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Varsi F, Ahmad S, Chakraborty M, Chandra A, Dugad SR, Goswami UD, Gupta SK, Hariharan B, Hayashi Y, Jagadeesan P, Jain A, Jain P, Kawakami S, Kojima H, Lipari P, Mahapatra S, Mohanty PK, Moharana R, Muraki Y, Nayak PK, Nonaka T, Oshima A, Pant BP, Pattanaik D, Paul S, Pradhan GS, Rameez M, Ramesh K, Reddy LV, Saha S, Sahoo R, Scaria R, Shibata S, Zuberi M. Evidence of a Hardening in the Cosmic Ray Proton Spectrum at around 166 TeV Observed by the GRAPES-3 Experiment. Phys Rev Lett 2024; 132:051002. [PMID: 38364164 DOI: 10.1103/physrevlett.132.051002] [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] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 10/16/2023] [Accepted: 01/04/2024] [Indexed: 02/18/2024]
Abstract
We present the measurement of the cosmic ray proton spectrum from 50 TeV to 1.3 PeV using 7.81×10^{6} extensive air shower events recorded by the ground-based GRAPES-3 experiment between 1 January 2014 and 26 October 2015 with a live time of 460 day. Our measurements provide an overlap with direct observations by satellite and balloon-based experiments. The electromagnetic and muon components in the shower were measured by a dense array of plastic scintillator detectors and a tracking muon telescope, respectively. The relative composition of the proton primary from the air shower data containing all primary particles was extracted using the multiplicity distribution of muons which is a sensitive observable for mass composition. The observed proton spectrum suggests a spectral hardening at ∼166 TeV and disfavors a single power law description of the spectrum up to the Knee energy (∼3 PeV).
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Affiliation(s)
- F Varsi
- Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - S Ahmad
- Aligarh Muslim University, Aligarh 202002, India
| | - M Chakraborty
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - A Chandra
- Aligarh Muslim University, Aligarh 202002, India
| | - S R Dugad
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - U D Goswami
- Dibrugarh University, Dibrugarh 786004, India
| | - S K Gupta
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - B Hariharan
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - Y Hayashi
- Graduate School of Science, Osaka Metropolitan University, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - P Jagadeesan
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - A Jain
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - P Jain
- Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - S Kawakami
- Graduate School of Science, Osaka Metropolitan University, Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - H Kojima
- College of Engineering, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - P Lipari
- INFN, Sezione Roma "Sapienza", Piazzale Aldo Moro 2, 00185 Roma, Italy
| | | | - P K Mohanty
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - R Moharana
- Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - Y Muraki
- Institute for Space-Earth Environmental Research, Nagoya University, Nagoya 464-8601, Japan
| | - P K Nayak
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - T Nonaka
- Institute for Cosmic Ray Research, Tokyo University, Kashiwa, Chiba 277-8582, Japan
| | - A Oshima
- College of Engineering, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - B P Pant
- Indian Institute of Technology Jodhpur, Jodhpur 342037, India
| | - D Pattanaik
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
- Utkal University, Bhubaneswar 751004, India
| | - S Paul
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - G S Pradhan
- Indian Institute of Technology Indore, Indore 453552, India
| | - M Rameez
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - K Ramesh
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - L V Reddy
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
| | - S Saha
- Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - R Sahoo
- Indian Institute of Technology Indore, Indore 453552, India
| | - R Scaria
- Indian Institute of Technology Indore, Indore 453552, India
| | - S Shibata
- College of Engineering, Chubu University, Kasugai, Aichi 487-8501, Japan
| | - M Zuberi
- Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400005, India
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Chakraborty M, Lara AG, Dang A, McCulloch KJ, Rainbow D, Carter D, Ngo LT, Solares E, Said I, Corbett-Detig RB, Gilbert LE, Emerson JJ, Briscoe AD. Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies. Proc Natl Acad Sci U S A 2023; 120:e2301411120. [PMID: 37552755 PMCID: PMC10438391 DOI: 10.1073/pnas.2301411120] [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: 01/26/2023] [Accepted: 06/16/2023] [Indexed: 08/10/2023] Open
Abstract
The acquisition of novel sexually dimorphic traits poses an evolutionary puzzle: How do new traits arise and become sex-limited? Recently acquired color vision, sexually dimorphic in animals like primates and butterflies, presents a compelling model for understanding how traits become sex-biased. For example, some Heliconius butterflies uniquely possess UV (ultraviolet) color vision, which correlates with the expression of two differentially tuned UV-sensitive rhodopsins, UVRh1 and UVRh2. To discover how such traits become sexually dimorphic, we studied Heliconius charithonia, which exhibits female-specific UVRh1 expression. We demonstrate that females, but not males, discriminate different UV wavelengths. Through whole-genome shotgun sequencing and assembly of the H. charithonia genome, we discovered that UVRh1 is present on the W chromosome, making it obligately female-specific. By knocking out UVRh1, we show that UVRh1 protein expression is absent in mutant female eye tissue, as in wild-type male eyes. A PCR survey of UVRh1 sex-linkage across the genus shows that species with female-specific UVRh1 expression lack UVRh1 gDNA in males. Thus, acquisition of sex linkage is sufficient to achieve female-specific expression of UVRh1, though this does not preclude other mechanisms, like cis-regulatory evolution from also contributing. Moreover, both this event, and mutations leading to differential UV opsin sensitivity, occurred early in the history of Heliconius. These results suggest a path for acquiring sexual dimorphism distinct from existing mechanistic models. We propose a model where gene traffic to heterosomes (the W or the Y) genetically partitions a trait by sex before a phenotype shifts (spectral tuning of UV sensitivity).
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
- Department of Biology, Texas A&M University, College Station, TX77843
| | | | - Andrew Dang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Kyle J. McCulloch
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN55108
| | - Dylan Rainbow
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - David Carter
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA92521
| | - Luna Thanh Ngo
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Edwin Solares
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Iskander Said
- Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, CA95064
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering and Genomics Institute, University of California, Santa Cruz, CA95064
| | | | - J. J. Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
| | - Adriana D. Briscoe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA92697
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Chakraborty M, Hasan MM, Kenreich JR, Jadwisienczak WM, Rahman F. Design and operation of a hybrid LED/LD-pumped phosphor-converted white-light lamp. Appl Opt 2023; 62:2266-2272. [PMID: 37132864 DOI: 10.1364/ao.484238] [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] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Illumination sources based on phosphors, pumped by laser diodes (LDs), have seen rapid developments over the past decade. Here, we present a new, to the best of our knowledge, design that features both spectral richness and the capability for high brightness. Complete design details and operational characterization have been described. This basic design can be extended in various ways to customize such lamps for different operational requirements. A hybrid arrangement of both LEDs and an LD is used to excite a mixture of two phosphors. The LEDs, in addition, provide a blue fill-in to enrich output radiation and to tune the chromaticity point inside the white region. The LD power, on the other hand, can be scaled up to generate very high brightness levels that are not achievable with pumping from LEDs alone. This capability is gained using a special transparent ceramic disk that carries the remote phosphor film. We also show that the radiation from our lamp is free from speckle-producing coherence.
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Chakraborty M, Kadir E, Gayen R. GO induced grain-boundary modification in transparent TiO2-GO nanocomposite thin films: Study by DC bias dependent impedance spectroscopy. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140116] [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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Chakravarty B, Kalapahar S, Sharma S, Chattopadhyay R, Ghosh S, Chakraborty M, Chakraborty R, Bose U, Chakraborty P. O-031 Activation of NLRP3 inflammasome enhances neutrophil extracellular traps in women with stage III/IV endometriosis: convergence of multiple signaling portray association between genetics and lesion type. Hum Reprod 2022. [DOI: 10.1093/humrep/deac104.031] [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: 11/14/2022] Open
Abstract
Abstract
Study question
Do NOD-like receptor pyrin-containing 3 (NLRP3) signaling affect neutrophil extracellular traps (NET)-osis in women with stage III/IV endometriosis?
Summary answer
Inflammasome activation whether due to pathogen (disease itself) or damage-associated molecular pattern (through NET) might be one mechanism involved in establishing perturbed endometrium in endometriosis.
What is known already
Endometriosis is characterized by number of processes like vascularization, hypernociception, and fibrosis, cardinal cause being inflammation. Recently, expression of inflammasome components, including NLRP3 and apoptosis signal-regulating kinase has been demonstrated in human endometrium cueing involvement in uterine innate immunity. Moreover, a novel extracellular killing mechanism, NET, is documented to reflect an inflammatory status in deep infiltrating endometriosis. Since, endometriosis demonstrates similarities with chronic inflammatory and autoimmune disorders; we postulated inflammatory responses in endometriosis may become modulated through a feed-forward loop of NET-induced specific cytokine production thus providing insights against potentiality of endometriotic cells to limit progression of the disease.
Study design, size, duration
Twenty-two consented women (24-39 years) with endometriosis (Group A) (Stages III–IV) (based on ASRM-2018 guidelines) and age-matched counterpart/s of male sub-fertility (Group B; control), free of uterine abnormalities (n = 18) were recruited between January to December 2021 from Institute of Reproductive Medicine, Kolkata. Eutopic endometrium, were collected from women undergoing diagnostic laparoscopy (Group A) or by curettage from women undergoing endometrial ablation (Group B). Serum was collected during window-of-implantation (LH + 7) for both the group/s.
Participants/materials, setting, methods
Pro-(IFN-g, TNF-a, IL-6, TGF-b) and anti-inflammatory (IL-10, IL-13, IL-4, IL-5) cytokines was evaluated by western blot. Expression level of inflammasome-related proteins (NLRP3, ASC, CASPASE1, PYCARD, IL-1-b) and mRNA expression was estimated by western-blot and quantitative-real-time PCR (qRT-PCR) respectively from tissue biopsies in Group A and B. SYTOX® green assay by flow-cytometry and neutrophil-elastase activity by immunofluorescence was done to quantify and characterize NET production in blood monocytes. P < 0.05 was considered statistically significant.
Main results and the role of chance
The mean (±SD) age of study population was 31.6±5.2 years. Hyperestrogenic milieu possibly stimulated (p < 0.001) pro-inflammatory molecules (IFN-g, TNF-a, IL-6, TGF-b) in endometriosis as observed by western-blot and qRT-PCR. A significant up-regulation (p < 0.001) was observed in relative mRNA expression of NLRP3 and PYCARD gene in Group A. However, caspase 1 expression documented non-significant variation in biopsies from endometriosis patients. Western blot corroborated the finding/s. The outcome of NLRP3 activation was supported by increased (p < 0.002) mRNA expression of IL-1b. NETs were detected significantly higher (p < 0.01) in 54.54% (12/22) patients in group A compared to control (16.66%; (3/18)). Moreover, quantification of NETs showed a significantly higher amount in endometriosis compared to group B (0.097 vs. 0.02, p < 0.03).
Spermann-rank correlation by SPSS version22 revealed positive correlation between IL-1b with NLRP3 (r = 0.56, p< 0.001), PYCARD (r = 0.11, p< 0.01); and caspase1 (r = 0.16, p< 0.01) and IL-1b (r = 0.47, p< 0.01) with NET-positive cell/s in endometriosis. Moreover, posterior cul-de-sac lesions correlated positively with NET-positive cell/s (r = 0.29; p < 0.01) cueing to possible prognostic marker/s. In summary, a coordinated-fashioned action of components of NLRP3 inflammasome machinery may regulate production of NET/s forming a complex network allowing communication between cell-types in order to maintain viability and development of endometrial lesion/s.
Limitations, reasons for caution
Our findings need to be replicated in larger study cohort/s, especially stratified by severity of endometriosis sub-groups and in women of different ethnicities. Another limitation is the missing information about NETs in normal functioning human endometrium throughout the menstrual cycle.
Wider implications of the findings
The proposed study aims to understand potential role of NLRP3 inflammasome complex as a “double-edged sword” in the development and pathophysiology of endometriosis. Therapeutic alternatives that aim to re-balance the pro- to anti-inflammatory milieu in the endometrium should consider the inflammasome as part of the equation.
Trial registration number
Not applicable
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Affiliation(s)
- B Chakravarty
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - S Kalapahar
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - S Sharma
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - R Chattopadhyay
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - S Ghosh
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - M Chakraborty
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
| | - R Chakraborty
- Melaka Manipal Medical College, Department of Microbiology, Manipal , India
| | - U Bose
- Melaka Manipal Medical College, Department of Pharmacology, Manipal , India
| | - P Chakraborty
- Institute of Reproductive Medicine, Department of Assisted Reproduction, Kolkata , India
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Kalapahar S, Chakraborty P, Shama S, Mitra I, Chattopadhyay R, Ghosh S, Chakraborty M, Chakravarty B. P-390 Serum homocysteine and uterine artery Doppler ultrasound in combination has better predictive accuracy in women with preeclampsia: useful tool for early screening in everyday practice. Hum Reprod 2022. [DOI: 10.1093/humrep/deac107.367] [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: 11/14/2022] Open
Abstract
Abstract
Study question
Is serum homocysteine combined with uterine-artery Doppler were effective in predicting preeclampsia (≥140mmHg/≥90mmHg blood pressure) in singleton pregnancy during 11–15 weeks of gestation?
Summary answer
Combination of serum homocysteine levels with uterine-artery Doppler is superior to individual presence of biochemical/ultrasound marker/s making the duo effective for early screening in preeclampsia.
What is known already
American College of Obstetricians and Gynecologists and National Institute for Care and Health Excellence recommend identifying patients who are at high risk of developing preeclampsia based on medical history. Recently, biochemical and ultrasound markers were investigated for prediction of preeclampsia, but none of them were predictably reliable, valid, and suitable for routine clinical use. Increased levels of homocysteine in 1st-trimester, seems to signal onset of preeclampsia later in pregnancy portraying severity of the disease as well. We aimed to identify predictive value of serum homocysteine combined with uterine-artery Doppler in singleton pregnancy during 11–15 weeks of gestation for preeclampsia.
Study design, size, duration
One hundred forty-two consented singleton pregnant women (28-45 years) at gestational age of 11–15 weeks, recruited between January to December 2021 from Institute of Reproductive Medicine, Kolkata were enrolled in the study. Women who used aspirin as a prophylaxis for preeclampsia or were diagnosed to have fetal, structural or chromosomal abnormalities were excluded from the study (n = 7). Maternal age, weight and height, mean arterial pressure, parity, and obstetric history were documented.
Participants/materials, setting, methods
Uterine-artery Doppler ultrasound and serum homocysteine levels were performed transabdominally and using ELISA respectively. Pregnancy outcomes were recorded. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) at optimal cut-off values were determined to predict preeclampsia. Optimal cut-off values for homocysteine levels were calculated using receiver operator characteristic curve (ROC). Chi-square test, Fisher’s exact test, unpaired t test, and Mann–Whitney U test were used when appropriate. P-value <0.05 was considered statistically significant.
Main results and the role of chance
16 cases had preeclampsia (11.26%) of whom 9 had early-onset preeclampsia (6.33%). Baseline characteristics including maternal-age (>35 or<), parity, body-mass- index, and gestational-age at measurement were not significantly different between two groups excepting higher (p < 0.001) mean arterial blood pressure (mmHg) at first trimester (97.2±6.4 vs. 81.1±7.2) in preeclampsia. Preeclamptic women had significantly higher (p < 0.001) serum homocysteine levels (μmol/l) (26.1±3.5 vs 10.2± 5.6) than normotensive pregnant women (n = 119). No difference in mean pulsatility (PI) of uterine-artery was observed (1.78±0.64 vs. 1.72±0.48) excluding significantly high (p > 0.02) in women with early-onset preeclampsia than control (2.11±0.81 vs. 1.39±0.92). However, lower (p < 0.01) gestational age (weeks) (35.4±2.1 vs. 37.6±1.4), and neonatal birth weight (gms) (2937.3±578.2 vs. 3227.6±421.5) with higher (p < 0.001) preterm delivery (25% vs 5.04%), low birth weight (25% vs 5.04%) and neonatal respiratory distress syndrome (12.5% vs. 0.84%) was documented in preeclampsia than control/s. The optimal cut-off value of serum homocysteine with PI levels, from ROC (AUC=0.735, p < 0.001) was superior to individual ROC (AUC=0.451; AUC=0.268). The sensitivity, specificity, PPV, and NPV were 67.7%, 70.5%, 1.7%, and 98.5%, respectively using a combination of abnormal serum homocysteine levels with abnormal uterine artery Doppler PI (above 95th percentile) and used as a predictive value for preeclampsia.
Limitations, reasons for caution
The limitation of this study was that there were small cases of early-onset preeclampsia. Additional studies with a larger sample size of early-onset preeclampsia and other models using serum homocysteine, combined with uterine artery Doppler, and maternal characteristic risk factors should be conducted.
Wider implications of the findings
Early screening of preeclampsia by using combination of serum homocysteine and uterine artery Doppler during first trimester (11–15 weeks) at the same visit may be more effective and allows the timing for using early low-dose aspirin prophylaxis in order to prevent preeclampsia.
Trial registration number
Not applicable
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Affiliation(s)
- S Kalapahar
- Institute of Reproductive Medicine, Department of Assisted Reproduction , Kolkata, India
| | - P Chakraborty
- Institute of Reproductive Medicine, Department of Assisted Reproduction , Kolkata, India
| | - S Shama
- Institute of Reproductive Medicine, Department of Assisted Reproduction , Kolkata, India
| | - I Mitra
- Indian Institute of Technology- Kharagpur, School of Medical Science and Technology , Kharagpur, India
| | - R Chattopadhyay
- Institute of Reproductive Medicine, Department of Assisted Reproduction , Kolkata, India
| | - S Ghosh
- Institute of Reproductive Medicine, Department of Assisted Reproduction , Kolkata, India
| | - M Chakraborty
- Institute of Reproductive Medicine, Department of Assisted Reproduction , Kolkata, India
| | - B Chakravarty
- Institute of Reproductive Medicine, Department of Assisted Reproduction , Kolkata, India
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Chakraborty M, Ramaiah A, Adolfi A, Halas P, Kaduskar B, Ngo LT, Jayaprasad S, Paul K, Whadgar S, Srinivasan S, Subramani S, Bier E, James AA, Emerson JJ. Author Correction: Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biol 2022; 20:96. [PMID: 35501892 PMCID: PMC9059397 DOI: 10.1186/s12915-022-01314-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Arunachalam Ramaiah
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.,Section of Cell and Developmental Biology, University of California, La Jolla, San Diego, CA, 92093-0335, USA.,Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Adriana Adolfi
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Paige Halas
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Bhagyashree Kaduskar
- Section of Cell and Developmental Biology, University of California, La Jolla, San Diego, CA, 92093-0335, USA.,Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Luna Thanh Ngo
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Suvratha Jayaprasad
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Kiran Paul
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Saurabh Whadgar
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Subhashini Srinivasan
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India.,Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Suresh Subramani
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India.,Section of Molecular Biology, University of California, La Jolla, San Diego, CA, 92093-0322, USA.,Tata Institute for Genetics and Society, University of California, La Jolla, San Diego, CA, 92093-0335, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, La Jolla, San Diego, CA, 92093-0335, USA.,Tata Institute for Genetics and Society, University of California, La Jolla, San Diego, CA, 92093-0335, USA
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA.,Tata Institute for Genetics and Society, University of California, La Jolla, San Diego, CA, 92093-0335, USA.,Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA. .,Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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Affiliation(s)
- S K Paul
- Department of Agronomy, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - N U Mahmud
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - D R Gupta
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M N Alam
- Bangladesh Sugarcrop Research Institute, Ishurdi 6620, Pabna, Bangladesh
| | - M Chakraborty
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - M T Islam
- Institute of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
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Agrawal S, Chakraborty P, Sinha A, Maiti A, Chakraborty M. ADRENAL HISTOPLASMOSIS: AN EASTERN INDIAN PERSPECTIVE. Acta Endocrinol (Buchar) 2022; 18:106-114. [PMID: 35975261 PMCID: PMC9365407 DOI: 10.4183/aeb.2022.106] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
CONTEXT The clinical presentation of histoplasmosis is varied. Due to its propensity for adrenal involvement, histoplasmosis is an important differential diagnosis in any patient presenting with adrenal mass, bilateral in particular. OBJECTIVE Data on clinical presentation, pattern of adrenal involvement, radiological appearance and long-term follow-up of adrenal histoplasmosis are relatively sparse; hence we looked at it. DESIGN This record based single-centre retrospective study was conducted in one of the tertiary care hospitals, situated in eastern India catering the Gangetic delta. SUBJECTS AND METHODS Data on demographic characters, presenting manifestations, biochemical & hormonal parameters and radiological appearance of confirmed adrenal histoplasmosis cases (n=9), admitted between 2015-2019 have been retrieved. The treatment outcome and condition of patients after 1-4 years of follow-up has also been discussed. RESULTS Four out of the nine (44.4%) patients had predisposing immunocompromised conditions in the form of diabetes and/or chronic alcoholism while rest were immunocompetent. Seven out of nine patients (77.8 %) had signs and symptoms suggestive of adrenal insufficiency, while two (22.2%) presented with only pyrexia of unknown origin. All of them had bilateral adrenal mass, though the radiologically appearances were different. All patients received anti-fungal agents with/without hydrocortisone and/or fludrocortisone. One patient died (11.1%), while majority responded favourably to treatment. Adrenocortical function did not recover completely. CONCLUSIONS The possibility of adrenal histoplasmosis should always be considered in patients presenting with bilateral adrenal mass, irrespective of adrenal morphology. Treatment is effective, but many of them require supplemental hydrocortisone for quite a long period, if not lifelong. Mineralocorticoid deficiency, however, is not permanent.
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Affiliation(s)
- S.S. Agrawal
- Endocrinology & Metabolism Medical College and Hospital Kolkata, West Bengal, India
| | - P.P. Chakraborty
- Endocrinology & Metabolism Medical College and Hospital Kolkata, West Bengal, India
| | - A. Sinha
- Endocrinology & Metabolism Medical College and Hospital Kolkata, West Bengal, India
| | - A. Maiti
- Endocrinology & Metabolism Medical College and Hospital Kolkata, West Bengal, India
| | - M. Chakraborty
- Microbiology, Medical College and Hospital Kolkata, Kolkata,West Bengal, India
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10
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Mahankar P, Chakraborty M, Bartakke S, Bafna V. Pearson syndrome- A case report. Pediatric Hematology Oncology Journal 2021. [DOI: 10.1016/j.phoj.2022.03.108] [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: 11/15/2022] Open
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11
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Durkin SM, Chakraborty M, Abrieux A, Lewald KM, Gadau A, Svetec N, Peng J, Kopyto M, Langer CB, Chiu JC, Emerson JJ, Zhao L. Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii. Mol Biol Evol 2021; 38:2532-2546. [PMID: 33586767 PMCID: PMC8136512 DOI: 10.1093/molbev/msab048] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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] [Indexed: 12/13/2022] Open
Abstract
Studying how novel phenotypes originate and evolve is fundamental to the field of evolutionary biology as it allows us to understand how organismal diversity is generated and maintained. However, determining the basis of novel phenotypes is challenging as it involves orchestrated changes at multiple biological levels. Here, we aim to overcome this challenge by using a comparative species framework combining behavioral, gene expression, and genomic analyses to understand the evolutionary novel egg-laying substrate-choice behavior of the invasive pest species Drosophila suzukii. First, we used egg-laying behavioral assays to understand the evolution of ripe fruit oviposition preference in D. suzukii compared with closely related species D. subpulchrella and D. biarmipes as well as D. melanogaster. We show that D. subpulchrella and D. biarmipes lay eggs on both ripe and rotten fruits, suggesting that the transition to ripe fruit preference was gradual. Second, using two-choice oviposition assays, we studied how D. suzukii, D. subpulchrella, D. biarmipes, and D. melanogaster differentially process key sensory cues distinguishing ripe from rotten fruit during egg-laying. We found that D. suzukii's preference for ripe fruit is in part mediated through a species-specific preference for stiff substrates. Last, we sequenced and annotated a high-quality genome for D. subpulchrella. Using comparative genomic approaches, we identified candidate genes involved in D. suzukii's ability to seek out and target ripe fruits. Our results provide detail to the stepwise evolution of pest activity in D. suzukii, indicating important cues used by this species when finding a host, and the molecular mechanisms potentially underlying their adaptation to a new ecological niche.
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Affiliation(s)
- Sylvia M Durkin
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
- Department of Integrative Biology and Museum of Vertebrate Zoology, University of California, Berkeley, Berkeley, CA, USA
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Antoine Abrieux
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, USA
| | - Kyle M Lewald
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, USA
| | - Alice Gadau
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Nicolas Svetec
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Junhui Peng
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Miriam Kopyto
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Christopher B Langer
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
| | - Joanna C Chiu
- Department of Entomology and Nematology, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Li Zhao
- Laboratory of Evolutionary Genetics and Genomics, The Rockefeller University, New York, NY, USA
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12
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Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ. Evolution of genome structure in the Drosophila simulans species complex. Genome Res 2021; 31:380-396. [PMID: 33563718 PMCID: PMC7919458 DOI: 10.1101/gr.263442.120] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 12/28/2020] [Indexed: 12/25/2022]
Abstract
The rapid evolution of repetitive DNA sequences, including satellite DNA, tandem duplications, and transposable elements, underlies phenotypic evolution and contributes to hybrid incompatibilities between species. However, repetitive genomic regions are fragmented and misassembled in most contemporary genome assemblies. We generated highly contiguous de novo reference genomes for the Drosophila simulans species complex (D. simulans, D. mauritiana, and D. sechellia), which speciated ∼250,000 yr ago. Our assemblies are comparable in contiguity and accuracy to the current D. melanogaster genome, allowing us to directly compare repetitive sequences between these four species. We find that at least 15% of the D. simulans complex species genomes fail to align uniquely to D. melanogaster owing to structural divergence-twice the number of single-nucleotide substitutions. We also find rapid turnover of satellite DNA and extensive structural divergence in heterochromatic regions, whereas the euchromatic gene content is mostly conserved. Despite the overall preservation of gene synteny, euchromatin in each species has been shaped by clade- and species-specific inversions, transposable elements, expansions and contractions of satellite and tRNA tandem arrays, and gene duplications. We also find rapid divergence among Y-linked genes, including copy number variation and recent gene duplications from autosomes. Our assemblies provide a valuable resource for studying genome evolution and its consequences for phenotypic evolution in these genetic model species.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Ching-Ho Chang
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
| | - Danielle E Khost
- Department of Biology, University of Rochester, Rochester, New York 14627, USA
- FAS Informatics and Scientific Applications, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Jeffrey Vedanayagam
- Department of Developmental Biology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA
| | - Jeffrey R Adrion
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | - Colin D Meiklejohn
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, Nebraska 68502, USA
| | | | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA
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13
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Chakraborty M, Ramaiah A, Adolfi A, Halas P, Kaduskar B, Ngo LT, Jayaprasad S, Paul K, Whadgar S, Srinivasan S, Subramani S, Bier E, James AA, Emerson JJ. Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biol 2021; 19:28. [PMID: 33568145 PMCID: PMC7876825 DOI: 10.1186/s12915-021-00963-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 11/17/2020] [Accepted: 01/19/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND The mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vector's genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution. RESULTS To access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element (TE) families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y chromosome in any mosquito. By tracking full-length mRNA for > 15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively throughout male development and adulthood, suggesting an important role. CONCLUSION Collectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate the development of genetic control strategies of malaria transmission.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Arunachalam Ramaiah
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Adriana Adolfi
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Paige Halas
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
| | - Bhagyashree Kaduskar
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
| | - Luna Thanh Ngo
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Suvratha Jayaprasad
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Kiran Paul
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Saurabh Whadgar
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Subhashini Srinivasan
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, KA, 560100, India
| | - Suresh Subramani
- Tata Institute for Genetics and Society, Center at inStem, Bangalore, Karnataka, 560065, India
- Section of Molecular Biology, University of California, San Diego, La Jolla, CA, 92093-0322, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
| | - Anthony A James
- Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, 92697, USA
- Tata Institute for Genetics and Society, University of California, San Diego, La Jolla, CA, 92093-0335, USA
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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14
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Liao Y, Zhang X, Chakraborty M, Emerson JJ. Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. Genome Res 2021; 31:397-410. [PMID: 33563719 PMCID: PMC7919452 DOI: 10.1101/gr.266130.120] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022]
Abstract
Topologically associating domains (TADs) were recently identified as fundamental units of three-dimensional eukaryotic genomic organization, although our knowledge of the influence of TADs on genome evolution remains preliminary. To study the molecular evolution of TADs in Drosophila species, we constructed a new reference-grade genome assembly and accompanying high-resolution TAD map for D. pseudoobscura Comparison of D. pseudoobscura and D. melanogaster, which are separated by ∼49 million years of divergence, showed that ∼30%-40% of their genomes retain conserved TADs. Comparative genomic analysis of 17 Drosophila species revealed that chromosomal rearrangement breakpoints are enriched at TAD boundaries but depleted within TADs. Additionally, genes within conserved TADs show lower expression divergence than those located in nonconserved TADs. Furthermore, we found that a substantial proportion of long genes (>50 kbp) in D. melanogaster (42%) and D. pseudoobscura (26%) constitute their own TADs, implying transcript structure may be one of the deterministic factors for TAD formation. By using structural variants (SVs) identified from 14 D. melanogaster strains, its three closest sibling species from the D. simulans species complex, and two obscura clade species, we uncovered evidence of selection acting on SVs at TAD boundaries, but with the nature of selection differing between SV types. Deletions are depleted at TAD boundaries in both divergent and polymorphic SVs, suggesting purifying selection, whereas divergent tandem duplications are enriched at TAD boundaries relative to polymorphism, suggesting they are adaptive. Our findings highlight how important TADs are in shaping the acquisition and retention of structural mutations that fundamentally alter genome organization.
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Affiliation(s)
- Yi Liao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Xinwen Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California 92697, USA.,Center for Complex Biological Systems, University of California, Irvine, California 92697, USA
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15
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Linder RA, Majumder A, Chakraborty M, Long A. Two Synthetic 18-Way Outcrossed Populations of Diploid Budding Yeast with Utility for Complex Trait Dissection. Genetics 2020; 215:323-342. [PMID: 32241804 PMCID: PMC7268983 DOI: 10.1534/genetics.120.303202] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 01/06/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
Advanced-generation multiparent populations (MPPs) are a valuable tool for dissecting complex traits, having more power than genome-wide association studies to detect rare variants and higher resolution than F2 linkage mapping. To extend the advantages of MPPs in budding yeast, we describe the creation and characterization of two outbred MPPs derived from 18 genetically diverse founding strains. We carried out de novo assemblies of the genomes of the 18 founder strains, such that virtually all variation segregating between these strains is known, and represented those assemblies as Santa Cruz Genome Browser tracks. We discovered complex patterns of structural variation segregating among the founders, including a large deletion within the vacuolar ATPase VMA1, several different deletions within the osmosensor MSB2, a series of deletions and insertions at PRM7 and the adjacent BSC1, as well as copy number variation at the dehydrogenase ALD2 Resequenced haploid recombinant clones from the two MPPs have a median unrecombined block size of 66 kb, demonstrating that the population is highly recombined. We pool-sequenced the two MPPs to 3270× and 2226× coverage and demonstrated that we can accurately estimate local haplotype frequencies using pooled data. We further downsampled the pool-sequenced data to ∼20-40× and showed that local haplotype frequency estimates remained accurate, with median error rates 0.8 and 0.6% at 20× and 40×, respectively. Haplotypes frequencies are estimated much more accurately than SNP frequencies obtained directly from the same data. Deep sequencing of the two populations revealed that 10 or more founders are present at a detectable frequency for > 98% of the genome, validating the utility of this resource for the exploration of the role of standing variation in the architecture of complex traits.
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Affiliation(s)
- Robert A Linder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine, California 92697-2525
| | - Arundhati Majumder
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine, California 92697-2525
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine, California 92697-2525
| | - Anthony Long
- Department of Ecology and Evolutionary Biology, School of Biological Sciences, University of California, Irvine, California 92697-2525
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16
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Jaggi N, Nirwan P, Chakraborty M. Process improvement to effectively manage and reduce sharps injuries in a Tertiary Hospital in Northern India. J Healthc Qual Res 2020; 35:141-148. [PMID: 32446644 DOI: 10.1016/j.jhqr.2020.03.007] [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: 12/19/2019] [Revised: 02/29/2020] [Accepted: 03/17/2020] [Indexed: 11/26/2022]
Abstract
INTRODUCTION AND OBJECTIVES Needle stick injuries are associated with a 0.3-30% risk of transmission of Human Immunodeficiency virus, Hepatitis C virus, and Hepatitis B virus. Despite causing psychological trauma they also involve a huge financial burden. A robust process improvement (RPI) toolkit was introduced in order to effectively manage and reduce needle stick injuries, as well as an attempt to report prevalence, post-exposure management, and associated economic burden. MATERIALS AND METHODS Prospective Observational Study (2015-2018) has been design in a Corporate Tertiary Care Hospital. The participants included were needle stick injuries exposed staff. RPI toolkit was implemented (2015-2018) focusing on root cause analysis, availability of safety engineered devices, immunization and post-exposure management of needle stick injuries exposed staff. The main outcome measure was needle stick injuries incidence. RESULTS A total of 211 needle stick injuries were reported (mean - 52.72/year, needle stick injury incidence - 13.18/year/100 beds). Yearly trends showed a decrease of 21.3% in injuries from 2015 (61) to 2018 (48). Half (106, 50%) of the total injuries were reported among nurses. Use of hypodermic needles was involved in 116 (55%) injuries, with 114 (54%) occurring due to nonadherence to hospital policies. Overall, 204 staff had protective immunity, and 135 (64%) of these had completed their Hepatitis B immunizations. The source was known in 165 (78%) cases, and 113 of these cases had an injury from a source with negative viral markers. A 6-month follow-up was completed in 90 cases. No seroconversion was reported. Overall costs incurred in post-exposure prophylaxis was approximately €30,000 (mean cost €143.50/needle stick injury). CONCLUSION Nurses are most at risk of needle stick injury in healthcare settings. Implementation of RPI toolkit led to a 21.3% reduction in sharps injury incidences. These injuries incur huge financial burden on the hospital. Appropriate immunization strategies saved about €1360 expenditure on post-exposure prophylaxis.
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Affiliation(s)
- N Jaggi
- Artemis Hospital, Sector 51, Gurugram, Haryana 122001, India
| | - P Nirwan
- Artemis Hospital, Sector 51, Gurugram, Haryana 122001, India.
| | - M Chakraborty
- Artemis Hospital, Sector 51, Gurugram, Haryana 122001, India
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17
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Heras J, Chakraborty M, Emerson JJ, German DP. Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish. Proc Biol Sci 2020; 287:20192327. [PMID: 32070255 PMCID: PMC7062031 DOI: 10.1098/rspb.2019.2327] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 10/03/2019] [Accepted: 01/26/2020] [Indexed: 01/30/2023] Open
Abstract
Adopting a new diet is a significant evolutionary change, and can profoundly affect an animal's physiology, biochemistry, ecology and genome. To study this evolutionary transition, we investigated the physiology and genomics of digestion of a derived herbivorous fish, Cebidichthys violaceus. We sequenced and assembled its genome (N50 = 6.7 Mb) and digestive transcriptome, and revealed the molecular changes related to digestive enzymes (carbohydrases, proteases and lipases), finding abundant evidence of molecular adaptation. Specifically, two gene families experienced expansion in copy number and adaptive amino acid substitutions: amylase and carboxyl ester lipase (cel), which are involved in the digestion of carbohydrates and lipids, respectively. Both show elevated levels of gene expression and increased enzyme activity. Because carbohydrates are abundant in the prickleback's diet and lipids are rare, these findings suggest that such dietary specialization involves both exploiting abundant resources and scavenging rare ones, especially essential nutrients, like essential fatty acids.
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Affiliation(s)
- Joseph Heras
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA 92697-2525, USA
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18
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Sah RP, Chakraborty M, Prasad K, Pandit M, Tudu VK, Chakravarty MK, Narayan SC, Rana M, Moharana D. Impact of water deficit stress in maize: Phenology and yield components. Sci Rep 2020; 10:2944. [PMID: 32076012 PMCID: PMC7031221 DOI: 10.1038/s41598-020-59689-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [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: 03/07/2019] [Accepted: 01/27/2020] [Indexed: 11/09/2022] Open
Abstract
Fifteen million farmers in India engaged in Maize cultivation. India would require 45 MMT of Maize by 2022. But, only 15% of cultivated area of maize is under irrigation and water shortage has been a challenge for sustainability of maize production. Water deficit stress (WDS) during pre-flowering and grain filling stages massively affects the plant performance due to imprecise traits function. Thus, the effect of WDS on non-drought tolerant (NDT) and drought tolerant (DT) maize lines were investigated. WDS increased the flowering days, days to maturity, anthesis silk interval, decreased the leaf number, abnormal expression of secondary stress responsive traits, loss of normal root architecture which overall lead to a reduction in GY/ha. WDS at flowering and grain filling stage leads to significant yield penalty especially in NDT lines than DT lines. The yield penalty was ranged from 34.28 to 66.15% in NDT and 38.48 to 55.95% in DT lines due to WDS. Using multiple statistics, traits which improve WDS tolerance in maize were identified viz; number of leaves, number of stomata on lower surface of leaf, leaf angle at ear forming node internodal length between 3rd and 4th leaf from top, flag leaf length, flag leaf width, ear per plants, leaf senescence, pollen stainability, root fresh weight and root length. These traits would help in trait specific breeding in maize for WDS tolerance.
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Affiliation(s)
- R P Sah
- ICAR-National Rice Research Institute, Cuttack, Odisha, India.,Department of Genetics and Plant Breeding, Birsa Agricultural University, Kanke, Ranchi, Jharkhand, India
| | - M Chakraborty
- Department of Genetics and Plant Breeding, Birsa Agricultural University, Kanke, Ranchi, Jharkhand, India.
| | - K Prasad
- Department of Genetics and Plant Breeding, Birsa Agricultural University, Kanke, Ranchi, Jharkhand, India
| | - M Pandit
- Department of Genetics and Plant Breeding, Birsa Agricultural University, Kanke, Ranchi, Jharkhand, India
| | - V K Tudu
- Department of Genetics and Plant Breeding, Birsa Agricultural University, Kanke, Ranchi, Jharkhand, India
| | - M K Chakravarty
- Department of Entomology, Birsa Agricultural University, Kanke, Ranchi, Jharkhand, India
| | - S C Narayan
- Department of Genetics and Plant Breeding, Birsa Agricultural University, Kanke, Ranchi, Jharkhand, India
| | - M Rana
- Indian Grassland and Fodder Research Institute, Jhansi, Uttar Pradesh, India
| | - D Moharana
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
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19
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Hossaini F, Munshi S, Chakraborty M. Antimicrobial effects of different extracts of medicinally used green leafy vegetables collected from local market of Dhaka, Bangladesh. Food Res 2020. [DOI: 10.26656/fr.2017.4(3).017] [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: 11/12/2022] Open
Abstract
The present study was carried out to determine the antimicrobial efficacy of green leafy
vegetable samples which are traditionally used as medicinal herbs. Therefore, three
samples each of Neem (Azadirachta indica, leaves), Ivy Gourd (Coccinia grandis, leaves),
Water Spinach (Ipomoea aquatica, leaves) and Skunkvine (Paederia foetida, leaves) were
collected and subjected to microbiological analysis, and agar well diffusion and
microdilution assays to check antimicrobial activity. The samples contained total viable
bacteria and fungi up to 107
and 105 CFU/g, respectively. Staphylococcus spp., Klebsiella
spp. and Pseudomonas spp. were recovered in all the samples. All the samples showed
potential antibacterial activity against most of the tested bacteria, especially their ethanolic
and methanolic extracts. Although, crude and hot water extracts almost had no effect on
the bacterial growth. The MIC value of the samples was found in a range of 3 mg/mL to
12 mg/mL and the average MIC value was recorded to be 6 mg/mL. Overall, the findings
of the present study justified the therapeutic potential of the tested green leafy vegetable
samples.
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20
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Solares EA, Chakraborty M, Miller DE, Kalsow S, Hall K, Perera AG, Emerson JJ, Hawley RS. Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing. G3 (Bethesda) 2018; 8:3143-3154. [PMID: 30018084 PMCID: PMC6169397 DOI: 10.1534/g3.118.200162] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [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] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/03/2018] [Indexed: 12/27/2022]
Abstract
Accurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, inversion, and translocation of sequences. In the past 10 years, high-throughput short reads have greatly expanded our ability to assay sequence variation due to single nucleotide polymorphisms. However, a recent de novo assembly of a second Drosophila melanogaster reference genome has revealed that short read genotyping methods miss hundreds of structural variants, including those affecting phenotypes. While genomes assembled using high-coverage long reads can achieve high levels of contiguity and completeness, concerns about cost, errors, and low yield have limited widespread adoption of such sequencing approaches. Here we resequenced the reference strain of D. melanogaster (ISO1) on a single Oxford Nanopore MinION flow cell run for 24 hr. Using only reads longer than 1 kb or with at least 30x coverage, we assembled a highly contiguous de novo genome. The addition of inexpensive paired reads and subsequent scaffolding using an optical map technology achieved an assembly with completeness and contiguity comparable to the D. melanogaster reference assembly. Comparison of our assembly to the reference assembly of ISO1 uncovered a number of structural variants (SVs), including novel LTR transposable element insertions and duplications affecting genes with developmental, behavioral, and metabolic functions. Collectively, these SVs provide a snapshot of the dynamics of genome evolution. Furthermore, our assembly and comparison to the D. melanogaster reference genome demonstrates that high-quality de novo assembly of reference genomes and comprehensive variant discovery using such assemblies are now possible by a single lab for under $1,000 (USD).
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Affiliation(s)
- Edwin A Solares
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA
| | - Danny E Miller
- Stowers Institute for Medical Research, Kansas City, MO
- MD-PhD Physician Scientist Training Program, University of Kansas Medical Center, Kansas City, KS
| | - Shannon Kalsow
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA
| | - Kate Hall
- Stowers Institute for Medical Research, Kansas City, MO
| | | | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California Irvine, CA
| | - R Scott Hawley
- Stowers Institute for Medical Research, Kansas City, MO
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS
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Patel TN, Chakraborty M, Bhattacharya P. Microsatellite Instability in Chronic Myeloid Leukemia using D17S261 and D3S643 markers: A Pilot Study in Gujarat Population. Indian J Cancer 2018; 54:426-429. [PMID: 29469071 DOI: 10.4103/ijc.ijc_275_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
CONTEXT Tumor progresses through a series of genetic alterations that involve proto-oncogenes and tumor suppressor genes - the gatekeeper, caretakers, and landscaper genes. Microsatellites are short tandem repeat sequences, present over the span of human genome and are known to be variable at multiple loci due to errors in DNA Mismatch Repair machinery. AIM The present study was aimed to evaluate the association between Microsatellite Instability (MSI) and evolution of Chronic Myeloid Leukemia (CML) - genetically a rare event but profound in this pilot study. SETTINGS AND DESIGNS We explore the possibility of MSI in primary CML patients confirmed by t(9;22) using capillary electrophoresis. Fifteen CML patients and healthy individual samples, respectively, were used to study the markers D17S261 and D3S643. MATERIALS AND METHODS The DNA was amplified using tagged and nontagged primers and further subjected to bioanalysis and fragment analysis. RESULTS While the results from bioanalyzer fluctuated, fragment analysis indicated the presence of microsatellite variability in 80% of the patients' samples as compared to no MSI in normal individuals for both the markers. CONCLUSION These findings suggest that MSI is a genetic event that may have a role in CML progression or evolution. Further studies are warranted to understand the plausible underlying causes.
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Affiliation(s)
- T N Patel
- Departments of Integrative Biology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - M Chakraborty
- Departments of Biomedical Genetics, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - P Bhattacharya
- Departments of Integrative Biology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Sharma N, Chakraborty M, Neog NK, Bandyopadhyay M. Development and characterization of a helicon plasma source. Rev Sci Instrum 2018; 89:083508. [PMID: 30184689 DOI: 10.1063/1.5030624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
The Helicon Plasma Source (HeliPS) designed and developed at the Centre of Plasma Physics-Institute for Plasma Research is a versatile helicon plasma device, which operates in a wide range of magnetic field configurations from 50 G to 500 G. This device is dedicated to perform a broad range of research activities. The main objective for development of the HeliPS is to carry out studies on ion-ion plasmas in electronegative gases. In the near future, ion-ion plasmas will be formed in electronegative gases in the downstream of the plasma production region. Although the system is primarily designed to carry out ion-ion plasma experiments, the same system can also be used for experimental studies on some basic helicon plasma properties such as wave propagation, wave coupling, and plasma instability. At present, argon plasma is produced with a RF power supply of 13.56 MHz frequency. External circuit parameters, such as antenna current, plasma resistance (Rp), and internal parameters, such as electron density and temperature, are measured. The details of the experimental setup development, device characteristic, as well as preliminary plasma production and characterization to confirm occurrence of the helicon plasma in the system are presented in this article.
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Affiliation(s)
- N Sharma
- Centre of Plasma Physics-Institute for Plasma Research, Tepesia, Sonapur, Kamrup, Assam 782402, India
| | - M Chakraborty
- Centre of Plasma Physics-Institute for Plasma Research, Tepesia, Sonapur, Kamrup, Assam 782402, India
| | - N K Neog
- Centre of Plasma Physics-Institute for Plasma Research, Tepesia, Sonapur, Kamrup, Assam 782402, India
| | - M Bandyopadhyay
- Institute for Plasma Research, HBNI, Bhat, Gandhinagar 382428, Gujarat, India
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Chakraborty M, VanKuren NW, Zhao R, Zhang X, Kalsow S, Emerson JJ. Hidden genetic variation shapes the structure of functional elements in Drosophila. Nat Genet 2018; 50:20-25. [PMID: 29255259 PMCID: PMC5742068 DOI: 10.1038/s41588-017-0010-y] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [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: 03/15/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022]
Abstract
Mutations that add, subtract, rearrange, or otherwise refashion genome structure often affect phenotypes, although the fragmented nature of most contemporary assemblies obscures them. To discover such mutations, we assembled the first new reference-quality genome of Drosophila melanogaster since its initial sequencing. By comparing this new genome to the existing D. melanogaster assembly, we created a structural variant map of unprecedented resolution and identified extensive genetic variation that has remained hidden until now. Many of these variants constitute candidates underlying phenotypic variation, including tandem duplications and a transposable element insertion that amplifies the expression of detoxification-related genes associated with nicotine resistance. The abundance of important genetic variation that still evades discovery highlights how crucial high-quality reference genomes are to deciphering phenotypes.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
| | - Nicholas W VanKuren
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Roy Zhao
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, USA
| | - Xinwen Zhang
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Graduate Program in Mathematical, Computational and Systems Biology, University of California, Irvine, CA, USA
| | - Shannon Kalsow
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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Chakraborty M, Mukhopadhyay S, Dasgupta A, Patsa S, Anjum N, Ray JG. A new approach of oral cancer detection using bilateral texture features in digital infrared thermal images. Annu Int Conf IEEE Eng Med Biol Soc 2017; 2016:1377-1380. [PMID: 28268582 DOI: 10.1109/embc.2016.7590964] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Oral cancer is one of the most prevalent form of cancer and its severity is aggrandized specially among the socio-economically backward population in developing countries. A major fraction of patient population is unable to avail diagnosis for oral cancer due to scarcity of state-of-the-art infrastructure and experienced oral and maxillofacial pathologist. Contemporary gold standard of oral cancer confirmation relies on biopsy report. But biopsy is invasive and thus patients are usually reluctant to undergo this test. Moreover, biopsy yields considerable false negatives if investigated tissue is not collected precisely from the carcinogenic location. Till date, there is dearth of computer aided pre-screening tool for detection of oral cancer. The paper presents Digital Infrared Thermal Imaging as a viable modality for early screening of oral cancer. This is the pioneering attempt to discriminate normal subjects from patients by leveraging discriminating texture features on oral thermograms. Statistically significant texture features were selected from a) both halves of frontal face and b) right and left profile faces. Due to disparity of distribution of facial temperature between normal subjects and patients, the corresponding texture features form discriminative class specific local clusters. Such local conglomeration was exploited using k-means and fuzzy k-means clustering. We adopt the concept of cluster prototype classifier which assigns label to each cluster according to majority class labels within that cluster. Highest classification accuracy of 86.12% is attained on fusion of features from left and right half of frontal face of precancerous subject followed by fuzzy k-means guided cluster prototype classification. The proposed work outperforms our previously developed pre-screening framework by upto 6.5%. Such promising results boosts the viability of our approach.
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Affiliation(s)
| | - M. Chakraborty
- Metallurgical Engineering Department, Indian Institute of Technology, Kharagpur 721302, India
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Bhat R, Chakraborty M, Glimm T, Stewart TA, Newman SA. Deep phylogenomics of a tandem-repeat galectin regulating appendicular skeletal pattern formation. BMC Evol Biol 2016; 16:162. [PMID: 27538950 PMCID: PMC4989294 DOI: 10.1186/s12862-016-0729-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 02/08/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND A multiscale network of two galectins Galectin-1 (Gal-1) and Galectin-8 (Gal-8) patterns the avian limb skeleton. Among vertebrates with paired appendages, chondrichthyan fins typically have one or more cartilage plates and many repeating parallel endoskeletal elements, actinopterygian fins have more varied patterns of nodules, bars and plates, while tetrapod limbs exhibit tandem arrays of few, proximodistally increasing numbers of elements. We applied a comparative genomic and protein evolution approach to understand the origin of the galectin patterning network. Having previously observed a phylogenetic constraint on Gal-1 structure across vertebrates, we asked whether evolutionary changes of Gal-8 could have critically contributed to the origin of the tetrapod pattern. RESULTS Translocations, duplications, and losses of Gal-8 genes in Actinopterygii established them in different genomic locations from those that the Sarcopterygii (including the tetrapods) share with chondrichthyans. The sarcopterygian Gal-8 genes acquired a potentially regulatory non-coding motif and underwent purifying selection. The actinopterygian Gal-8 genes, in contrast, did not acquire the non-coding motif and underwent positive selection. CONCLUSION These observations interpreted through the lens of a reaction-diffusion-adhesion model based on avian experimental findings can account for the distinct endoskeletal patterns of cartilaginous, ray-finned, and lobe-finned fishes, and the stereotypical limb skeletons of tetrapods.
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Affiliation(s)
- Ramray Bhat
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Present Address: Department of Molecular Reproduction, Development and Genetics, Indian Institute of Science, Bangalore, 560012 India
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 USA
| | - Tilmann Glimm
- Department of Mathematics, Western Washington University, Bellingham, WA 98229 USA
| | - Thomas A. Stewart
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520 USA
- Minnesota Center for Philosophy of Science, University of Minnesota, Minneapolis, MN 55455 USA
| | - Stuart A. Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, NY 10595 USA
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Affiliation(s)
- S N Biswas
- Department of General Medicine, Midnapore Medical College and Hospital, Medinipur, West Bengal, India
| | - P P Chakraborty
- Department of General Medicine, Midnapore Medical College and Hospital, Medinipur, West Bengal, India
| | - M Chakraborty
- Department of Microbiology, Calcutta School of Tropical Medicine, Kolkata, West Bengal, India
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Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res 2016; 44:e147. [PMID: 27458204 PMCID: PMC5100563 DOI: 10.1093/nar/gkw654] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [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: 12/11/2015] [Accepted: 07/09/2016] [Indexed: 01/19/2023] Open
Abstract
Genome assemblies that are accurate, complete and contiguous are essential for identifying important structural and functional elements of genomes and for identifying genetic variation. Nevertheless, most recent genome assemblies remain incomplete and fragmented. While long molecule sequencing promises to deliver more complete genome assemblies with fewer gaps, concerns about error rates, low yields, stringent DNA requirements and uncertainty about best practices may discourage many investigators from adopting this technology. Here, in conjunction with the platinum standard Drosophila melanogaster reference genome, we analyze recently published long molecule sequencing data to identify what governs completeness and contiguity of genome assemblies. We also present a hybrid meta-assembly approach that achieves remarkable assembly contiguity for both Drosophila and human assemblies with only modest long molecule sequencing coverage. Our results motivate a set of preliminary best practices for obtaining accurate and contiguous assemblies, a ‘missing manual’ that guides key decisions in building high quality de novo genome assemblies, from DNA isolation to polishing the assembly.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - James G Baldwin-Brown
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA
| | - Anthony D Long
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA.,Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
| | - J J Emerson
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA 92697, USA .,Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA
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Raut AN, Nandanwar SU, Suryawanshi YR, Chakraborty M, Jauhari S, Mukhopadhyay S, Shenoy KT, Bajaj HC. Liquid phase selective hydrogenation of phenol to cyclohexanone over Ru/Al2O3 nanocatalyst under mild conditions. Kinet Catal 2016. [DOI: 10.1134/s0023158416010110] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chakraborty M, Reddy PS, Mustafa G, Rajesh G, Narasu VML, Udayasuriyan V, Rana D. Transgenic rice expressing the cry2AX1 gene confers resistance to multiple lepidopteran pests. Transgenic Res 2016; 25:665-78. [DOI: 10.1007/s11248-016-9954-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/23/2016] [Indexed: 10/22/2022]
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Chakraborty M, Sairam Reddy P, Laxmi Narasu M, Krishna G, Rana D. Agrobacterium-mediated genetic transformation of commercially elite rice restorer line using nptII gene as a plant selection marker. Physiol Mol Biol Plants 2016; 22:51-60. [PMID: 27186018 PMCID: PMC4840146 DOI: 10.1007/s12298-015-0334-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/15/2015] [Accepted: 12/06/2015] [Indexed: 05/29/2023]
Abstract
Transformation of commercially important indica cultivars remains challenging for the scientific community even though Agrobacterium-mediated transformation protocols for a few indica rice lines have been well established. We report successful transformation of a commercially important restorer line JK1044R of indica rice hybrid JKRH 401. While following existing protocol, we optimized several parameters for callusing, regeneration and genetic transformation of JK1044R. Calli generated from the rice scutellum tissue were used for transformation by Agrobacterium harboring pCAMBIA2201. A novel two tire selection scheme comprising of Geneticin (G418) and Paramomycin were deployed for selection of transgenic calli as well as regenerated plantlets that expressed neomycin phosphotransferase-II gene encoded by the vector. One specific combination of G418 (30 mg l(-1)) and Paramomycin (70 mg l(-1)) was very effective for calli selection. Transformed and selected calli were detected by monitoring the expression of the reporter gene uidA (GUS). Regenerated plantlets were confirmed through PCR analysis of nptII and gus genes specific primers as well as dot blot using gus gene specific as probe.
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Affiliation(s)
- M. Chakraborty
- />Department of Biotechnology, Jawaharlal Nehru Technological University (JNTU), Hyderabad, Telangana 500072 India
- />Biotechnology Division, J.K Agri. Genetics Pvt. Ltd., Hyderabad, Telangana 500016 India
| | - P. Sairam Reddy
- />Biotechnology Division, J.K Agri. Genetics Pvt. Ltd., Hyderabad, Telangana 500016 India
| | - M. Laxmi Narasu
- />Department of Biotechnology, Jawaharlal Nehru Technological University (JNTU), Hyderabad, Telangana 500072 India
| | - Gaurav Krishna
- />Biotechnology Division, J.K Agri. Genetics Pvt. Ltd., Hyderabad, Telangana 500016 India
- />Jacob School of Biotechnology & Bioengineering, Sam Higginbottom Institute of Agriculture, Technology & Sciences (Formerly Allahabad Agricultural Institute), Deemed University, Allahabad, 211007 Uttar Pradesh India
| | - Debashis Rana
- />Biotechnology Division, J.K Agri. Genetics Pvt. Ltd., Hyderabad, Telangana 500016 India
- />Bayer CropScience-Seeds, Bayer (South East Asia) Pte Ltd, Singapore, Singapore
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Chakraborty M, Fry JD. Evidence that Environmental Heterogeneity Maintains a Detoxifying Enzyme Polymorphism in Drosophila melanogaster. Curr Biol 2015; 26:219-223. [PMID: 26748852 DOI: 10.1016/j.cub.2015.11.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/28/2022]
Abstract
Environmental heterogeneity is thought to be an important process maintaining genetic variation in populations [1-4]: if alternative alleles are favored in different environments, a stable polymorphism can be maintained [1, 5, 6]. This situation has been hypothesized to occur in genes encoding multi-substrate enzymes [7], in which changes that increase activity with one substrate typically decrease activity with others [8-10], but examples of polymorphisms maintained by this mechanism are rare. Here, we present evidence that a polymorphism in an enzyme gene in Drosophila melanogaster is maintained by such a trade-off. The mitochondrially localized aldehyde dehydrogenase in D. melanogaster has two important functions: detoxifying acetaldehyde derived from dietary ethanol [11] and detoxifying larger aldehydes produced as byproducts of oxidative phosphorylation [12]. A derived variant of the enzyme, Leu479Phe, is present in moderate frequencies in most temperate populations but is rare in more ethanol-averse tropical populations. Using purified recombinant protein, we show that the Leu-Phe substitution increases turnover rate of acetaldehyde but decreases turnover rate of larger aldehydes. Furthermore, using transgenic fly lines, we show that the substitution increases lifetime fitness on medium supplemented with an ecologically relevant ethanol concentration but decreases fitness on medium lacking ethanol. The strong, opposing selection pressures, coupled with documented highly variable ethanol concentrations in breeding sites of temperate populations, implicate an essential role for environmental heterogeneity in maintaining the polymorphism.
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Affiliation(s)
- Mahul Chakraborty
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - James D Fry
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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Singh SK, Rajawat AS, Rathore BP, Bahuguna IM, Chakraborty M. Detection of Glacier Lakes Buried under Snow by RISAT-1 SAR in the Himalayan Terrain. CURR SCI INDIA 2015. [DOI: 10.18520/cs/v109/i9/1735-1739] [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: 11/15/2022]
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Singh SK, Rajawat AS, Rathore BP, Bahuguna IM, Chakraborty M. Detection of Glacier Lakes Buried under Snow by RISAT-1 SAR in the Himalayan Terrain. CURR SCI INDIA 2015. [DOI: 10.18520/v109/i9/1735-1739] [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: 11/15/2022]
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Nandanwar SU, Dabbawala AA, Chakraborty M, Bajaj HC, Mukhopadhyay S, Shenoy KT. Partial hydrogenation of benzene to cyclohexene over Ru/γ-Al2O3 nanocatalyst via w/o microemulsion using boric acid and ethanolamine additives. Res Chem Intermed 2015. [DOI: 10.1007/s11164-015-2102-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Patel RR, Barad JM, Nandanwar SU, Dabbawala AA, Chakraborty M, Parikh PA, Baja HC. Cellulose supported ruthenium nanoclusters as an efficient and recyclable catalytic system for benzene hydrogenation under mild conditions. Kinet Catal 2015. [DOI: 10.1134/s002315841502007x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Chakraborty M, Fry JD. Parallel functional changes in independent testis-specific duplicates of Aldehyde dehydrogenase in Drosophila. Mol Biol Evol 2015; 32:1029-38. [PMID: 25564519 DOI: 10.1093/molbev/msu407] [Citation(s) in RCA: 7] [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] [Indexed: 02/06/2023] Open
Abstract
A large proportion of duplicates, originating from ubiquitously expressed genes, acquire testis-biased expression. Identifying the underlying cause of this observation requires determining whether the duplicates have altered functions relative to the parental genes. Typically, statistical methods are used to test for positive selection, signature of which in protein sequence of duplicates implies functional divergence. When assumptions are violated, however, such tests can lead to false inference of positive selection. More convincing evidence for naturally selected functional changes would be the occurrence of structural changes with similar functional consequences in independent duplicates of the same gene. We investigated two testis-specific duplicates of the broadly expressed enzyme gene Aldehyde dehydrogenase (Aldh) that arose in different Drosophila lineages. The duplicates show a typical pattern of accelerated amino acid substitutions relative to their broadly expressed paralogs, with statistical evidence for positive selection in both cases. Importantly, in both duplicates, width of the entrance to the substrate binding site, known a priori to influence substrate specificity, and otherwise conserved throughout the genus Drosophila, has been reduced, resulting in narrowing of the entrance. Protein structure modeling suggests that the reduction of the size of the enzyme's substrate entry channel, which is likely to shift substrate specificity toward smaller aldehydes, is accounted for by the positively selected parallel substitutions in one duplicate but not the other. Evolution of the testis-specific duplicates was accompanied by reduction in expression of the ancestral Aldh in males, supporting the hypothesis that the duplicates may have helped resolve intralocus sexual conflict over Aldh function.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - James D Fry
- Department of Biology, University of Rochester
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Bala N, Saha S, Chakraborty M, Maiti M, Das S, Basu R, Nandy P. Green synthesis of zinc oxide nanoparticles using Hibiscus subdariffa leaf extract: effect of temperature on synthesis, anti-bacterial activity and anti-diabetic activity. RSC Adv 2015. [DOI: 10.1039/c4ra12784f] [Citation(s) in RCA: 324] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Particle size dependent anti-bacterial and anti-diabetic activities of green synthesized ZnO nanoparticles.
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Affiliation(s)
- Niranjan Bala
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
| | - S. Saha
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
| | - M. Chakraborty
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
| | - M. Maiti
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
| | - S. Das
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
| | - R. Basu
- Department of Physics
- Jogamaya Devi College
- Kolkata 700 026
- India
| | - P. Nandy
- Centre for Interdisciplinary Research and Education
- Kolkata 700 068
- India
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Majumdar P, Singh SB, Dhara S, Chakraborty M. Influence of boron addition to Ti-13Zr-13Nb alloy on MG63 osteoblast cell viability and protein adsorption. Mater Sci Eng C Mater Biol Appl 2014; 46:62-8. [PMID: 25491960 DOI: 10.1016/j.msec.2014.10.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 09/02/2014] [Accepted: 10/02/2014] [Indexed: 10/24/2022]
Abstract
Cell proliferation, cell morphology and protein adsorption on near β-type Ti-13Zr-13Nb (TZN) alloy and Ti-13Zr-13Nb-0.5B (TZNB) composite have been investigated and compared to evaluate the effect of boron addition which has been added to the Ti alloy to improve their poor tribological properties by forming in situ TiB precipitates. MG63 cell proliferation on substrates with different chemistry but the same topography was compared. The MTT assay test showed that the cell viability on the TZN alloy was higher than the boron containing TZNB composite after 36 h of incubation and the difference was pronounced after 7 days. However, both the materials showed substantially higher cell attachment than the control (polystyrene). For the same period of incubation in fetal bovine serum (FBS), the amount of protein adsorbed on the surface of boron free TZN samples was higher than that in the case of boron containing TZNB composite. The presence of boron in the TZN alloy influenced protein adsorption and cell response and they are lower in TZNB than in TZN as a result of the associated difference in chemical characteristics.
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Affiliation(s)
- P Majumdar
- School of Mechanical Science, Indian Institute of Technology, Bhubaneswar, India.
| | - S B Singh
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology, Kharagpur, India
| | - S Dhara
- School Medical Science and Technology, Indian Institute of Technology, Kharagpur, India
| | - M Chakraborty
- School of Mechanical Science, Indian Institute of Technology, Bhubaneswar, India
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Abstract
Prototype galectins, endogenously expressed animal lectins with a single carbohydrate recognition domain, are well-known regulators of tissue properties such as growth and adhesion. The earliest discovered and best studied of the prototype galectins is Galectin-1 (Gal-1). In the Gallus gallus (chicken) genome, Gal-1 is represented by two homologs: Gal-1A and Gal-1B, with distinct biochemical properties, tissue expression, and developmental functions. We investigated the origin of the Gal-1A/Gal-1B divergence to gain insight into when their developmental functions originated and how they could have contributed to vertebrate phenotypic evolution. Sequence alignment and phylogenetic tree construction showed that the Gal-1A/Gal-1B divergence can be traced back to the origin of the sauropsid lineage (consisting of extinct and extant reptiles and birds) although lineage-specific duplications also occurred in the amphibian and actinopterygian genomes. Gene synteny analysis showed that sauropsid gal-1b (the gene for Gal-1B) and its frog and actinopterygian gal-1 homologs share a similar chromosomal location, whereas sauropsid gal-1a has translocated to a new position. Surprisingly, we found that chicken Gal-1A, encoded by the translocated gal-1a, was more similar in its tertiary folding pattern than Gal-1B, encoded by the untranslocated gal-1b, to experimentally determined and predicted folds of nonsauropsid Gal-1s. This inference is consistent with our finding of a lower proportion of conserved residues in sauropsid Gal-1Bs, and evidence for positive selection of sauropsid gal-1b, but not gal-1a genes. We propose that the duplication and structural divergence of Gal-1B away from Gal-1A led to specialization in both expression and function in the sauropsid lineage.
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Affiliation(s)
- Ramray Bhat
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - I S Mian
- Department of Computer Science, University College London, United Kingdom
| | - Stuart A Newman
- Department of Cell Biology and Anatomy, New York Medical College, Valhalla, New York
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Sellappan B, Chakraborty M, Cherian S. Congenital hypothyroidism presenting as pseudo-obstruction in preterm infants. BMJ Case Rep 2014; 2014:bcr2013201082. [PMID: 24832703 PMCID: PMC4025204 DOI: 10.1136/bcr-2013-201082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/16/2014] [Indexed: 11/03/2022] Open
Abstract
Congenital hypothyroidism (CH) presenting as acute pseudo-obstruction is uncommon. We report two premature infants presenting with acute bowel obstruction subsequently diagnosed to have CH. Both responded well to medical management with thyroid supplementation.
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Affiliation(s)
- B Sellappan
- Neonatal Unit, University Hospital of Wales, Cardiff, UK
| | - M Chakraborty
- Neonatal Unit, University Hospital of Wales, Cardiff, UK
| | - S Cherian
- Neonatal Unit, University Hospital of Wales, Cardiff, UK
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Kumar A, Koch A, Borthakur R, Chakraborty M, De A, Phukan A, Bez G, Lal R. Synthesis and spectroscopic characterization of monometallic molybdenum (VI) complexes derived from bis(2-hydroxy-1-naphthaldehyde)succinoyldihydrazone. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2014.01.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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43
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Vadakkekara R, Chakraborty M, Parikh PA. Synthesis, characterization, and application of monodisperse gelatin-stabilized silver nanospheres in reduction of aromatic nitro compounds. Colloid J 2014. [DOI: 10.1134/s1061933x14010153] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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De D, Chakraborty M, Majumdar S, Giri S. Bandgap engineering through nanocrystalline magnetic alloy grafting on reduced graphene oxide. Phys Chem Chem Phys 2014; 16:19661-7. [DOI: 10.1039/c4cp02259a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Grafting of nanocrystalline Co80Ni20on reduced graphene oxide causes a significantly large moment (1.2μB), ∼10 times localization of conductivity and significant magnetoconductance of hybrid-materials, which is promising toward spintronic applications.
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Affiliation(s)
- D. De
- Department of Solid State Physics
- Indian Association for the Cultivation of Science
- Kolkata 700 032, India
- Department of Physics
- NITMAS
| | - M. Chakraborty
- Department of Solid State Physics
- Indian Association for the Cultivation of Science
- Kolkata 700 032, India
- Department of Physics
- Indian Institute of Technology
| | - S. Majumdar
- Department of Solid State Physics
- Indian Association for the Cultivation of Science
- Kolkata 700 032, India
| | - S. Giri
- Department of Solid State Physics
- Indian Association for the Cultivation of Science
- Kolkata 700 032, India
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Suryawanshi YR, Chakraborty M, Jauhari S, Mukhopadhyay S, Shenoy KT, Shridharkrishna R. Microwave irradiation solvothermal technique: an optimized protocol for size-control synthesis of Ru nanoparticles. Cryst Res Technol 2013. [DOI: 10.1002/crat.201200412] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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46
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Nandanwar SU, Chakraborty M, Mukhopadhyay S, Shenoy KT. Benzene hydrogenation over highly active monodisperse Ru/γ-Al2O3 nanocatalyst synthesized by (w/o) reverse microemulsion. Reac Kinet Mech Cat 2012. [DOI: 10.1007/s11144-012-0526-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Raji V, Chakraborty M, Parikh PA. Synthesis of Starch-Stabilized Silver Nanoparticles and Their Antimicrobial Activity. Particulate Science and Technology 2012. [DOI: 10.1080/02726351.2011.626510] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Majumdar P, Singh S, Dhara S, Chakraborty M. Influence of in situ TiB reinforcements and role of heat treatment on mechanical properties and biocompatibility of Ti-alloys. J Mech Behav Biomed Mater 2012; 10:1-12. [DOI: 10.1016/j.jmbbm.2012.02.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2011] [Revised: 02/13/2012] [Accepted: 02/19/2012] [Indexed: 10/28/2022]
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Yu T, Jain A, Chakraborty M, Wilson N, Hill A. Factors Influencing the Likelihood of Female Medical Students Pursuing Surgery: A Critical Review. J Surg Res 2012. [DOI: 10.1016/j.jss.2011.11.908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Mukherjee S, Chakraborty M, Panda A, Bhattacharya S, Moulik S. Physicochemistry of bis-alkyltrimethylammonium dichromate, tungstate and molybdate amphiphiles: Synthesis, characterization, behaviors at the air–water interface and self-aggregation in aqueous medium. Colloids Surf A Physicochem Eng Asp 2011. [DOI: 10.1016/j.colsurfa.2011.07.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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