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Basu A, Basu S, Ghosh K, Mullick S, Datta S. PO-310 CLINICAL FEASIBILITY OF COBALT 60 HDR INTRACAVITARY BRACHYTHERAPY IN CARCINOMA CERVIX: A PRELIMINARY REPORT. Radiother Oncol 2012. [DOI: 10.1016/s0167-8140(12)72276-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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77
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Basu S, Basu A, Ghosh K, Datta S, Mullick S. PO-417 A PHASE I FEASIBILITY STUDY FOR HDR INTERSTITIAL BRACHYTHERAPY USING 60CO FOR DIFFERENT SITES. Radiother Oncol 2012. [DOI: 10.1016/s0167-8140(12)72383-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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78
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Brito JP, Singh E, Basu A. Iatrogenic heart block during treatment of a patient with Cushing's syndrome: report of a case. Endocrine 2012; 41:344. [PMID: 22124942 DOI: 10.1007/s12020-011-9567-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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79
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Bhattacharyya J, Chowdhury AH, Ray S, Jha JK, Das S, Gayen S, Chakraborty A, Mitra J, Maiti MK, Basu A, Sen SK. Native polyubiquitin promoter of rice provides increased constitutive expression in stable transgenic rice plants. PLANT CELL REPORTS 2012; 31:271-9. [PMID: 21996937 DOI: 10.1007/s00299-011-1161-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2011] [Revised: 09/16/2011] [Accepted: 09/22/2011] [Indexed: 05/04/2023]
Abstract
The rice Ubiquitin1 (Ubi1) promoter was tested to evaluate its capacity to express the heterologous gusA gene encoding β-glucuronidase in transgenic rice tissue relative to the commonly used Ubi1 corn promoter and the rice gibberellic acid insensitive (GAI) gene promoter element. Experimental results showed increased expression of gusA gene in rice tissue when driven by the native Ubi1 promoter when compared to the use of corn Ubi1 promoter. Results further indicated that the cis-regulatory elements present in the native promoter element might have been responsible for high expression. However, the gusA gene expression level when driven by the rice GAI promoter was notably lower than both Ubi1 promoters. The present study, thus, for the first time helped to demonstrate that the native Ubi1 promoter is a promising genetic element in transgenic approaches for constitutive expression of any gene in rice tissue.
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Samanta P, Sadhukhan S, Das S, Joshi A, Sen SK, Basu A. Isolation of RNA from field-grown jute (Corchorus capsularis) plant in different developmental stages for effective downstream molecular analysis. Mol Biotechnol 2012; 49:109-15. [PMID: 21327574 DOI: 10.1007/s12033-011-9376-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Jute (Corchorus capsularis), as a natural fibre producing plant species, ranks next to cotton only. Today, biotechnological approach has been considered as most accepted means for any genetic improvement of plant species. However, genetic control of the fibre development in jute has not yet been explored sufficiently for desired genetic improvement. One of the major impediments in exploring the genetic architecture in this crop at molecular level is the availability of good quality RNA from field-grown plant tissues mostly due to the presence of high amount of mucilage and phenolics. Development of a suitable RNA isolation method is becoming essential for deciphering developmental stage-specific gene expression pattern related to fibre formation in this crop species. A combination of modified hot borate buffer followed by isopycnic centrifugation (termed as HBIC) was adopted and found to be the best isolation method yielding sufficient quantity (~350-500 μg/gm fresh tissue) and good quality (A(260/280) ratio 1.88 to 1.91) RNA depending on the developmental stage of stem tissue from field-grown jute plant. The poly A(+) RNA purified from total RNA isolated by the present method was found amenable to efficient RT-PCR and cDNA library construction. The present development of RNA isolation was found to be appropriate for gene expression analysis related to fibre formation in this economically important jute plant in near future.
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Basu A, Horvath R, Esisi B, Birchall D, Chinnery PF. Recurrent stroke-like episodes in X-linked Charcot-Marie-Tooth disease. Neurology 2011; 77:1205-6. [PMID: 21900630 DOI: 10.1212/wnl.0b013e31822f046e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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82
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Ghosh A, Bera S, Ghosal S, Ray S, Basu A, Ray M. Differential inhibition/inactivation of mitochondrial complex I implicates its alteration in malignant cells. BIOCHEMISTRY (MOSCOW) 2011; 76:1051-60. [DOI: 10.1134/s0006297911090100] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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83
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Banerjee K, Basu A, Guin R, Sengupta D. Radon (222Rn) level variations on a regional scale from the Singhbhum Shear Zone, India: A comparative evaluation between influence of basement U-activity and porosity. Radiat Phys Chem Oxf Engl 1993 2011. [DOI: 10.1016/j.radphyschem.2010.12.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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84
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Werhwein EA, Mohamed EA, Curry TB, Basu A, Rizza RA, Basu R, Joyner MJ. Is blood pressure control in humans mediated by the peripheral chemoreceptors? FASEB J 2011. [DOI: 10.1096/fasebj.25.1_supplement.1076.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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85
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Sarkar N, Basu A. Fluctuations and symmetries in two-dimensional active gels. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:44. [PMID: 21533956 DOI: 10.1140/epje/i2011-11044-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 12/21/2010] [Indexed: 05/30/2023]
Abstract
Motivated by the unique physical properties of biological active matter, e.g., cytoskeletal dynamics in eukaryotic cells, we set up effective two-dimensional (2d) coarse-grained hydrodynamic equations for the dynamics of thin active gels with polar or nematic symmetries. We use the well-known three-dimensional (3d) descriptions (K. Kruse et al., Eur. Phys. J. E 16, 5 (2005); A. Basu et al., Eur. Phys. J. E 27, 149 (2008)) for thin active-gel samples confined between parallel plates with appropriate boundary conditions to derive the effective 2d constitutive relations between appropriate thermodynamic fluxes and generalised forces for small deviations from equilibrium. We consider three distinct cases, characterised by spatial symmetries and boundary conditions, and show how such considerations dictate the structure of the constitutive relations. We use these to study the linear instabilities, calculate the correlation functions and the diffusion constant of a small tagged particle, and elucidate their dependences on the activity or nonequilibrium drive.
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Aston DE, Berven CA, Williams BC, Basu A. Mathematical analysis of effects on the electrostatic double layer of nanoscale surfaces in microfluidic channels. CAN J CHEM ENG 2011. [DOI: 10.1002/cjce.20475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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87
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Mandal A, Huang W, Bhandari S, Basu A. Goodness-of-fit testing in growth curve models: A general approach based on finite differences. Comput Stat Data Anal 2011. [DOI: 10.1016/j.csda.2010.09.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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88
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Mandal A, Bhandari S, Basu A. Minimum disparity estimation based on combined disparities: Asymptotic results. J Stat Plan Inference 2011. [DOI: 10.1016/j.jspi.2010.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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89
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Basu A, Rahaman MS, Islam MR. Extension of the pore diffusion approach for modelling binary adsorption of lead and arsenic ions in a fixed-bed column packed with atlantic cod fish scales. CAN J CHEM ENG 2010. [DOI: 10.1002/cjce.20420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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90
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Batal I, Lunz JG, Aggarwal N, Zeevi A, Sasatomi E, Basu A, Tan H, Shapiro R, Randhawa P. A critical appraisal of methods to grade transplant glomerulitis in renal allograft biopsies. Am J Transplant 2010; 10:2442-52. [PMID: 20977635 DOI: 10.1111/j.1600-6143.2010.03261.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Transplant glomerulitis is an increasingly recognized lesion in renal transplant biopsies. To develop a refined grading system, we defined glomerulitis by the presence of ≥5 leukocytes/glomerulus and evaluated 111 biopsies using three different grading systems: (i) percentage of glomerular involvement, (ii) peak inflammation in the most severely affected glomerulus and (iii) presence/absence of endocapillary occlusion by inflammatory cells. Endocapillary occlusion had no impact on graft survival, but was associated with increased serum creatinine, proteinuria and subsequent transplant glomerulopathy. Grading based on either percent or peak glomerular involvement correlated with graft failure and peritubular capillaritis. However, the percent glomerular involvement method had the additional advantage of displaying associations with: concurrent proteinuria, focal or diffuse immunoperoxidase peritubular capillary C4d staining, 1-year postbiopsy serum creatinine, subsequent detection of donor-specific antibody and development of transplant glomerulopathy. Patients with >75% glomerular involvement also revealed persistent high-grade glomerulitis on follow-up biopsies despite antirejection treatment. In conclusion, grading of glomerulitis is a meaningful exercise, and a quantification system based on percentage of glomerular involvement shows the most robust associations with clinical parameters and prognosis.
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Nordstrom KN, Verneuil E, Arratia PE, Basu A, Zhang Z, Yodh AG, Gollub JP, Durian DJ. Microfluidic rheology of soft colloids above and below jamming. PHYSICAL REVIEW LETTERS 2010; 105:175701. [PMID: 21231059 DOI: 10.1103/physrevlett.105.175701] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Indexed: 05/07/2023]
Abstract
The rheology near jamming of a suspension of soft colloidal spheres is studied using a custom microfluidic rheometer that provides the stress versus strain rate over many decades. We find non-Newtonian behavior below the jamming concentration and yield-stress behavior above it. The data may be collapsed onto two branches with critical scaling exponents that agree with expectations based on Hertzian contacts and viscous drag. These results support the conclusion that jamming is similar to a critical phase transition, but with interaction-dependent exponents.
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Basu A, Ramakrishnan S, Petre C, Koziol S, Brink S, Hasler PE. Neural dynamics in reconfigurable silicon. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2010; 4:311-319. [PMID: 23853376 DOI: 10.1109/tbcas.2010.2055157] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A neuromorphic analog chip is presented that is capable of implementing massively parallel neural computations while retaining the programmability of digital systems. We show measurements from neurons with Hopf bifurcations and integrate and fire neurons, excitatory and inhibitory synapses, passive dendrite cables, coupled spiking neurons, and central pattern generators implemented on the chip. This chip provides a platform for not only simulating detailed neuron dynamics but also uses the same to interface with actual cells in applications such as a dynamic clamp. There are 28 computational analog blocks (CAB), each consisting of ion channels with tunable parameters, synapses, winner-take-all elements, current sources, transconductance amplifiers, and capacitors. There are four other CABs which have programmable bias generators. The programmability is achieved using floating gate transistors with on-chip programming control. The switch matrix for interconnecting the components in CABs also consists of floating-gate transistors. Emphasis is placed on replicating the detailed dynamics of computational neural models. Massive computational area efficiency is obtained by using the reconfigurable interconnect as synaptic weights, resulting in more than 50 000 possible 9-b accurate synapses in 9 mm(2).
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Jha SS, Jha JK, Chattopadhyaya B, Basu A, Sen SK, Maiti MK. Cloning and characterization of cDNAs encoding for long-chain saturated acyl-ACP thioesterases from the developing seeds of Brassica juncea. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2010; 48:476-480. [PMID: 20356753 DOI: 10.1016/j.plaphy.2010.02.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Revised: 02/10/2010] [Accepted: 02/15/2010] [Indexed: 05/29/2023]
Abstract
Four types of cDNAs corresponding to the fatty acyl-acyl carrier protein (ACP) thioesterase (Fat) enzyme were isolated from the developing seeds of Brassica juncea, a widely cultivated species amongst the oil-seed crops. The mature polypeptides deduced from the cDNAs showed sequence identity with the FatB class of plant thioesterases. Southern hybridization revealed the presence of at least four copies of BjFatB gene in the genome of this amphidiploid species. Western blot and RT-PCR analyses showed that the BjFatB class thioesterase is expressed poorly in flowers and leaves, but significantly in seeds at the mid-maturation stage. The enzymatic activities of different BjFatB isoforms were established upon heterologous expression of the four BjFatB CDSs in Escherichia coli K27fadD88, a mutant strain of fatty acid beta-oxidation pathway. The substrate specificity of each BjFatB isoform was determined in vivo by fatty acid profile analyses of the culture supernatant and membrane lipid of the recombinant K27fadD88 and E. coli DH10B (fadD(+)) clones, respectively. The BjFatB1 and BjFatB3 were predominantly active on C18:0-ACP substrate, whereas BjFatB2 and BjFatB4 were specific towards C18:0-ACP as well as C16:0-ACP. These novel FatB genes may find potential application in metabolic engineering of crop plants through their over-expression in seed tissues to generate stearate-rich vegetable fats/oils of commercial importance.
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Das S, Sen S, Chakraborty A, Chakraborti P, Maiti MK, Basu A, Basu D, Sen SK. An unedited 1.1 kb mitochondrial orfB gene transcript in the wild abortive cytoplasmic male sterility (WA-CMS) system of Oryza sativa L. subsp. indica. BMC PLANT BIOLOGY 2010; 10:39. [PMID: 20193092 PMCID: PMC2848759 DOI: 10.1186/1471-2229-10-39] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 03/02/2010] [Indexed: 05/21/2023]
Abstract
BACKGROUND The application of hybrid rice technology has significantly increased global rice production during the last three decades. Approximately 90% of the commercially cultivated rice hybrids have been derived through three-line breeding involving the use of WA-CMS lines. It is believed that during the 21st century, hybrid rice technology will make significant contributions to ensure global food security. This study examined the poorly understood molecular basis of the WA-CMS system in rice. RESULTS RFLPs were detected for atp6 and orfB genes in sterile and fertile rice lines, with one copy of each in the mt-genome. The RNA profile was identical in both lines for atp6, but an additional longer orfB transcript was identified in sterile lines. 5' RACE analysis of the long orfB transcript revealed it was 370 bp longer than the normal transcript, with no indication it was chimeric when compared to the genomic DNA sequence. cDNA clones of the longer orfB transcript in sterile lines were sequenced and the transcript was determined unedited. Sterile lines were crossed with the restorer and maintainer lines, and fertile and sterile F1 hybrids were respectively generated. Both hybrids contained two types of orfB transcripts. However, the long transcript underwent editing in the fertile F1 hybrids and remained unedited in the sterile lines. Additionally, the editing of the 1.1 kb orfB transcript co-segregated with fertility restoring alleles in a segregating population of F2 progeny; and the presence of unedited long orfB transcripts was detected in the sterile plants from the F2 segregating population. CONCLUSION This study helped to assign plausible operative factors responsible for male-sterility in the WA cytoplasm of rice. A new point of departure to dissect the mechanisms governing the CMS-WA system in rice has been identified, which can be applied to further harness the opportunities afforded by hybrid vigor in rice.
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96
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Basu A, Mandal A, Pardo L. Hypothesis testing for two discrete populations based on the Hellinger distance. Stat Probab Lett 2010. [DOI: 10.1016/j.spl.2009.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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97
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Shapiro R, Lunz J, Zeevi A, Basu A, Mapara M, Randhawa P, Tan HP, Sharma V, Humar A. 1.7 year follow-up after bortezomib therapy for refractory antibody mediated rejection. CLINICAL TRANSPLANTS 2010:405-407. [PMID: 21696058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In summary, 1.7 years after transplantation, bortezomib rescue has been durably effective in salvaging our patient with refractory antibody mediated rejection. The only price has been persistently high levels of BK viruria. The presence of ongoing and even recurrent donor specific antibody has made it difficult to reduce immunosuppression further, and the concern that the high levels of BK viruria will eventually progress to viremia and nephropathy necessitates continued therapy with very low dose cidofovir and leflunomide. The absence of C1q binding DSA with stable renal function may provide some reserved optimism that the DSA that is detectable by convention Luminex assay may have reduced pathological implications. However, more data and prolonged follow-up are needed to determine whether or not non-complement binding DSA has an adverse pathological role.
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Dasgupta T, Basu A, Bhowmick P, Mitra P. A Framework for the Automatic Generation of Indian Sign Language. JOURNAL OF INTELLIGENT SYSTEMS 2010. [DOI: 10.1515/jisys.2010.19.2.125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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99
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Basu A, Smith M, Ahmed A. Retrospective Analysis of Laparoscopic Bilateral Pelvic Lymphadenectomy in Patients with Cervical Carcinoma. J Minim Invasive Gynecol 2009. [DOI: 10.1016/j.jmig.2009.08.338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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100
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Badwal S, Pal L, Basu A, Saxena S. Multiple synchronous spinal extra-osseous intradural chordomas: is it a distinct entity? Br J Neurosurg 2009; 20:99-103. [PMID: 16753627 DOI: 10.1080/02688690600682614] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Chordomas are most commonly of extradural origin and are associated with bone destruction. Extra-osseous intradural chordomas are extremely rare and most of the cases described are located near the clivus. We report an extremely rare case of multiple extra-osseous intraspinal chordomas in a 36-year-old male patient with autopsy findings. This case highlights that behaviour of spinal intradural chordomas is not universally low grade, but is variable and aggressive.
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