochondrial DNA transcription initiation. J Biol Chem 2020; 295:18406-18425. [PMID: 33127643 PMCID: PMC7939475 DOI: 10.1074/jbc.rev120.011202] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized compartments that produce requisite ATP to fuel cellular functions and serve as centers of metabolite processing, cellular signaling, and apoptosis. To accomplish these roles, mitochondria rely on the genetic information in their small genome (mitochondrial DNA) and the nucleus. A growing appreciation for mitochondria's role in a myriad of human diseases, including inherited genetic disorders, degenerative diseases, inflammation, and cancer, has fueled the study of biochemical mechanisms that control mitochondrial function. The mitochondrial transcriptional machinery is different from nuclear machinery. The in vitro re-constituted transcriptional complexes of Saccharomyces cerevisiae (yeast) and humans, aided with high-resolution structures and biochemical characterizations, have provided a deeper understanding of the mechanism and regulation of mitochondrial DNA transcription. In this review, we will discuss recent advances in the structure and mechanism of mitochondrial transcription initiation. We will follow up with recent discoveries and formative findings regarding the regulatory events that control mitochondrial DNA transcription, focusing on those involved in cross-talk between the mitochondria and nucleus.
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Affiliation(s)
- Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA; Graduate School of Biomedical Sciences, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | | | - Kalyan Das
- Department of Microbiology, Immunology, and Transplantation, Rega Institute for Medical Research, KU Leuven, Leuven, Belgium
| | | | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, New Jersey, USA.
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Gu W, Martinez S, Nguyen H, Xu H, Herdewijn P, De Jonghe S, Das K. Tenofovir-Amino Acid Conjugates Act as Polymerase Substrates-Implications for Avoiding Cellular Phosphorylation in the Discovery of Nucleotide Analogues. J Med Chem 2020; 64:782-796. [PMID: 33356231 DOI: 10.1021/acs.jmedchem.0c01747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleotide analogues are used for treating viral infections such as HIV, hepatitis B, hepatitis C, influenza, and SARS-CoV-2. To become polymerase substrates, a nucleotide analogue must be phosphorylated by cellular kinases which is rate-limiting. The goal of this study is to develop dNTP/NTP analogues directly from nucleotides. Tenofovir (TFV) analogues were synthesized by conjugating with amino acids. We demonstrate that some conjugates act as dNTP analogues and HIV-1 reverse transcriptase (RT) catalytically incorporates the TFV part as the chain terminator. X-ray structures in complex with HIV-1 RT/dsDNA showed binding of the conjugates at the polymerase active site, however, in different modes in the presence of Mg2+ versus Mn2+ ions. The adaptability of the compounds is seemingly essential for catalytic incorporation of TFV by RT. 4d with a carboxyl sidechain demonstrated the highest incorporation. 4e showed weak incorporation and rather behaved as a dNTP-competitive inhibitor. This result advocates the feasibility of designing NTP/dNTP analogues by chemical substitutions to nucleotide analogues.
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Affiliation(s)
- Weijie Gu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium.,KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Sergio Martinez
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Hoai Nguyen
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Hongtao Xu
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
| | - Kalyan Das
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, Herestraat 49, 3000 Leuven, Belgium
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37
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De Wijngaert B, Sultana S, Singh A, Dharia C, Vanbuel H, Shen J, Vasilchuk D, Martinez SE, Kandiah E, Patel SS, Das K. Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase. Mol Cell 2020; 81:268-280.e5. [PMID: 33278362 DOI: 10.1016/j.molcel.2020.11.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023]
Abstract
Mitochondrial RNA polymerase (mtRNAP) is crucial in cellular energy production, yet understanding of mitochondrial DNA transcription initiation lags that of bacterial and nuclear DNA transcription. We report structures of two transcription initiation intermediate states of yeast mtRNAP that explain promoter melting, template alignment, DNA scrunching, abortive synthesis, and transition into elongation. In the partially melted initiation complex (PmIC), transcription factor MTF1 makes base-specific interactions with flipped non-template (NT) nucleotides "AAGT" at -4 to -1 positions of the DNA promoter. In the initiation complex (IC), the template in the expanded 7-mer bubble positions the RNA and NTP analog UTPαS, while NT scrunches into an NT loop. The scrunched NT loop is stabilized by the centrally positioned MTF1 C-tail. The IC and PmIC states coexist in solution, revealing a dynamic equilibrium between two functional states. Frequent scrunching/unscruching transitions and the imminent steric clashes of the inflating NT loop and growing RNA:DNA with the C-tail explain abortive synthesis and transition into elongation.
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Affiliation(s)
- Brent De Wijngaert
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Shemaila Sultana
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Anupam Singh
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Chhaya Dharia
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Hans Vanbuel
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Daniel Vasilchuk
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA
| | - Sergio E Martinez
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Eaazhisai Kandiah
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38043 Grenoble, France
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ 08854, USA.
| | - Kalyan Das
- Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium.
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Chaturvedi K, Khubber S, Singha S, Goel H, Barba FJ, Das K. Prediction and qualitative analysis of sensory perceptions over temporal vectors using combination of artificial neural networks and fuzzy logic: Validation on Indian cheese (paneer). J FOOD PROCESS PRES 2020. [DOI: 10.1111/jfpp.14955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kartikey Chaturvedi
- Department of Basic and Applied Sciences National Institute of Food Technology Entrepreneurship and Management Sonipat India
| | | | - Siddhartha Singha
- Centre for Rural Technology Indian Institute of Technology Guwahati India
| | - Himanshu Goel
- Department of Basic and Applied Sciences National Institute of Food Technology Entrepreneurship and Management Sonipat India
| | - Francisco J. Barba
- Nutrition and Food Science Area, Preventive Medicine and Public Health, Food Sciences, Toxicology and Forensic Medicine Department Faculty of Pharmacy Universitat de València València Spain
| | - Kalyan Das
- Department of Basic and Applied Sciences National Institute of Food Technology Entrepreneurship and Management Sonipat India
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Leek NJ, Neason M, Kreilkamp BAK, de Bezenac C, Ziso B, Elkommos S, Das K, Marson AG, Keller SS. Thalamohippocampal atrophy in focal epilepsy of unknown cause at the time of diagnosis. Eur J Neurol 2020; 28:367-376. [PMID: 33012040 DOI: 10.1111/ene.14565] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/13/2020] [Accepted: 09/24/2020] [Indexed: 01/02/2023]
Abstract
BACKGROUND AND PURPOSE Patients with chronic focal epilepsy may have atrophy of brain structures important for the generation and maintenance of seizures. However, little research has been conducted in patients with newly diagnosed focal epilepsy (NDfE), despite it being a crucial point in time for understanding the underlying biology of the disorder. We aimed to determine whether patients with NDfE show evidence of volumetric abnormalities of subcortical structures. METHODS Eighty-two patients with NDfE and 40 healthy controls underwent magnetic resonance imaging scanning using a standard clinical protocol. Volume estimation of the left and right hippocampus, thalamus, caudate nucleus, putamen and cerebral hemisphere was performed for all participants and normalised to whole brain volume. Volumes lower than two standard deviations below the control mean were considered abnormal. Volumes were analysed with respect to patient clinical characteristics, including treatment outcome 12 months after diagnosis. RESULTS Volume of the left hippocampus (p(FDR-corr) = 0.04) and left (p(FDR-corr) = 0.002) and right (p(FDR-corr) = 0.04) thalamus was significantly smaller in patients relative to controls. Relative to the normal volume limits in controls, 11% patients had left hippocampal atrophy, 17% had left thalamic atrophy and 9% had right thalamic atrophy. We did not find evidence of a relationship between volumes and future seizure control or with other clinical characteristics of epilepsy. CONCLUSIONS Volumetric abnormalities of structures known to be important for the generation and maintenance of focal seizures are established at the time of epilepsy diagnosis and are not necessarily a result of the chronicity of the disorder.
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Affiliation(s)
- N J Leek
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - M Neason
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - B A K Kreilkamp
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - C de Bezenac
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - B Ziso
- The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - S Elkommos
- St. George's University Hospitals NHS Foundation Trust, London, UK
| | - K Das
- The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - A G Marson
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - S S Keller
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.,The Walton Centre NHS Foundation Trust, Liverpool, UK
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Das K, Das S, Mohapatra A. A Novel Energy-efficient Sensor Cloud Model using Data Prediction and Forecasting Techniques. Karbala International Journal of Modern Science 2020. [DOI: 10.33640/2405-609x.1650] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Affiliation(s)
- Ujjwal Das
- OM, QM and IS Area IIM Udaipur Rajasthan India
| | - Kalyan Das
- Department of Mathematics IIT Bombay Powai India
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42
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Sohn BK, Basu U, Lee SW, Cho H, Shen J, Deshpande A, Johnson LC, Das K, Patel SS, Kim H. The dynamic landscape of transcription initiation in yeast mitochondria. Nat Commun 2020; 11:4281. [PMID: 32855416 PMCID: PMC7452894 DOI: 10.1038/s41467-020-17793-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/14/2020] [Indexed: 01/24/2023] Open
Abstract
Controlling efficiency and fidelity in the early stage of mitochondrial DNA transcription is crucial for regulating cellular energy metabolism. Conformational transitions of the transcription initiation complex must be central for such control, but how the conformational dynamics progress throughout transcription initiation remains unknown. Here, we use single-molecule fluorescence resonance energy transfer techniques to examine the conformational dynamics of the transcriptional system of yeast mitochondria with single-base resolution. We show that the yeast mitochondrial transcriptional complex dynamically transitions among closed, open, and scrunched states throughout the initiation stage. Then abruptly at position +8, the dynamic states of initiation make a sharp irreversible transition to an unbent conformation with associated promoter release. Remarkably, stalled initiation complexes remain in dynamic scrunching and unscrunching states without dissociating the RNA transcript, implying the existence of backtracking transitions with possible regulatory roles. The dynamic landscape of transcription initiation suggests a kinetically driven regulation of mitochondrial transcription.
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Affiliation(s)
- Byeong-Kwon Sohn
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Urmimala Basu
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Seung-Won Lee
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Hayoon Cho
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Jiayu Shen
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Aishwarya Deshpande
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Laura C Johnson
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Kalyan Das
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Rutgers University, Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
| | - Hajin Kim
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea.
- Institute for Basic Science, Ulsan, Republic of Korea.
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Das A, Ghosh S, Das K, Dutta I, Basu T, Das M. Re:(In) visible impact of inadequate WaSH Provision on COVID-19 incidences can be not be ignored in large and megacities of India. Public Health 2020; 185:34-36. [PMID: 32521329 PMCID: PMC7253972 DOI: 10.1016/j.puhe.2020.05.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022]
Affiliation(s)
- A Das
- Department of Geography, University of Gour Banga, Malda, India.
| | - S Ghosh
- Department of Geography, Kazi Nazrul University, Asansol, India.
| | - K Das
- Department of Geography, University of Gour Banga, Malda, India.
| | - I Dutta
- Department of Geography, University of Gour Banga, Malda, India.
| | - T Basu
- Department of Geography, University of Gour Banga, Malda, India.
| | - M Das
- Department of Geography, University of Gour Banga, Malda, India.
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Macerollo A, Hammersley B, Bonello M, Somerset J, Bhargava D, Das K, Osman-Farah J, Eldridge PR, Alusi SH. Deep brain stimulation for post-thalamic stroke complex movement disorders. Neurol Sci 2020; 42:337-342. [PMID: 32654009 DOI: 10.1007/s10072-020-04572-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 07/02/2020] [Indexed: 11/30/2022]
Affiliation(s)
- A Macerollo
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK. .,Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK.
| | - B Hammersley
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK
| | - M Bonello
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK
| | - J Somerset
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK
| | - D Bhargava
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK
| | - K Das
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK
| | - J Osman-Farah
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK
| | - P R Eldridge
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK
| | - S H Alusi
- The Walton Centre for Neurology and Neurosurgery, Liverpool, UK
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McLean KA, Ahmed WUR, Akhbari M, Claireaux HA, English C, Frost J, Henshall DE, Khan M, Kwek I, Nicola M, Rehman S, Varghese S, Drake TM, Bell S, Nepogodiev D, McLean KA, Drake TM, Glasbey JC, Borakati A, Drake TM, Kamarajah S, McLean KA, Bath MF, Claireaux HA, Gundogan B, Mohan M, Deekonda P, Kong C, Joyce H, Mcnamee L, Woin E, Burke J, Khatri C, Fitzgerald JE, Harrison EM, Bhangu A, Nepogodiev D, Arulkumaran N, Bell S, Duthie F, Hughes J, Pinkney TD, Prowle J, Richards T, Thomas M, Dynes K, Patel M, Patel P, Wigley C, Suresh R, Shaw A, Klimach S, Jull P, Evans D, Preece R, Ibrahim I, Manikavasagar V, Smith R, Brown FS, Deekonda P, Teo R, Sim DPY, Borakati A, Logan AE, Barai I, Amin H, Suresh S, Sethi R, Bolton W, Corbridge O, Horne L, Attalla M, Morley R, Robinson C, Hoskins T, McAllister R, Lee S, Dennis Y, Nixon G, Heywood E, Wilson H, Ng L, Samaraweera S, Mills A, Doherty C, Woin E, Belchos J, Phan V, Chouari T, Gardner T, Goergen N, Hayes JDB, MacLeod CS, McCormack R, McKinley A, 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JCK, Atkin G, Azizi A, Cargill Z, China Z, Elliot J, Jebakumar R, Lam J, Mudalige G, Onyerindu C, Renju M, Babu VS, Hussain M, Joji N, Lovett B, Mownah H, Ali B, Cresswell B, Dhillon AK, Dupaguntla YS, Hungwe C, Lowe-Zinola JD, Tsang JCH, Bevan K, Cardus C, Duggal A, Hossain S, McHugh M, Scott M, Chan F, Evans R, Gurung E, Haughey B, Jacob-Ramsdale B, Kerr M, Lee J, McCann E, O'Boyle K, Reid N, Hayat F, Hodgson S, Johnston R, Jones W, Khan M, Linn T, Long S, Seetharam P, Shaman S, Smart B, Anilkumar A, Davies J, Griffith J, Hughes B, Islam Y, Kidanu D, Mushaini N, Qamar I, Robinson H, Schramm M, Tan CY, Apperley H, Billyard C, Blazeby JM, Cannon SP, Carse S, Göpfert A, Loizidou A, Parkin J, Sanders E, Sharma S, Slade G, Telfer R, Huppatz IW, Worley E, Chandramoorthy L, Friend C, Harris L, Jain P, Karim MJ, Killington K, McGillicuddy J, Rafferty C, Rahunathan N, Rayne T, Varathan Y, Verma N, Zanichelli D, Arneill M, Brown F, Campbell B, Crozier L, Henry J, McCusker C, Prabakaran P, Wilson R, Asif U, Connor M, Dindyal S, Math N, Pagarkar A, Saleem H, Seth I, Sharma S, Standfield N, Swartbol T, Adamson R, Choi JE, El Tokhy O, Ho W, Javaid NR, Kelly M, Mehdi AS, Menon D, Plumptre I, Sturrock S, Turner J, Warren O, Crane E, Ferris B, Gadsby C, Smallwood J, Vipond M, Wilson V, Amarnath T, Doshi A, Gregory C, Kandiah K, Powell B, Spoor H, Toh C, Vizor R, Common M, Dunleavy K, Harris S, Luo C, Mesbah Z, Kumar AP, Redmond A, Skulsky S, Walsh T, Daly D, Deery L, Epanomeritakis E, Harty M, Kane D, Khan K, Mackey R, McConville J, McGinnity K, Nixon G, Ang A, Kee JY, Leung E, Norman S, Palaniappan SV, Sarathy PP, Yeoh T, Frost J, Hazeldine P, Jones L, Karbowiak M, Macdonald C, Mutarambirwa A, Omotade A, Runkel M, Ryan G, Sawers N, Searle C, Suresh S, Vig S, Ahmad A, McGartland R, Sim R, Song A, Wayman J, Brown R, Chang LH, Concannon K, Crilly C, Arnold TJ, Burgin A, Cadden F, Choy CH, Coleman M, Lim D, Luk J, Mahankali-Rao P, Prudence-Taylor AJ, Ramakrishnan D, Russell J, Fawole A, Gohil J, Green B, Hussain A, McMenamin L, McMenamin L, Tang M, Azmi F, Benchetrit S, Cope T, Haque A, Harlinska A, Holdsworth R, Ivo T, Martin J, Nisar T, Patel A, Sasapu K, Trevett J, Vernet G, Aamir A, Bird C, Durham-Hall A, Gibson W, Hartley J, May N, Maynard V, Johnson S, Wood CM, O'Brien M, Orbell J, Stringfellow TD, Tenters F, Tresidder S, Cheung W, Grant A, Tod N, Bews-Hair M, Lim ZH, Lim SW, Vella-Baldacchino M, Auckburally S, Chopada A, Easdon S, Goodson R, McCurdie F, Narouz M, Radford A, Rea E, Taylor O, Yu T, Alfa-Wali M, Amani L, Auluck I, Bruce P, Emberton J, Kumar R, Lagzouli N, Mehta A, Murtaza A, Raja M, Dennahy IS, Frew K, Given A, He YY, Karim MA, MacDonald E, McDonald E, McVinnie D, Ng SK, Pettit A, Sim DPY, Berthaume-Hawkins SD, Charnley R, Fenton K, Jones D, Murphy C, Ng JQ, Reehal R, Robinson H, Seraj SS, Shang E, Tonks A, White P, Yeo A, Chong P, Gabriel R, Patel N, Richardson E, Symons L, Aubrey-Jones D, Dawood S, Dobrzynska M, Faulkner S, Griffiths H, Mahmood F, Patel P, Perry M, Power A, Simpson R, Ali A, Brobbey P, Burrows A, Elder P, Ganyani R, Horseman C, Hurst P, Mann H, Marimuthu K, McBride S, Pilsworth E, Powers N, Stanier P, Innes R, Kersey T, Kopczynska M, Langasco N, Patel N, Rajagopal R, Atkins B, Beasley W, Lim ZC, Gill A, Ang HL, Williams H, Yogeswara T, Carter R, Fam M, Fong J, Latter J, Long M, Mackinnon S, McKenzie C, Osmanska J, Raghuvir V, Shafi A, Tsang K, Walker L, Bountra K, Coldicutt O, Fletcher D, Hudson S, Iqbal S, Bernal TL, Martin JWB, Moss-Lawton F, Smallwood J, Vipond M, Cardwell A, Edgerton K, Laws J, Rai A, Robinson K, Waite K, Ward J, Youssef H, Knight C, Koo PY, Lazarou A, Stanger S, Thorn C, Triniman MC, Botha A, Boyles L, Cumming S, Deepak S, Ezzat A, Fowler AJ, Gwozdz AM, Hussain SF, Khan S, Li H, Morrell BL, Neville J, Nitiahpapand R, Pickering O, Sagoo H, Sharma E, Welsh K, Denley S, Khan S, Agarwal M, Al-Saadi N, Bhambra R, Gupta A, Jawad ZAR, Jiao LR, Khan K, Mahir G, Singagireson S, Thoms BL, Tseu B, Wei R, Yang N, Britton N, Leinhardt D, Mahfooz M, Palkhi A, Price M, Sheikh S, Barker M, Bowley D, Cant M, Datta U, Farooqi M, Lee A, Morley G, Amin MN, Parry A, Patel S, Strang S, Yoganayagam N, Adlan A, Chandramoorthy S, Choudhary Y, Das K, Feldman M, France B, Grace R, Puddy H, Soor P, Ali M, Dhillon P, Faraj A, Gerard L, Glover M, Imran H, Kim S, Patrick Y, Peto J, Prabhudesai A, Smith R, Tang A, Vadgama N, Dhaliwal R, Ecclestone T, Harris A, Ong D, Patel D, Philp C, Stewart E, Wang L, Wong E, Xu Y, Ashaye T, Fozard T, Galloway F, Kaptanis S, Mistry P, Nguyen T, Olagbaiye F, Osman M, Philip Z, Rembacken R, Tayeh S, Theodoropoulou K, Herman A, Lau J, Saha A, Trotter M, Adeleye O, Cave D, Gunwa T, Magalhães J, Makwana S, Mason R, Parish M, Regan H, Renwick P, Roberts G, Salekin D, Sivakumar C, Tariq A, Liew I, McDade A, Stewart D, Hague M, Hudson-Peacock N, Jackson CES, James F, Pitt J, Walker EY, Aftab R, Ang JJ, Anwar S, Battle J, Budd E, Chui J, Crook H, Davies P, Easby S, Hackney E, Ho B, Imam SZ, Rammell J, Andrews H, Perry C, Schinle P, Ahmed P, Aquilina T, Balai E, Church M, Cumber E, Curtis A, Davies G, Dennis Y, Dumann E, Greenhalgh S, Kim P, King S, Metcalfe KHM, Passby L, Redgrave N, Soonawalla Z, Waters S, Zornoza A, Gulzar I, Hole J, Hull K, Ishaq H, Karaj J, Kelkar A, Love E, Patel S, Thakrar D, Vine M, Waterman A, Dib NP, Francis N, Hanson M, Ingleton R, Sadanand KS, Sukirthan N, Arnell S, Ball M, Bassam N, Beghal G, Chang A, Dawe V, George A, Huq T, Hussain A, Ikram B, Kanapeckaite L, Khan M, Ramjas D, Rushd A, Sait S, Serry M, Yardimci E, Capella S, Chenciner L, Episkopos C, Karam E, McCarthy C, Moore-Kelly W, Watson N, Ahluwalia V, Barnfield J, Ben-Gal O, Bloom I, Gharatya A, Khodatars K, Merchant N, Moonan A, Moore M, Patel K, Spiers H, Sundaram K, Turner J, Bath MF, Black J, Chadwick H, Huisman L, Ingram H, Khan S, Martin L, Metcalfe M, Sangal P, Seehra J, Thatcher A, Venturini S, Whitcroft I, Afzal Z, Brown S, Gani A, Gomaa A, Hussein N, Oh SY, Pazhaniappan N, Sharkey E, Sivagnanasithiyar T, Williams C, Yeung J, Cruddas L, Gurjar S, Pau A, Prakash R, Randhawa R, Chen L, Eiben I, Naylor M, Osei-Bordom D, Trenear R, Bannard-Smith J, Griffiths N, Patel BY, Saeed F, Abdikadir H, Bennett M, Church R, Clements SE, Court J, Delvi A, Hubert J, Macdonald B, Mansour F, Patel RR, Perris R, Small S, Betts A, Brown N, Chong A, Croitoru C, Grey A, Hickland P, Ho C, Hollington D, McKie L, Nelson AR, Stewart H, Eiben P, Nedham M, Ali I, Brown T, Cumming S, Hunt C, Joyner C, McAlinden C, Roberts J, Rogers D, Thachettu A, Tyson N, Vaughan R, Verma N, Yasin T, Andrew K, Bhamra N, Leong S, Mistry R, Noble H, Rashed F, Walker NR, Watson L, Worsfold M, Yarham E, Abdikadir H, Arshad A, Barmayehvar B, Cato L, Chan-lam N, Do V, Leong A, Sheikh Z, Zheleniakova T, Coppel J, Hussain ST, Mahmood R, Nourzaie R, Prowle J, Sheik-Ali S, Thomas A, Alagappan A, Ashour R, Bains H, Diamond J, Gordon J, Ibrahim B, Khalil M, Mittapalli D, Neo YN, Patil P, Peck FS, Reza N, Swan I, Whyte M, Chaudhry S, Hernon J, Khawar H, O'Brien J, Pullinger M, Rothnie K, Ujjal S, Bhatte S, Curtis J, Green S, Mayer A, Watkinson G, Chapple K, Hawthorne T, Khaliq M, Majkowski L, Malik TAM, Mclauchlan K, En BNW, Parton S, Robinson SD, Saat MI, Shurovi BN, Varatharasasingam K, Ward AE, Behranwala K, Bertelli M, Cohen J, Duff F, Fafemi O, Gupta R, Manimaran M, Mayhew J, Peprah D, Wong MHY, Farmer N, Houghton C, Kandhari N, Khan K, Ladha D, Mayes J, McLennan F, Panahi P, Seehra H, Agrawal R, Ahmed I, Ali S, Birkinshaw F, Choudhry M, Gokani S, Harrogate S, Jamal S, Nawrozzadeh F, Swaray A, Szczap A, Warusavitarne J, Abdalla M, Asemota N, Cullum R, Hartley M, Maxwell-Armstrong C, Mulvenna C, Phillips J, Yule A, Ahmed L, Clement KD, Craig N, Elseedawy E, Gorman D, Kane L, Livie J, Livie V, Moss E, Naasan A, Ravi F, Shields P, Zhu Y, Archer M, Cobley H, Dennis R, Downes C, Guevel B, Lamptey E, Murray H, Radhakrishnan A, Saravanabavan S, Sardar M, Shaw C, Tilliridou V, Wright R, Ye W, Alturki N, Helliwell R, Jones E, Kelly D, Lambotharan S, Scott K, Sivakumar R, Victor L, Boraluwe-Rallage H, Froggatt P, Haynes S, Hung YMA, Keyte A, Matthews L, Evans E, Haray P, John I, Mathivanan A, Morgan L, Oji O, Okorocha C, Rutherford A, Spiers H, Stageman N, Tsui A, Whitham R, Amoah-Arko A, Cecil E, Dietrich A, Fitzpatrick H, Guy C, Hair J, Hilton J, Jawad L, McAleer E, Taylor Z, Yap J, Akhbari M, Debnath D, Dhir T, Elbuzidi M, Elsaddig M, Glace S, Khawaja H, Koshy R, Lal K, Lobo L, McDermott A, Meredith J, Qamar MA, Vaidya A, Acquaah F, Barfi L, Carter N, Gnanappiragasam D, Ji C, Kaminski F, Lawday S, Mackay K, Sulaiman SK, Webb R, Ananthavarathan P, Dalal F, Farrar E, Hashemi R, Hossain M, Jiang J, Kiandee M, Lex J, Mason L, Matthews JH, McGeorge E, Modhwadia S, Pinkney T, Radotra A, Rickard L, Rodman L, Sales A, Tan KL, Bachi A, Bajwa DS, Battle J, Brown LR, Butler A, Calciu A, Davies E, Gardner I, Girdlestone T, Ikogho O, Keelan G, O'Loughlin P, Tam J, Elias J, Ngaage M, Thompson J, Bristow S, Brock E, Davis H, Pantelidou M, Sathiyakeerthy A, Singh K, Chaudhry A, Dickson G, Glen P, Gregoriou K, Hamid H, Mclean A, Mehtaji P, Neophytou G, Potts S, Belgaid DR, Burke J, Durno J, Ghailan N, Hanson M, Henshaw V, Nazir UR, Omar I, Riley BJ, Roberts J, Smart G, Van Winsen K, Bhatti A, Chan M, D'Auria M, Green S, Keshvala C, Li H, Maxwell-Armstrong C, Michaelidou M, Simmonds L, Smith C, Wimalathasan A, Abbas J, Cairns C, Chin YR, Connelly A, Moug S, Nair A, Svolkinas D, Coe P, Subar D, Wang H, Zaver V, Brayley J, Cookson P, Cunningham L, Gaukroger A, Ho M, Hough A, King J, O'Hagan D, Widdison A, Brown R, Brown B, Chavan A, Francis S, Hare L, Lund J, Malone N, Mavi B, McIlwaine A, Rangarajan S, Abuhussein N, Campbell HS, Daniels J, Fitzgerald I, Mansfield S, Pendrill A, Robertson D, Smart YW, Teng T, Yates J, Belgaumkar A, Katira A, Kossoff J, Kukran S, Laing C, Mathew B, Mohamed T, Myers S, Novell R, Phillips BL, Thomas M, Turlejski T, Turner S, Varcada M, Warren L, Wynell-Mayow W, Church R, Linley-Adams L, Osborn G, Saunders M, Spencer R, Srikanthan M, Tailor S, Tullett A, Ali M, Al-Masri S, Carr G, Ebhogiaye O, Heng S, Manivannan S, Manley J, McMillan LE, Peat C, Phillips B, Thomas S, Whewell H, Williams G, Bienias A, Cope EA, Courquin GR, Day L, Garner C, Gimson A, Harris C, Markham K, Moore T, Nadin T, Phillips C, Subratty SM, Brown K, Dada J, Durbacz M, Filipescu T, Harrison E, Kennedy ED, Khoo E, Kremel D, Lyell I, Pronin S, Tummon R, Ventre C, Walls L, Wootton E, Akhtar A, Davies E, El-Sawy D, Farooq M, Gaddah M, Griffiths H, Katsaiti I, Khadem N, Leong K, Williams I, Chean CS, Chudek D, Desai H, Ellerby N, Hammad A, Malla S, Murphy B, Oshin O, Popova P, Rana S, Ward T, Abbott TEF, Akpenyi O, Edozie F, El Matary R, English W, Jeyabaladevan S, Morgan C, Naidu V, Nicholls K, Peroos S, Prowle J, Sansome S, Torrance HD, Townsend D, Brecher J, Fung H, Kazmi Z, Outlaw P, Pursnani K, Ramanujam N, Razaq A, Sattar M, Sukumar S, Tan TSE, Chohan K, Dhuna S, Haq T, Kirby S, Lacy-Colson J, Logan P, Malik Q, McCann J, Mughal Z, Sadiq S, Sharif I, Shingles C, Simon A, Burnage S, Chan SSN, Craig ARJ, Duffield J, Dutta A, Eastwood M, Iqbal F, Mahmood F, Mahmood W, Patel C, Qadeer A, Robinson A, Rotundo A, Schade A, Slade RD, De Freitas M, Kinnersley H, McDowell E, Moens-Lecumberri S, Ramsden J, Rockall T, Wiffen L, Wright S, Bruce C, Francois V, Hamdan K, Limb C, Lunt AJ, Manley L, Marks M, Phillips CFE, Agnew CJF, Barr CJ, Benons N, Hart SJ, Kandage D, Krysztopik R, Mahalingam P, Mock J, Rajendran S, Stoddart MT, Clements B, Gillespie H, Lee S, McDougall R, Murray C, O'Loane R, Periketi S, Tan S, Amoah R, Bhudia R, Dudley B, Gilbert A, Griffiths B, Khan H, McKigney N, Roberts B, Samuel R, Seelarbokus A, Stubbing-Moore A, Thompson G, Williams P, Ahmed N, Akhtar R, Chandler E, Chappelow I, Gil H, Gower T, Kale A, Lingam G, Rutler L, Sellahewa C, Sheikh A, Stringer H, Taylor R, Aglan H, Ashraf MR, Choo S, Das E, Epstein J, Gentry R, Mills D, Poolovadoo Y, Ward N, Bull K, Cole A, Hack J, Khawari S, Lake C, Mandishona T, Perry R, Sleight S, Sultan S, Thornton T, Williams S, Arif T, Castle A, Chauhan P, Chesner R, Eilon T, Kamarajah S, Kambasha C, Lock L, Loka T, Mohammad F, Motahariasl S, Roper L, Sadhra SS, Sheikh A, Toma T, Wadood Q, Yip J, Ainger E, Busti S, Cunliffe L, Flamini T, Gaffing S, Moorcroft C, Peter M, Simpson L, Stokes E, Stott G, Wilson J, York J, Yousaf A, Borakati A, Brown M, Goaman A, Hodgson B, Ijeomah A, Iroegbu U, Kaur G, Lowe C, Mahmood S, Sattar Z, Sen P, Szuman A, Abbas N, Al-Ausi M, Anto N, Bhome R, Eccles L, Elliott J, Hughes EJ, Jones A, Karunatilleke AS, Knight JS, Manson CCF, Mekhail I, Michaels L, Noton TM, Okenyi E, Reeves T, Yasin IH, Banfield DA, Harris R, Lim D, Mason-Apps C, Roe T, Sandhu J, Shafiq N, Stickler E, Tam JP, Williams LM, Ainsworth P, Boualbanat Y, Doull C, Egan E, Evans L, Hassanin K, Ninkovic-Hall G, Odunlami W, Shergill M, Traish M, Cummings D, Kershaw S, Ong J, Reid F, Toellner H, Alwandi A, Amer M, George D, Haynes K, Hughes K, Peakall L, Premakumar Y, Punjabi N, Ramwell A, Sawkins H, Ashwood J, Baker A, Baron C, Bhide I, Blake E, De Cates C, Esmail R, Hosamuddin H, Kapp J, Nguru N, Raja M, Thomson F, Ahmed H, Aishwarya G, Al-Huneidi R, Ali S, Aziz R, Burke D, Clarke B, Kausar A, Maskill D, Mecia L, Myers L, Smith ACD, Walker G, Wroe N, Donohoe C, Gibbons D, Jordan P, Keogh C, Kiely A, Lalor P, McCrohan M, Powell C, Foley MP, Reynolds J, Silke E, Thorpe O, Kong JTH, White C, Ali Q, Dalrymple J, Ge Y, Khan H, Luo RS, Paine H, Paraskeva B, Parker L, Pillai K, Salciccioli J, Selvadurai S, Sonagara V, Springford LR, Tan L, Appleton S, Leadholm N, Zhang Y, Ahern D, Cotter M, Cremen S, Durrigan T, Flack V, Hrvacic N, Jones H, Jong B, Keane K, O'Connell PR, O'sullivan J, Pek G, Shirazi S, Barker C, Brown A, Carr W, Chen Y, Guillotte C, Harte J, Kokayi A, Lau K, McFarlane S, Morrison S, Broad J, Kenefick N, Makanji D, Printz V, Saito R, Thomas O, Breen H, Kirk S, Kong CH, O'Kane A, Eddama M, Engledow A, Freeman SK, Frost A, Goh C, Lee G, Poonawala R, Suri A, Taribagil P, Brown H, Christie S, Dean S, Gravell R, Haywood E, Holt F, Pilsworth E, Rabiu R, Roscoe HW, Shergill S, Sriram A, Sureshkumar A, Tan LC, Tanna A, Vakharia A, Bhullar S, Brannick S, Dunne E, Frere M, Kerin M, Kumar KM, Pratumsuwan T, Quek R, Salman M, Van Den Berg N, Wong C, Ahluwalia J, Bagga R, Borg CM, Calabria C, Draper A, Farwana M, Joyce H, Khan A, Mazza M, Pankin G, Sait MS, Sandhu N, Virani N, Wong J, Woodhams K, Croghan N, Ghag S, Hogg G, Ismail O, John N, Nadeem K, Naqi M, Noe SM, Sharma A, Tan S, Begum F, Best R, Collishaw A, Glasbey J, Golding D, Gwilym B, Harrison P, Jackman T, Lewis N, Luk YL, Porter T, Potluri S, Stechman M, Tate S, Thomas D, Walford B, Auld F, Bleakley A, Johnston S, Jones C, Khaw J, Milne S, O'Neill S, Singh KKR, Smith R, Swan A, Thorley N, Yalamarthi S, Yin ZD, Ali A, Balian V, Bana R, Clark K, Livesey C, McLachlan G, Mohammad M, Pranesh N, Richards C, Ross F, Sajid M, Brooke M, Francombe J, Gresly J, Hutchinson S, Kerrigan K, Matthews E, Nur S, Parsons L, Sandhu A, Vyas M, White F, Zulkifli A, Zuzarte L, Al-Mousawi A, Arya J, Azam S, Yahaya AA, Gill K, Hallan R, Hathaway C, Leptidis I, McDonagh L, Mitrasinovic S, Mushtaq N, Pang N, Peiris GB, Rinkoff S, Chan L, Christopher E, Farhan-Alanie MMH, Gonzalez-Ciscar A, Graham CJ, Lim H, McLean KA, Paterson HM, Rogers A, Roy C, Rutherford D, Smith F, Zubikarai G, Al-Khudairi R, Bamford M, Chang M, Cheng J, Hedley C, Joseph R, Mitchell B, Perera S, Rothwell L, Siddiqui A, Smith J, Taylor K, Wright OW, Baryan HK, Boyd G, Conchie H, Cox L, Davies J, Gardner S, Hill N, Krishna K, Lakin F, Scotcher S, Alberts J, Asad M, Barraclough J, Campbell A, Marshall D, Wakeford W, Cronbach P, D'Souza F, Gammeri E, Houlton J, Hall M, Kethees A, Patel R, Perera M, Prowle J, Shaid M, Webb E, Beattie S, Chadwick M, El-Taji O, Haddad S, Mann M, Patel M, Popat K, Rimmer L, Riyat H, Smith H, Anandarajah C, Cipparrone M, Desai K, Gao C, Goh ET, Howlader M, Jeffreys N, Karmarkar A, Mathew G, Mukhtar H, Ozcan E, Renukanthan A, Sarens N, Sinha C, Woolley A, Bogle R, Komolafe O, Loo F, Waugh D, Zeng R, Crewe A, Mathias J, Mills A, Owen A, Prior A, Saunders I, Baker A, Crilly L, McKeon J, Ubhi HK, Adeogun A, Carr R, Davison C, Devalia S, Hayat A, Karsan RB, Osborne C, Scott K, Weegenaar C, Wijeyaratne M, Babatunde F, Barnor-Ahiaku E, Beattie G, Chitsabesan P, Dixon O, Hall N, Ilenkovan N, Mackrell T, Nithianandasivam N, Orr J, Palazzo F, Saad M, Sandland-Taylor L, Sherlock J, Ashdown T, Chandler S, Garsaa T, Lloyd J, Loh SY, Ng S, Perkins C, Powell-Chandler A, Smith F, Underhill R. Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study. Br J Surg 2020; 107:1023-1032. [PMID: 32026470 DOI: 10.1002/bjs.11453] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/21/2019] [Accepted: 11/08/2019] [Indexed: 01/14/2023]
Abstract
BACKGROUND This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. METHODS This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery. RESULTS A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498). CONCLUSION There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.
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Tuske S, Zheng J, Olson ED, Ruiz FX, Pascal BD, Hoang A, Bauman JD, Das K, DeStefano JJ, Musier-Forsyth K, Griffin PR, Arnold E. Integrative structural biology studies of HIV-1 reverse transcriptase binding to a high-affinity DNA aptamer. Curr Res Struct Biol 2020; 2:116-129. [PMID: 33870216 PMCID: PMC8052095 DOI: 10.1016/j.crstbi.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/03/2020] [Accepted: 06/19/2020] [Indexed: 02/07/2023] Open
Abstract
The high-resolution crystal structure of HIV-1 reverse transcriptase (RT) bound to a 38-mer DNA hairpin aptamer with low pM affinity was previously described. The high-affinity binding aptamer contained 2'-O-methyl modifications and a seven base-pair GC-rich tract and the structure of the RT-aptamer complex revealed specific contacts between RT and the template strand of the aptamer. Similar to all crystal structures of RT bound to nucleic acid template-primers, the aptamer bound RT with a bend in the duplex DNA. To understand the structural basis for the ultra-high-affinity aptamer binding, an integrative structural biology approach was used. Hydrogen-deuterium exchange coupled to liquid chromatography-mass spectrometry (HDX-MS) was used to examine the structural dynamics of RT alone and in the presence of the DNA aptamer. RT was selectively labeled with 15N to unambiguously identify peptides from each subunit. HDX of unliganded RT shows a mostly stable core. The p66 fingers and thumb subdomains, and the RNase H domain are relatively dynamic. HDX indicates that both the aptamer and a scrambled version significantly stabilize regions of RT that are dynamic in the absence of DNA. No substantial differences in RT dynamics are observed between aptamer and scrambled aptamer binding, despite a large difference in binding affinity. Small-angle X-ray scattering and circular dichroism spectroscopy were used to investigate the aptamer conformation in solution and revealed a pre-bent DNA that possesses both A- and B-form helical character. Both the 2'-O-methyl modifications and the GC tract appear to contribute to an energetically favorable conformation for binding to RT that contributes to the aptamer's ultra-high affinity for RT. The X-ray structure of RT with an RNA/DNA version of the aptamer at 2.8 Å resolution revealed a potential role of the hairpin positioning in affinity. Together, the data suggest that both the 2'-O-methyl modifications and the GC tract contribute to an energetically favorable conformation for high-affinity binding to RT.
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Affiliation(s)
- Steve Tuske
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Erik D. Olson
- Department of Chemistry and Biochemistry, Center for RNA Biology, And Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Bruce D. Pascal
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Anthony Hoang
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Joseph D. Bauman
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Kalyan Das
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jeffrey J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, MD, 20740, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, And Center for Retrovirus Research, The Ohio State University, Columbus, OH, 43210, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine, And Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, 08854, USA
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Das A, Ghosh S, Das K, Basu T, Das M, Dutta I. Modeling the effect of area deprivation on COVID-19 incidences: a study of Chennai megacity, India. Public Health 2020; 185:266-269. [PMID: 32707468 PMCID: PMC7290224 DOI: 10.1016/j.puhe.2020.06.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/06/2020] [Accepted: 06/08/2020] [Indexed: 11/17/2022]
Abstract
Objectives Socio-economic inequalities may affect coronavirus disease 2019 (COVID-19) incidence. The goal of the research was to explore the association between deprivation of socio-economic status (SES) and spatial patterns of COVID-19 incidence in Chennai megacity for unfolding the disease epidemiology. Study design This is an ecological (or contextual) study for electoral wards (subcities) of Chennai megacity. Methods Using data of confirmed COVID-19 cases from May 15, 2020, to May 21, 2020, for 155 electoral wards obtained from the official website of the Chennai Municipal Corporation, we examined the incidence of COVID-19 using two count regression models, namely, Poisson regression (PR) and negative binomial regression (NBR). As explanatory factors, we considered area deprivation that represented the deprivation of SES. An index of multiple deprivations (IMD) was developed to measure the area deprivation using an advanced local statistic, geographically weighted principal component analysis. Based on the availability of appropriately scaled data, five domains (i.e., poor housing condition, low asset possession, poor availability of WaSH services, lack of household amenities and services, and gender disparity) were selected as components of the IMD in this study. Results The hot spot analysis revealed that area deprivation was significantly associated with higher incidences of COVID-19 in Chennai megacity. The high variations (adjusted R2: 72.2%) with the lower Bayesian Information Criteria (BIC) (124.34) and Akaike's Information Criteria (AIC) (112.12) for NBR compared with PR suggests that the NBR model better explains the relationship between area deprivation and COVID-19 incidences in Chennai megacity. NBR with two-sided tests and P <0.05 were considered statistically significant. The outcome of the PR and NBR models suggests that when all other variables were constant, according to NBR, the relative risk (RR) of COVID-19 incidences was 2.19 for the wards with high housing deprivation or, in other words, the wards with high housing deprivation having 119% higher probability (RR = e0.786 = 2.19, 95% confidence interval [CI] = 1.98 to 2.40), compared with areas with low deprivation. Similarly, in the wards with poor availability of WaSH services, chances of having COVID-19 incidence was 90% higher than in the wards with good WaSH services (RR = e0.642 = 1.90, 95% CI = 1.79 to 2.00). Spatial risks of COVID-19 were predominantly concentrated in the wards with higher levels of area deprivation, which were mostly located in the northeastern parts of Chennai megacity. Conclusions We formulated an area-based IMD, which was substantially related to COVID-19 incidences in Chennai megacity. This study highlights that the risks of COVID-19 tend to be higher in areas with low SES and that the northeastern part of Chennai megacity is predominantly high-risk areas. Our results can guide measures of COVID-19 control and prevention by considering spatial risks and area deprivation. COVID-19 cases was modelled using Poisson regression and negative binomial regression. An IMD was devised using geographically weighted principal component analysis. Area deprivation in Chennai has both positive and inverse associations with the COVID-19.
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Affiliation(s)
- A Das
- Department of Geography, University of Gour Banga, Malda, India.
| | - S Ghosh
- Department of Geography, Kazi Nazrul University, Asansol, India.
| | - K Das
- Department of Geography, University of Gour Banga, Malda, India.
| | - T Basu
- Department of Geography, University of Gour Banga, Malda, India.
| | - M Das
- Department of Geography, University of Gour Banga, Malda, India.
| | - I Dutta
- Department of Geography, University of Gour Banga, Malda, India.
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Omara M, Abdelgadir E, Khan F, Latif MF, Alawadi F, Koury M, Elshourbagy D, Hamza D, Kumar S, Das K, Malik Q, Tirmazy SH. Incidence of Immune Related Adverse Events in Patients Treated with Immune Checkpoint Inhibitors, Case Series from Two Tertiary Care Centeers in Dubai, UAE. Tumori 2020. [DOI: 10.1177/0300891620914156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Introduction: Immune checkpoint inhibitors (ICI) represent a major component of systemic therapy in advanced malignancy. Studies have reported unique spectrum of toxicity profile of ICI as compared to systemic chemotherapy. Aim of this study is to evaluate toxicities of ICI in our population and to compare this with published data. Material and Methods: We retrospectively reviewed medical records of patients treated with ICI at Dubai hospital and American hospital Dubai from November 2015 to April 2019. After patient identification from hospitals cancer registry, data regarding patients’ demographics, cancer type, type of ICI, adverse events, and duration of treatment were collected. Results: Forty-Five patients were identified with median age of 60 (27-80) years. 27 (60%) patients were male and 18 (40%) were female. Underlying diagnosis was lung cancer (n=25), renal cell cancer (n=6), melanoma (n=5), bladder cancer (n=3), Hodgkins lymphoma (n=3) and other malignancies (n=3). Majority of patients received Nivolumab (n=20, 44%) followed by Pembrolizumab (n=19, 42%), Atezolizumab (n=4, 9%) and Durvalumab (n=2, 5%) respectively. Thyroid dysfunction was the most common side effect observed in 17 (38%) patients including hypothyroidism (n=12, 27%) and hyperthyroidism (n=5, 11%). 53 % patients treated with Nivolumab developed thyroid dysfunction as compared to Pembrolizumab (22%). 7 patients (16%) had elevated liver enzymes. Grade II and III hepatotoxicity was noted in 1 patient (2.2 %) each. One patient (2.2 %) developed grade II skin toxicity. One patient (2.2 %) developed grade III colitis. Grade II, III and IV pneumonitis was observed in 2 (4.4 %), 1 (2.2%) and 1 (2.2%) patient respectively. Immune mediated adverse events were managed according to standard guidelines and 2 patients (4.4 %) had treatment discontinuation due to grade IV Pneumonitis and grade III Colitis. Conclusion: Our study reports relatively higher incidence of thyroid adverse events in patients treated with ICI. The incidence of grade III-IV immune related toxicity remains low. Overall treatment with ICI was tolerated reasonably well and toxicity was manageable.
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Affiliation(s)
- M Omara
- Oncology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
- Oncology Department Suez Canal University Hospital, Ismailia, Egypt
| | - Elamin Abdelgadir
- Endocrinology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
| | - F Khan
- Oncology department American Hospital Dubai – UAE
| | - M F Latif
- Oncology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
| | - Fatheya Alawadi
- Endocrinology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
| | - M Koury
- Oncology department American Hospital Dubai – UAE
| | - D. Elshourbagy
- Oncology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
- Oncology Department Tanta University Hospital, Tanta - Egypt
| | - Dina Hamza
- Oncology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
| | - S. Kumar
- Oncology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
| | - K. Das
- Oncology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
| | - Quayom Malik
- Oncology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
| | - S H Tirmazy
- Oncology department Dubai Hospital, Dubai Health Authority, Dubai – UAE
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Bhattacharyya A, Sarma P, Das K, Agarwal B, Medhi J, Das Mohapatra SS. Safety and efficacy of riboflavin-assisted collagen cross-linking of cornea in progressive keratoconus patients: A prospective study in North East India. Indian J Pharmacol 2020; 51:157-167. [PMID: 31391683 PMCID: PMC6644189 DOI: 10.4103/ijp.ijp_75_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
INTRODUCTION: Riboflavin- and ultraviolet (UV)-A-mediated collagen cross-linking of the cornea is a frequently used therapeutic measure for the treatment of progressive keratoconus (PK). First, riboflavin increases cross-linking and second, it serves as a protective shield to other deep ocular structures. However, pharmacogenomic variation in riboflavin efficacy is reported. As the Northeast Indian population represents a genetically diverse group of population compared to mainstream India, we have assessed the efficacy of the procedure in a northeastern population with PK. METHODS: In this study, 78 eyes with PK were included (n = 39 in the treatment arm and n = 39 in the control arm). The primary objective was to evaluate the effect of corneal collagen cross-linking using riboflavin (C3R) (epithelium off) on maximum keratometry. The secondary objectives were evaluation of change in corneal topography parameters, i.e., minimum keratometry (Kmin), simulated keratometry (Sim K), subjective refraction (cylinder power, spherical power, and spherical equivalent [SE]), uncorrected visual acuity (UCVA), best-corrected visual acuity (BCVA), and contrast sensitivity (CS) and safety (intraocular pressure, endothelial cell density, and percentage hexagonality) at 1, 3, and 6 months following C3R procedure. RESULTS: Statistically significant improvement was noted in Kmin (6 months), Sim K (3 and 6 months), cylinder power (3 and 6 months), spherical power (3 and 6 months), SE (3 and 6 months), BCVA (6 months), and UCVA (1, 6 months) in the C3R group (n = 39) when compared to the control group (n = 39). The mean CS decreased at 1 month and gradually improved to achieve statistically significant value at 6 months in the C3R group (P < 0.05). CONCLUSION: Riboflavin-assisted C3R treatment showed promising efficacy in the treatment of PK patients in our population. As the collagen turnover rate of cornea is 2–3 years and the progression of PK is highly variable, we need long-term studies to evaluate the efficacy of C3R over time, requirement of repeat therapy, and safety of repeat cross-linking.
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Affiliation(s)
| | - Phulen Sarma
- Department of Pharmacology, PGIMER, Chandigarh, India
| | - Kalyan Das
- Department of Ophthalmology, Cornea Services, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
| | - Balmukund Agarwal
- Department of Ophthalmology, Cornea Services, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
| | - Jnanankar Medhi
- Department of Ophthalmology, Cornea Services, Sri Sankaradeva Nethralaya, Guwahati, Assam, India
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Harlalka S, Roy UK, Majumdar G, Das K, Mandal P. An Open Label Prospective Study on Evaluation of Safety and Efficacy of Cilnidipine Over Amlodipine in Stage 1 Hypertensive Patients. Kathmandu Univ Med J (KUMJ) 2020; 18:42-48. [PMID: 33582687] [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: 06/12/2023]
Abstract
Background Calcium channel blockers are considered the first line drug over renin-angiotensinaldosterone system inhibitor in black population and with renin-angiotensinaldosterone system inhibitor in non-black population with Hypertension. Amlodipine has longer biological half life and lower potential to stimulate SNS. But, is associated with reflex tachycardia and pedal oedema. Cilnidipine has potent inhibitory both on voltage gated L-type and N-type calcium channels with better anti-proteinuric effect and good tolerability. Hence, our study compared the efficacy, safety and compliance of cilnidipine over amlodipine in Stage 1 hypertensive subjects. Objective To find out antihypertensive and renoprotective effect of cilnidipine. Method The study was open-label, single centre, prospective, parallel design, randomized controlled was done in Outdoor Patient Department (OPD) of Medicine and Department of Pharmacology in Burdwan Medical College and Hospital (BMCH). Patients with stage 1 HTN received cilnidipine while the other group received amlodipine. There were 4 follow-up visits for each participant consisting of baseline, 1 week, 6 weeks and after 12 weeks. Clinical parameters including pulse rate, blood pressure and ankle oedema noted also laboratory investigations were done. Safety parameters with adverse events and compliance by traditional pill count method. Result Blood pressure was effectively decreased by both amlodipine and cilnidipine. Cilnidipine significantly decreased Pulse Rate while amlodipine increased it and the difference in Pulse Rate comparing both the groups was statistically significant. None of the ADRs were statistically significant except pedal oedema. Pedal oedema was noted only in amlodipine arm and was statistically significant. Compliance to both the drugs was excellent. Total cost of therapy was higher with cilnidipine. Conclusion Though amlodipine is preferred drug, cilnidipine should be a better alternative when we consider subjects with sympathetic over activity, proteinuria or pedal oedema.
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Affiliation(s)
- S Harlalka
- Department of Pharmacology, Burdwan Medical College and Hospital, India
| | - U K Roy
- Department of Pharmacology, Burdwan Medical College and Hospital, India
| | - G Majumdar
- Department of Pharmacology, Burdwan Medical College and Hospital, India
| | - K Das
- Department of Pharmacology, Burdwan Medical College and Hospital, India
| | - P Mandal
- Department of Pharmacology, Burdwan Medical College and Hospital, India
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