149 results on '"Pillai, Manoj"'
Search Results
102. Solid Oxide Fuel Cell with Oxide Anode-Side Support
- Author
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Pillai, Manoj R., primary, Jiang, Yi, additional, Mansourian, Negar, additional, Kim, Ilwon, additional, Bierschenk, David M., additional, Zhu, Huayang, additional, Kee, Robert J., additional, and Barnett, Scott A., additional
- Published
- 2008
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103. Integration site analysis in transgenic mice by thermal asymmetric interlaced (TAIL)-PCR: segregating multiple-integrant founder lines and determining zygosity
- Author
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Pillai, Manoj M., primary, Venkataraman, Gopalakrishnan M., additional, Kosak, Steven, additional, and Torok-Storb, Beverly, additional
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- 2007
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104. Electrochemical Partial Oxidation of Methane in Solid Oxide Fuel Cells: Effect of Anode Reforming Activity
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Pillai, Manoj R., primary, Bierschenk, David M., additional, and Barnett, Scott A., additional
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- 2007
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105. Reduced expression of inducible gelatinase B/matrix metalloproteinase-9 in monocytes from patients with myelodysplastic syndrome: correlation of inducible levels with the percentage of cytogenetically marked cells and with marrow cellularity
- Author
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Iwata, Mineo, primary, Pillai, Manoj, additional, Ramakrishnan, Aravind, additional, Hackman, Robert C., additional, Deeg, H. Joachim, additional, Opdenakker, Ghislain, additional, and Torok-Storb, Beverly, additional
- Published
- 2006
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- View/download PDF
106. Monocyte-derived CXCL7 peptides in the marrow microenvironment
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Pillai, Manoj M., primary, Iwata, Mineo, additional, Awaya, Norihiro, additional, Graf, Lynn, additional, and Torok-Storb, Beverly, additional
- Published
- 2006
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107. Primary Marrow-Derived Stromal Cells: Isolation and Manipulation.
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Ramakrishnan, Aravind, Torok-Storb, Beverly, and Pillai, Manoj M.
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- 2013
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108. Inducible Levels of Gelatinase B/Matrix Metalloproteinase-9 Gene Expression in Monocytes Are Associated with Marrow Cellularity in Myelodysplastic Syndrome (MDS).
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Iwata, Mineo, primary, Pillai, Manoj, primary, Deeg, H. Joachim, primary, Opdenakker, Ghislain, primary, and Torok-Storb, Beverly, primary
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- 2005
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109. Human Marrow Stromal Cells Activate Monocytes to Secrete CXCL7 Peptides, Which Alter the Composition of the Hematopoietic Microenvironment (ME).
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Pillai, Manoj M., primary, Iwata, Mineo, additional, Dahlen, Debra D., additional, and Torok-Storb, Beverly, additional
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- 2004
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110. Expression and Function of IL-7 Receptors in Marrow Stromal Cells
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Pillai, Manoj, primary, Torok-Storb, Beverly, additional, and Iwata, Mineo, additional
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- 2004
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111. Low power dual edge triggered flip-flop.
- Author
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Bhargavaram, Dasari and Pillai, Manoj Gopala Krishna
- Abstract
Flip-flops are critical timing elements in digital circuits which have a large impact on circuit speed and power consumption. The performance of the Flip-Flop is an important element to determine the performance of the whole synchronous circuit. The pulse generator can be shared among many flip-flops to reduce the power dissipation. Firstly, in the Dual edge static pulsed flip-flop suffers from high leakage current leads to more power consumption. Secondly, Dual edge trigger sense amplifier flip-flop having unnecessary transitions which causes power consumption. Thirdly, Dual edge trigger NAND keeper flip-flop keeper technique is used to pull up the voltage to VDD having full swing and this keeper transistor width is high and which consumes more power. The power consumption of the Dual edge nand keeper flip-flop is 347uW. Lastly, Dual edge trigger pulsed flip-flop is introduced by employing a technique called conditional switching for further power reduction. The circuits are designed in a 0.18-um standard CMOS process with a 1.8V power supply voltage. [ABSTRACT FROM PUBLISHER]
- Published
- 2012
112. The Fanconi Anemia pathway protein complex FANCI/FANCD2 couples the DNA damage response to R-loop regulation through SRSF1-mediated mRNA export
- Author
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Olazabal-Herrero, Anne, He, Boxue, Kwon, Youngho, Gupta, Abhishek K., Dutta, Arijit, Huang, Yuxin, Boddu, Prajwal, Liang, Zhuobin, Liang, Fengshan, Teng, Yaqun, Lan, Li, Chen, Xiaoyong, Pei, Huadong, Pillai, Manoj M., Sung, Patrick, and Kupfer, Gary M.
- Abstract
Fanconi anemia (FA) is characterized by congenital abnormalities, bone marrow failure, and cancer susceptibility. The central FA protein complex FANCI/FANCD2 (ID2) is activated by monoubiquitination and recruits DNA repair proteins for interstrand crosslink (ICL) repair and replication fork protection. Defects in the FA pathway leads to R-loop accumulation that contribute to genomic instability. Here, we report that the splicing factor SRSF1 and FANCD2 interact physically and act together to suppress R-loop formation via mRNA export regulation. We show that SRSF1 stimulates FANCD2 monoubiquitination in an RNA-dependent fashion. In turn, FANCD2 monoubiquitination proves crucial for the assembly of the SRSF1-NXF1 nuclear export complex and mRNA export. Importantly, several SRSF1 cancer-associated mutants fail to interact with FANCD2, leading to inefficient FANCD2 monoubiquitination, decreased mRNA export, and R-loop accumulation. We propose a model wherein SRSF1 and FANCD2 interaction links DNA damage response to the avoidance of pathogenic R-loops via regulation of mRNA export.
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- 2023
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113. Photochemistry of Anils in NaY Zeolite
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Casades, Isabel, primary, Álvaro, Mercedes, additional, García, Hermenegildo, additional, and Pillai, Manoj Narayana, additional
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- 2002
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114. Topological quenching of 2,4,6-triphenylpyrylium tetrafluoborate in anionic micelles
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Sanjuán, Ana, primary, Pillai, Manoj Narayana, additional, Alvaro, Mercedes, additional, and Garcı́a, Hermenegildo, additional
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- 2001
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115. Influence of dietary fiber from coconut kernel (cocos nucifera) on the 1,2-dimethylhydrazine-induced lipid peroxidation in rats
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Pillai, Manoj G, primary, Thampi, B.S.H, additional, Menon, Venugopal P, additional, and Leelamma, S, additional
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- 1999
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116. Characterization of triacylglycerol biosynthesis in subcellular fractions of an oleaginous fungus, Mortierella ramanniana var. angulispora
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Pillai, Manoj G, primary, Certik, Milan, additional, Nakahara, Toro, additional, and Kamisaka, Yasushi, additional
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- 1998
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117. Structure and interfacial stability of (111)-oriented InAsSb/InAs strained-layer multiquantum well structures
- Author
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Theiring, Scott C., primary, Pillai, Manoj R., additional, Barnett, Scott A., additional, and Wessels, Bruce W., additional
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- 1997
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118. Low Latency Message-Passing for Reflective Memory Networks.
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Sivasubramaniam, Anand, Lauria, Mario, Jacunski, Matt, Moorthy, Vijay, Ware, Peter P., Pillai, Manoj, Panda, Dhabaleswar K., and Sadayappan, P.
- Abstract
In this paper we present an efficient design for message passing over a reflective memory network. First, we consider the attributes of reflective memory communication networks and the requirements to efficiently build message-passing functionality on these networks. We then introduce the Bill-Board Protocol, a lock-free protocol which provides low-latency send, receive, and multicast functionality to higher-level applications over reflective memory networks. The communication protocol and an implementation on SCRAMNet is described in detail. Lastly, the performance of this protocol is demonstrated. [ABSTRACT FROM AUTHOR]
- Published
- 1999
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119. Marrow Stromal Cell Infusion Rescues Hematopoiesis in Lethally Irradiated Mice despite Rapid Clearance after Infusion.
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Xiaodong Yang, Balakrishnan, Ilango, Torok-Storb, Beverly, and Pillai, Manoj M.
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MESENCHYMAL stem cells ,INFUSION therapy ,HEMATOPOIESIS ,LABORATORY mice ,CELLULAR therapy ,TOTAL body irradiation ,HISTOCHEMISTRY ,IRRADIATION - Abstract
Marrow stromal cells (MSCs, also termed mesenchymal stem cells) have been proposed as a promising cellular therapy for tissue injury including radiation-induced marrow failure, but evidence for a direct effect is lacking. To assess the effects of MSCs on survival after lethal irradiation, we infused syngeneic MSCs (either as immortalized MSCs clones or primary MSCs) intravenously into wild-type C57/Bl6 mice within 24 hours of lethal total body irradiation (TBI). Mice receiving either of the MSC preparations had significantly improved survival when compared to controls. In vivo imaging, immune histochemistry, and RT-PCR employed to detect MSCs indicated that the infused MSCs were predominantly localized to the lungs and rapidly cleared following infusion. Our results suggest that a single infusion of MSCs can improve survival after otherwise lethal TBI but the effect is not due to a direct interaction with, or contribution to, the damaged marrow by MSCs [ABSTRACT FROM AUTHOR]
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- 2012
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120. Commodity Futures Markets, Warehouse Receipts and the Dynamics of Warehousing Infrastructure: The Indian Scenario.
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Pillai, Manoj
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AGRICULTURAL economics ,GROSS domestic product ,INDIAN economy ,FOOD security ,COMMODITY exchanges ,WAREHOUSES ,ECONOMIC policy ,FINANCE - Abstract
Agriculture is an important component of the Indian Economy. It contributes to about 21% of India's Gross Domestic Product (GDP), 11% of total exports and provides employment to around 60% of the work force and is directly related to self-reliance, meeting the food and nutritional security of the people, equitable distribution of income and wealth in rural areas, reduction of poverty and improvement in the quality of life. The liberalized economic policies resulted in a commendable growth of some sectors of the economy, but when it comes to agricultural development, the growth scenario presents a dismal and bleak picture. There has been a consistent decline in the growth of the agricultural sector since 1990 compared to the 1980s. Commodity markets and warehouse financing are innovative initiatives devised specifically to revive and resurrect the agricultural sector with the twin objectives of providing price discovery and risk mitigation to the farmers. This article delves into all the relevant aspects of warehouse finance and warehouse infrastructure in India. [ABSTRACT FROM AUTHOR]
- Published
- 2010
121. Stability and coking of direct-methane solid oxide fuel cells: Effect of CO2 and air additions
- Author
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Pillai, Manoj, Lin, Yuanbo, Zhu, Huayang, Kee, Robert J., and Barnett, Scott A.
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SOLID oxide fuel cells , *METHANE , *CARBON dioxide , *AIR , *ANODES , *MIXTURES , *STABILITY (Mechanics) , *OXIDATION - Abstract
Abstract: This paper concerns the stability of anode-supported solid oxide fuel cells (SOFCs), operated with fuel mixtures of methane–CO2 and methane–air. Stability, which was evaluated in terms of voltage decrease at constant current density, was affected by coke deposits. Chemically inert anode barrier layers were shown to enhance stability and to slow catalytic endothermic reforming reactions within the Ni–YSZ anode that otherwise caused deleterious temperature variations and cell cracking. Increasing the amount of CO2 added to CH4 fuel led to a wider stable operating range, yet had relatively little effect on SOFC performance. Button cells operated at 800 C with fuel streams of 75% CH4 and 25% CO2 achieved maximum power densities above 1W/cm2. Adding air to methane also increased stability. In the case of air addition, SOFC temperature increased as a consequence of exothermic partial-oxidation reforming chemistry. Models were developed to predict temperature and gas-composition profiles within the button cells. The simulation results were used to assist interpretation of the experimental observations. [Copyright &y& Elsevier]
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- 2010
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122. Fuel-flexible operation of a solid oxide fuel cell with Sr0.8La0.2TiO3 support
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Pillai, Manoj R., Kim, Ilwon, Bierschenk, David M., and Barnett, Scott A.
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SOLID oxide fuel cells , *STRONTIUM compounds , *ANODES , *CATHODES , *NATURAL gas , *OXIDATION-reduction reaction , *SEMICONDUCTOR doping - Abstract
Abstract: Solid oxide fuel cells with Sr0.8La0.2TiO3 anode-side supports, Ni- Sm-doped ceria adhesion layer, Ni- Y2O3-stabilized ZrO2 (YSZ) anode active layer, YSZ electrolyte, and La0.8Sr0.2MnO3(LSM)–YSZ cathode are described. These cells are stable in simulated natural gas at current densities as low as 0.2Acm−2. This represents much-improved stability against coking in natural gas, compared with conventional Ni–YSZ anode-supported SOFCs which rapidly coke, even at higher current densities. Cell operation in H2 fuel with 50–100ppm, H2S results in an initial decrease in cell power density, but no long-term degradation occurs and full recovery to the initial performance level is observed after dry H2 fuel flow is restored. Degradation is not observed during or after seven redox cycles between H2 and air. [Copyright &y& Elsevier]
- Published
- 2008
- Full Text
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123. Methane Partial Oxidation Using A (La0.6Sr0.4)(Ga0.8Mg0.05Co0.15)O3–δ Membrane.
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Yuanbo Lin, Pillai, Manoj, Bierschenk, David, Stevens, Blake, and Barnett, Scott
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LANTHANUM compounds , *MEMBRANE reactors , *METHANE , *OXIDATION , *SYNTHESIS gas - Abstract
This article describes results on methane partial oxidation in (La0.6Sr0.4)(Ga0.8Mg0.05Co0.15)O3 ceramic membrane reactors. The thin membranes were fabricated by co-firing with porous composite NiO–La-doped Ceria (LDC) supports. A La0.6Sr0.4Fe0.2Co0.8O3-based composite layer on the air side of the membrane promoted fast oxygen reduction. Electrical measurements indicated that LSGMC showed good mixed conductivity and that oxygen transport was co-limited by bulk and interfacial processes. The O2 permeation rate during methane partial oxidation at 750 °C was ≈10–12 sccm/cm2, with a maximum syngas production rate of 60–70 sccm/cm2. [ABSTRACT FROM AUTHOR]
- Published
- 2008
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124. India's Tryst with TRIPS Continues!
- Author
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Pillai, Manoj, Kumar, Sushil, Kumar, Rajeev, and Agarwal, Pallavi
- Abstract
The article reports on India's compliance with trade-related aspects of intellectual property rights (TRIPS) and its effort to read further limitations into TRIPS as of 2005. It states that the Expert Committee can limit interpretation of TRIPS as against the Patents Act if it views the patentability exclusion of microorganisms and non-new chemical entity (NCE) product inventions will violate TRIPS provisions. Otherwise, amendments to the Patents Act will reportedly require more explanation.
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- 2006
125. The Patents (Amendment) Act, 2005 and TRIPS Compliance—A Critique.
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Pillai, Manoj
- Abstract
This article comments on the passing of the Patents (Amendment) Act, 2005 and the TRIPS Agreement. It explores the controversial Section 5 of the Indian Patents Act that provided only limited term process patent protection for inventions relating to food, drug, and medicine. The provision enabled the development of a generic pharmaceutical industry in India.
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- 2005
126. Biosynthesis of Triacylglycerol Molecular Species in an Oleaginous Fungus, Mortierella ramanniana var. angulispora.
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Pillai, Manoj G., Ahmad, Ateeque, Yokochi, Toshihiro, Nakahara, Toro, and Kamisaka, Yasushi
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- 2002
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127. Liquid-Hydrocarbon Internal Reforming In Catalyst-Assisted SOFCs
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Kim, Ilwon, Pillai, Manoj R., and Barnett, Scott A.
- Abstract
Direct internal reforming of hydrocarbon fuels such as gasoline and diesel has been problematic due to coking on Ni-based SOFC anodes. This paper describes stable direct internal reforming SOFCs (Ni-YSZ/YSZ/LSM-YSZ) using anode reforming catalysts. Button cells were tested with a separate catalyst piece placed against the anode. Button cell power densities of ~ 0.5W/cm2 at ~ 800oC have been demonstrated with n-dodecane and n-tridecane mixed with H2O-CO2-air. Life tests with n-dodecane showed stable operation for > 140 h. Flattened-tube segmented-in- series modules with 14 cells on each side were tested with a catalyst layer coating on the fuel side of the zirconia support tube. For iso-octane mixed with either air or H2O-CO2-air, a stable maximum power density of ~ 0.6W/cm2 was obtained at ~ 800oC.
- Published
- 2007
128. Reduced expression of inducible gelatinase B/matrix metalloproteinase-9 in monocytes from patients with myelodysplastic syndrome: correlation of inducible levels with the percentage of cytogenetically marked cells and with marrow cellularity
- Author
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Iwata, Mineo, Pillai, Manoj, Ramakrishnan, Aravind, Hackman, Robert C., Deeg, H. Joachim, Opdenakker, Ghislain, and Torok-Storb, Beverly
- Abstract
Regulatory molecules produced by stromal cells are often membrane bound until cleaved by matrix metalloproteinases (MMPs); cleavage can either activate or inactivate regulatory functions. We report here that marrow stromal cells induce the expression of MMP-9 in monocytes. Induction was contact independent and could be reproduced with recombinant MCP-1/CCL2, whereas IL-6, M-CSF, G-CSF, GM-CSF, IL-8/CXCL8, SDF-1/CXCL12, and MGSA/CXCL1 did not have this effect. Stroma-induced levels of MMP-9 in the monocyte population from healthy donors were relatively consistent, whereas induced levels varied significantly (P < .001) in the CD14+ population from 27 patients with myelodysplastic syndrome (MDS). In patients with a clonal chromosomal marker, the level of inducible MMP-9 expression in the monocyte population was inversely correlated with the percentage of marker-positive cells (n = 11, P = .01), suggesting that the ability to induce MMP-9 may be compromised in clonally derived monocytes. The inducible levels of MMP-9 were also inversely correlated with marrow cellularity observed in biopsies from MDS patients (P < .001). We conclude that monocytes can express MMP-9 in response to stromal factors and that this response may be significantly decreased in MDS-derived monocytes.
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- 2007
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129. Study of pancreatic lipase inhibition kinetics and LC–QTOF–MS‐based identification of bioactive constituents of Momordica charantia fruits.
- Author
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Chanda, Joydeb, Mukherjee, Pulok K., Biswas, Rajarshi, Malakar, Dipankar, and Pillai, Manoj
- Abstract
The different parts of Momordica charantia have been reported to have several therapeutic applications against hyperglycemia and hypercholesterolemia associated with pancreatic lipase (PL). Inhibition of this enzyme prevents the absorption of dietary triglyceride in the intestine, and thus exerts an anti‐obesity effect. This study aimed to investigate the bioactive constituents of the fruits of M. charantia (MCF) extract and fractions against pancreatic PL followed by study of their inhibition kinetics. The PL inhibitory assay was performed spectrophotometrically by measuring the change in absorbance of the products at 405 nm, using p‐nitrophenylcaprylate as substrate. The results indicated that the ethyl acetate fraction of MCF (EFMC) offered significant, dose‐dependent inhibition against PL, compared with the positive control, Orlistat. The enzyme kinetics study revealed the inhibition to be a mixed type in nature. Additionally, the total phenol and flavonoid content of the fractions was estimated. A positive correlation between phenolic content of EFMC and its PL inhibitory activity was established statistically, which implied that higher inhibition potential was contributed by the phenolic compounds. The identification of the bioactive constituents was further confirmed by LC–QTOF–MS study. This finding suggested that phenolic compounds of MCF can serve as functional food components to address obesity‐related disorders linked with PL. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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130. Building the Foundations of Process Safety in Design.
- Author
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Jessup, James, Barlow, Julian, Peake, Damian, and Pillai, Manoj
- Subjects
PROCESS safety management ,PROJECT management ,ENGINEERING design ,PETROLEUM engineering ,PETROLEUM industry - Abstract
The article describes a behavior-based process-safety program aimed at entrenching process safety in the hearts and minds of design engineers and positively influencing behaviors. The program was created before embarking on front-end engineering design (FEED) of the Al Karaana petrochemical project. It discusses nine foundations of projects process safety.
- Published
- 2015
131. Shotgun approach reveals distinctive lipid profiles in brassica oilseeds: A high-resolution ESI-ToF-MS study.
- Author
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Kumar, Sujith, Shabeer, Ahammed, Rashid, Faraz, Mawlong, Ibandalin, Rani, Reema, Singh, Vijay Veer, Mog, Babli, and Pillai, Manoj
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EDIBLE fats & oils , *RAPESEED , *FREE fatty acids , *OILSEEDS , *MASS spectrometry - Abstract
Members of Brassica seed oil are important sources of nutritionally superior edible oil. There are no comprehensive reports on complete lipidomic profile of these oilseed crops. In this study, the lipidomic profiling of edible oil from 7 different cultivated species of Brassica seed oils was performed by shotgun approach using electrospray High Resolution Time of Flight-Mass Spectrometry (ESI-ToF-MS). The mass spectrum under positive polarity revealed 1098 lipids under different lipid classes including sphingolipids, phospholipids and different storage lipids. Under negative polarity, 70 lipids including free fatty acids (FFA), cardiolipins and phospholipids were detected. Erucic acid in FFA form was found to be most abundant in both Yellow and Brown sarson. Brassica napus contains almost all forms of cardiolipins (CL). Out of 26 different species of cardiolipins detected in negative ion mode, CL 56:1 (FA 18:1) and CL 56:1 (FA 22:1) were present only in brown sarson. Similarly, CL 56:2 (FA 18:2) and CL 56:1 (FA 22:1) were present only in Yellow and Brown sarson. These findings enhance our understanding of the nutritional diversity in Brassica seed oils, emphasizing the significance of lipidomic analysis for elucidating the molecular composition of edible oils. [ABSTRACT FROM AUTHOR]
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- 2024
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132. Synthesis of GaNxAs1-x thin films by pulsed laser melting and rapid thermal annealing of N+-implanted GaAs
- Author
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Liliental-Weber, Zuzanna, Scarpulla, Michael A., Dubon, Oscar D., Jr., Jasinski, Jacek, Yu, Kin Man, Wu, Jay, Pillai, Manoj R., Aziz, Michael, Walukiewicz, Wladek, and J. W., Beeman
- Abstract
We present a systematic investigation on the formation of the highly mismatched alloy GaNxAs1–x using N+-implantation followed by a combination of pulsed laser melting and rapid thermal annealing. Thin films of GaNxAs1–x with x as high as 0.016 and an activation efficiency of the implanted N up to 50% have been synthesized with structural and optical properties comparable to films grown by epitaxial deposition techniques with similar substitutional N content. The effects of N+ implantation dose, laser energy fluence, and rapid thermal annealing temperature on the N incorporation as well as optical and structural properties of the GaNxAs1–x films are discussed., Engineering and Applied Sciences
- Published
- 2003
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133. Ferromagnetic Ga1-xMnx as Films Produced by Ion Implantation and Pulsed Laser Melting
- Author
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Ridgway, Mark C., Dubon, Oscar D., Monteiro, Orthon, Aziz, Michael, Scarpulla, Michael A., Yu, Kin Man, and Pillai, Manoj R.
- Abstract
We demonstrate the formation of ferromagnetic Ga1-xMnxAs films by Mn ion implantation into GaAs followed by pulsed-laser melting. Irradiation with a single excimer laser pulse results in the epitaxial regrowth of the implanted layer with Mn substitutional fraction up to 80% and effective Curie temperature up to 29 K for samples with a maximum Mn concentration of x'0.03. A remanent magnetization persisting above 85 K has been observed for samples with x'0.10, in which 40% of the Mn resides on substitutional lattice sites. We find that the ferromagnetism in Ga1-xMnxAs is rather robust to the presence of structural defects., Engineering and Applied Sciences
- Published
- 2003
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134. Enhanced Nitrogen Incorporation by Pulsed Laser Annealing of GaNxAs1-x Formed by N Ion Implantation
- Author
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Aziz, Michael, Walukiewicz, Wladek, Pillai, Manoj R., Beeman, J. W., Yu, Kin Man, Scarpulla, Michael A., and Dubon, Oscar D.
- Abstract
We demonstrate that pulsed laser annealing followed by rapid thermal annealing greatly enhances incorporation of substitutional N in N+-implanted GaAs. Films implanted to 1.8% N exhibit a fundamental band gap of 1.26 eV (a band gap reduction of 160 meV), corresponding to an N activation efficiency of 50%. The optical and crystalline quality of the synthesized film is comparable to GaNxAs1-x thin films of similar composition grown by epitaxial growth techniques. Compared to films produced by N+ implantation and rapid thermal annealing only, the introduction of pulsed laser annealing improves N incorporation by a factor of 5. Moreover, we find that the synthesized films are thermally stable up to an annealing temperature of 950 °C., Engineering and Applied Sciences
- Published
- 2002
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135. Co-generation of Electricity and Syngas under Electrochemical Partial Oxidation using Novel SOFCs
- Author
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Kim, Ilwon, Pillai, Manoj, McDonald, Nikkia, Shastry, Tejas, and Barnett, Scott
- Abstract
Generation of syngas from natural gas is an important process in industry, because syngas is a popular precursor for production of variety of different chemicals. Currently, syngas is produced by steam or partial oxidation reforming. Electrochemical Partial Oxidation (EPOX) is a novel process where fuels like methane and natural gas, are partially oxidized under SOFC operation to co-generate electricity and syngas. In the view point of SOFC commercialization, such process could significantly off-set the manufacturing costs of SOFC generators, due to production of valuable syngas during the life of the generators. We have previously demonstrated high electrical power densities and syngas generation rates under EPOx operation using Ni-YSZ button cells. In this work, SOFCs featuring novel fuel barriers are used for EPOX operations. These SOFCs are well suited for EPOx due to their stable performances under direct hydrocarbon fueled operations and relatively high performances under intermediate temperatures. Flattened tubular design of SIS-SOFC in particular, would potentially simplify product gas collection compared to planar designs. The results on electrical tests and exhaust gas analysis using differentially pumped mass spectroscopy are presented. The effects of reforming catalysts, addition of steam or CO2 in the fuel stream are discussed. Finally the stability under long term testing are presented.
- Published
- 2009
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136. Generation of scalable cancer models by combining AAV-intron-trap, CRISPR/Cas9, and inducible Cre-recombinase.
- Author
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Boddu, Prajwal C., Gupta, Abhishek K., Kim, Jung-Sik, Neugebauer, Karla M., Waldman, Todd, and Pillai, Manoj M.
- Subjects
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CRISPRS , *INTRONS , *LOCUS (Genetics) , *CELL culture , *CELL growth , *GENOME editing , *CELL lines , *GENETIC mutation - Abstract
Scalable isogenic models of cancer-associated mutations are critical to studying dysregulated gene function. Nonsynonymous mutations of splicing factors, which typically affect one allele, are common in many cancers, but paradoxically confer growth disadvantage to cell lines, making their generation and expansion challenging. Here, we combine AAV-intron trap, CRISPR/Cas9, and inducible Cre-recombinase systems to achieve >90% efficiency to introduce the oncogenic K700E mutation in SF3B1, a splicing factor commonly mutated in multiple cancers. The intron-trap design of AAV vector limits editing to one allele. CRISPR/Cas9-induced double stranded DNA breaks direct homologous recombination to the desired genomic locus. Inducible Cre-recombinase allows for the expansion of cells prior to loxp excision and expression of the mutant allele. Importantly, AAV or CRISPR/Cas9 alone results in much lower editing efficiency and the edited cells do not expand due to toxicity of SF3B1-K700E. Our approach can be readily adapted to generate scalable isogenic systems where mutant oncogenes confer a growth disadvantage. Boddu et al combined AAV-intron trap, CRISPR/Cas9 and inducible Cre-recombinase systems to introduce the oncogenic K700E mutation in SF3B1, which is a splicing factor commonly mutated in multiple cancers, with more than 90% efficiency. Their approach can be readily adapted to generate scalable isogenic systems where mutant oncogenes are detrimental to cell culture growth. [ABSTRACT FROM AUTHOR]
- Published
- 2021
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137. Transcription elongation defects link oncogenic SF3B1 mutations to targetable alterations in chromatin landscape.
- Author
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Boddu, Prajwal C., Gupta, Abhishek K., Roy, Rahul, De La Peña Avalos, Bárbara, Olazabal-Herrero, Anne, Neuenkirchen, Nils, Zimmer, Joshua T., Chandhok, Namrata S., King, Darren, Nannya, Yasuhito, Ogawa, Seishi, Lin, Haifan, Simon, Matthew D., Dray, Eloise, Kupfer, Gary M., Verma, Amit, Neugebauer, Karla M., and Pillai, Manoj M.
- Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human diseases remains unexplored. Using isogenic cell lines, patient samples, and a mutant mouse model, we investigated how cancer-associated mutations in SF3B1 alter transcription. We found that these mutations reduce the elongation rate of RNA polymerase II (RNAPII) along gene bodies and its density at promoters. The elongation defect results from disrupted pre-spliceosome assembly due to impaired protein-protein interactions of mutant SF3B1. The decreased promoter-proximal RNAPII density reduces both chromatin accessibility and H3K4me3 marks at promoters. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC/H3K4me pathway, which, when modulated, reverse both transcription and chromatin changes. Our findings reveal how splicing factor mutant states behave functionally as epigenetic disorders through impaired transcription-related changes to the chromatin landscape. We also present a rationale for targeting the Sin3/HDAC complex as a therapeutic strategy. [Display omitted] • SF3B1 oncogenic mutations reduce RNAPII gene-body elongation rate and promoter density • RNAPII elongation defect is linked to disruption of the early spliceosome assembly • Chromatin landscape is altered, rendering these functionally epigenetic disorders • Sin3/HDAC pathway can be therapeutically targeted in SF3B1 mutant disease Boddu et al. reveal how common cancer-associated mutations in SF3B1, a core splicing factor, alter RNAPII transcription kinetics through impaired early spliceosome assembly. Transcription defects alter chromatin organization at gene promoters, which can be reversed by inhibiting the Sin3/HDAC complex, providing a potential therapeutic strategy. [ABSTRACT FROM AUTHOR]
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- 2024
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138. Accelerated identification of serine racemase inhibitor from Centella asiatica.
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Rani, Komal, Tyagi, Mitali, Mazumder, Mohit, Singh, Akanksha, Shanmugam, Annaian, Dalal, Krishna, Pillai, Manoj, Samudrala, Gourinath, Kumar, Saroj, and Srinivasan, Alagiri
- Subjects
- *
SERINE , *RACEMASES , *METHYL aspartate receptors , *NEUROLOGICAL disorders , *MEDICINAL plants - Abstract
Serine racemase (SR) converts the free form of L-serine into D-serine (DS) in the mammalian brain. The DS functions as a co-agonist of N-methyl D-aspartate (NMDA) receptor. The over- activation of NMDA receptor leads to many neurological disorders like stroke, amyotrophic lateral sclerosis, Alzheimer's disease and an effective inhibitor of SR could be a corrective method for the receptor over-activation. We report for the first time here a rapid way of purifying and identifying an inhibitor from medicinal plants known to have the neuro-protective effect. We have purified SR inhibitor from the methanolic extract of Centella asiatica by affinity method. High resolution mass spectrometry and infrared spectroscopy were used to identify the ligand to be madecassoside. We have shown the madecassoside binding in silico and its inhibition of recombinant human serine racemase in vitro and ex vivo. [ABSTRACT FROM AUTHOR]
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- 2020
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139. Systematic proteomics of endogenous human cohesin reveals an interaction with diverse splicing factors and RNA-binding proteins required for mitotic progression.
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Jung-Sik Kim, Xiaoyuan He, Jie Liu, Zhijun Duan, Taeyeon Kim, Gerard, Julia, Kim, Brian, Pillai, Manoj M., Lane, William S., Noble, William S., Budnik, Bogdan, and Waldman, Todd
- Subjects
- *
RNA-binding proteins , *RNA splicing , *PROTEOMICS , *DNA repair , *GENOME editing , *GENE expression - Abstract
The cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Cohesin is a ring complex composed of four core subunits and seven regulatory subunits. In an effort to comprehensively identify additional cohesin-interacting proteins, we used gene editing to introduce a dual epitope tag into the endogenous allele of each of 11 known components of cohesin in cultured human cells, and we performed MS analyses on dual-affinity purifications. In addition to reciprocally identifying all known components of cohesin, we found that cohesin interacts with a panoply of splicing factors and RNA-binding proteins (RBPs). These included diverse components of the U4/U6.U5 tri-small nuclear ribonucleoprotein complex and several splicing factors that are commonly mutated in cancer. The interaction between cohesin and splicing factors/RBPs was RNA- and DNA-independent, occurred in chromatin, was enhanced during mitosis, and required RAD21. Furthermore, cohesin-interacting splicing factors and RBPs followed the cohesin cycle and prophase pathway of cell cycle-regulated interactions with chromatin. Depletion of cohesin-interacting splicing factors and RBPs resulted in aberrant mitotic progression. These results provide a comprehensive view of the endogenous human cohesin interactome and identify splicing factors and RBPs as functionally significant cohesin-interacting proteins. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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140. Sputum Proteomics Reveals a Shift in Vitamin D-binding Protein and Antimicrobial Protein Axis in Tuberculosis Patients.
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Bishwal, Subasa C., Das, Mrinal K., Badireddy, Vinod K., Dabral, Deepti, Das, Aleena, Mahapatra, Alok R., Sahu, Sukanya, Malakar, Dipankar, Singh, I. Ibungo, Mazumdar, Himanghsu, Patgiri, Saurav J., Deka, Trinayan, Kapfo, Wetetsho, Liegise, Kevideme, Kupa, Rukuwe-u, Debnath, Sanjita, Bhowmik, Rajesh, Debnath, Rahul, Behera, Rajendra K., and Pillai, Manoj G.
- Abstract
Existing understanding of molecular composition of sputum and its role in tuberculosis patients is variously limited to its diagnostic potential. We sought to identify infection induced sputum proteome alteration in active/non tuberculosis patients (A/NTB) and their role in altered lung patho-physiology. Out of the study population (n = 118), sputum proteins isolated from discovery set samples (n = 20) was used for an 8-plex isobaric tag for relative and absolute concentration analysis. A minimum set of protein with at least log2(ATB/NTB) >±1.0 in ATB was selected as biosignature and validated in 32 samples. Predictive accuracy was calculated from area under the receiver operating characteristic curve (AUC of ROC) using a confirmatory set (n = 50) by Western blot analysis. Mass spectrometry analysis identified a set of 192 sputum proteins, out of which a signature of β-integrin, vitamin D binding protein:DBP, uteroglobin, profilin and cathelicidin antimicrobial peptide was sufficient to differentiate ATB from NTB. AUC of ROC of the biosignature was calculated to 0.75. A shift in DBP-antimicrobial peptide (AMP) axis in the lungs of tuberculosis patients is observed. The identified sputum protein signature is a promising panel to differentiate ATB from NTB groups and suggest a deregulated DBP-AMP axis in lungs of tuberculosis patients. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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141. PD-1H/VISTA mediates immune evasion in acute myeloid leukemia.
- Author
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Kim TK, Han X, Hu Q, Vandsemb EN, Fielder CM, Hong J, Kim KW, Mason EF, Plowman RS, Wang J, Wang Q, Zhang JP, Badri T, Sanmamed MF, Zheng L, Zhang T, Alawa J, Lee SW, Zeidan AM, Halene S, Pillai MM, Chandhok NS, Lu J, Xu ML, Gore SD, and Chen L
- Subjects
- Animals, Humans, Mice, Bone Marrow, Immunity, Cellular, Immunotherapy, Immune Evasion, Leukemia, Myeloid, Acute drug therapy
- Abstract
Acute myeloid leukemia (AML) presents a pressing medical need in that it is largely resistant to standard chemotherapy as well as modern therapeutics, such as targeted therapy and immunotherapy, including anti-programmed cell death protein (anti-PD) therapy. We demonstrate that programmed death-1 homolog (PD-1H), an immune coinhibitory molecule, is highly expressed in blasts from the bone marrow of AML patients, while normal myeloid cell subsets and T cells express PD-1H. In studies employing syngeneic and humanized AML mouse models, overexpression of PD-1H promoted the growth of AML cells, mainly by evading T cell-mediated immune responses. Importantly, ablation of AML cell-surface PD-1H by antibody blockade or genetic knockout significantly inhibited AML progression by promoting T cell activity. In addition, the genetic deletion of PD-1H from host normal myeloid cells inhibited AML progression, and the combination of PD-1H blockade with anti-PD therapy conferred a synergistic antileukemia effect. Our findings provide the basis for PD-1H as a potential therapeutic target for treating human AML.
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- 2024
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142. The FANCI/FANCD2 complex links DNA damage response to R-loop regulation through SRSF1-mediated mRNA export.
- Author
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Olazabal-Herrero A, He B, Kwon Y, Gupta AK, Dutta A, Huang Y, Boddu P, Liang Z, Liang F, Teng Y, Lan L, Chen X, Pei H, Pillai MM, Sung P, and Kupfer GM
- Subjects
- Humans, R-Loop Structures, Active Transport, Cell Nucleus, Fanconi Anemia Complementation Group Proteins metabolism, Fanconi Anemia Complementation Group D2 Protein genetics, Fanconi Anemia Complementation Group D2 Protein metabolism, Ubiquitination, DNA Repair, RNA, Messenger genetics, RNA, Messenger metabolism, DNA Damage, Serine-Arginine Splicing Factors genetics, Serine-Arginine Splicing Factors metabolism, Fanconi Anemia metabolism, Neoplasms
- Abstract
Fanconi anemia (FA) is characterized by congenital abnormalities, bone marrow failure, and cancer susceptibility. The central FA protein complex FANCI/FANCD2 (ID2) is activated by monoubiquitination and recruits DNA repair proteins for interstrand crosslink (ICL) repair and replication fork protection. Defects in the FA pathway lead to R-loop accumulation, which contributes to genomic instability. Here, we report that the splicing factor SRSF1 and FANCD2 interact physically and act together to suppress R-loop formation via mRNA export regulation. We show that SRSF1 stimulates FANCD2 monoubiquitination in an RNA-dependent fashion. In turn, FANCD2 monoubiquitination proves crucial for the assembly of the SRSF1-NXF1 nuclear export complex and mRNA export. Importantly, several SRSF1 cancer-associated mutants fail to interact with FANCD2, leading to inefficient FANCD2 monoubiquitination, decreased mRNA export, and R-loop accumulation. We propose a model wherein SRSF1 and FANCD2 interaction links DNA damage response to the avoidance of pathogenic R-loops via regulation of mRNA export., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2024
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143. Transcription elongation defects link oncogenic splicing factor mutations to targetable alterations in chromatin landscape.
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Boddu PC, Gupta A, Roy R, De La Pena Avalos B, Herrero AO, Neuenkirchen N, Zimmer J, Chandhok N, King D, Nannya Y, Ogawa S, Lin H, Simon M, Dray E, Kupfer G, Verma AK, Neugebauer KM, and Pillai MM
- Abstract
Transcription and splicing of pre-messenger RNA are closely coordinated, but how this functional coupling is disrupted in human disease remains unexplored. Here, we investigated the impact of non-synonymous mutations in SF3B1 and U2AF1, two commonly mutated splicing factors in cancer, on transcription. We find that the mutations impair RNA Polymerase II (RNAPII) transcription elongation along gene bodies leading to transcription-replication conflicts, replication stress and altered chromatin organization. This elongation defect is linked to disrupted pre-spliceosome assembly due to impaired association of HTATSF1 with mutant SF3B1. Through an unbiased screen, we identified epigenetic factors in the Sin3/HDAC complex, which, when modulated, normalize transcription defects and their downstream effects. Our findings shed light on the mechanisms by which oncogenic mutant spliceosomes impact chromatin organization through their effects on RNAPII transcription elongation and present a rationale for targeting the Sin3/HDAC complex as a potential therapeutic strategy., Highlights: Oncogenic mutations of SF3B1 and U2AF1 cause a gene-body RNAPII elongation defectRNAPII transcription elongation defect leads to transcription replication conflicts, DNA damage response, and changes to chromatin organization and H3K4me3 marksThe transcription elongation defect is linked to disruption of the early spliceosome formation through impaired interaction of HTATSF1 with mutant SF3B1.Changes to chromatin organization reveal potential therapeutic strategies by targeting the Sin3/HDAC pathway.
- Published
- 2023
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144. Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry.
- Author
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Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, and Karanicolas J
- Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.
- Published
- 2023
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145. Activation of targetable inflammatory immune signaling is seen in myelodysplastic syndromes with SF3B1 mutations.
- Author
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Choudhary GS, Pellagatti A, Agianian B, Smith MA, Bhagat TD, Gordon-Mitchell S, Sahu S, Pandey S, Shah N, Aluri S, Aggarwal R, Aminov S, Schwartz L, Steeples V, Booher RN, Ramachandra M, Samson M, Carbajal M, Pradhan K, Bowman TV, Pillai MM, Will B, Wickrema A, Shastri A, Bradley RK, Martell RE, Steidl UG, Gavathiotis E, Boultwood J, Starczynowski DT, and Verma A
- Subjects
- Child, Humans, Interleukin-1 Receptor-Associated Kinases genetics, Interleukin-1 Receptor-Associated Kinases metabolism, Mutation, NF-kappa B genetics, NF-kappa B metabolism, Protein Isoforms metabolism, RNA Splicing, Leukemia, Myeloid, Acute genetics, Leukemia, Myeloid, Acute pathology, Myelodysplastic Syndromes metabolism, Phosphoproteins metabolism, RNA Splicing Factors metabolism
- Abstract
Background: Mutations in the SF3B1 splicing factor are commonly seen in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML), yet the specific oncogenic pathways activated by mis-splicing have not been fully elucidated. Inflammatory immune pathways have been shown to play roles in the pathogenesis of MDS, though the exact mechanisms of their activation in splicing mutant cases are not well understood., Methods: RNA-seq data from SF3B1 mutant samples was analyzed and functional roles of interleukin-1 receptor-associated kinase 4 ( IRAK4) isoforms were determined. Efficacy of IRAK4 inhibition was evaluated in preclinical models of MDS/AML., Results: RNA-seq splicing analysis of SF3B1 mutant MDS samples revealed retention of full-length exon 6 of IRAK4 , a critical downstream mediator that links the Myddosome to inflammatory NF-kB activation. Exon 6 retention leads to a longer isoform, encoding a protein (IRAK4-long) that contains the entire death domain and kinase domain, leading to maximal activation of NF-kB. Cells with wild-type SF3B1 contain smaller IRAK4 isoforms that are targeted for proteasomal degradation. Expression of IRAK4-long in SF3B1 mutant cells induces TRAF6 activation leading to K63-linked ubiquitination of CDK2, associated with a block in hematopoietic differentiation. Inhibition of IRAK4 with CA-4948, leads to reduction in NF-kB activation, inflammatory cytokine production, enhanced myeloid differentiation in vitro and reduced leukemic growth in xenograft models., Conclusions: SF3B1 mutation leads to expression of a therapeutically targetable, longer, oncogenic IRAK4 isoform in AML/MDS models., Funding: This work was supported by Cincinnati Children's Hospital Research Foundation, Leukemia Lymphoma Society, and National Institute of Health (R35HL135787, RO1HL111103, RO1DK102759, RO1HL114582), Gabrielle's Angel Foundation for Cancer Research, and Edward P. Evans Foundation grants to DTS. AV is supported by Edward P. Evans Foundation, National Institute of Health (R01HL150832, R01HL139487, R01CA275007), Leukemia and Lymphoma Society, Curis and a gift from the Jane and Myles P. Dempsey family. AP and JB are supported by Blood Cancer UK (grants 13042 and 19004). GC is supported by a training grant from NYSTEM. We acknowledge support of this research from The Einstein Training Program in Stem Cell Research from the Empire State Stem Cell Fund through New York State Department of Health Contract C34874GG. MS is supported by a National Institute of Health Research Training and Career Development Grant (F31HL132420)., Competing Interests: GC, AP, BA, TB, SG, SS, SP, NS, SA, RA, SA, LS, VS, MC, KP, TB, MP, BW, AW, AS, EG, JB No competing interests declared, MS MS owns stock options in Poseida Therapeutics. The author has no other competing interests to declare, RB RB is a former employee of Curis, Inc, and holds patents patents related to CA-4948 (WO-2019089580-A1). RB also owns stocks in Curis, Inc. The author has no other competing interests to declare, MR MR is an employee of Aurigene Inc, MS MS owns stock options in Curis, Inc as an employee. The author has no other competing interests to declare, RB RKB is a named inventor on patent applications related to treating cancers with SF3B1 mutations filed by Fred Hutchinson Cancer Research Center (METHODS AND COMPOSITIONS COMPRISING BRD9 ACTIVATING THERAPIES FOR TREATING CANCERS AND RELATED DISORDERS - PCT/US2020/039645; SYNTHETIC INTRONS FOR TARGETED GENE EXPRESSION - PCT/US21/56273).The author has no other competing interests to declare, RM REM is an employee of Curis, Inc and has received honoria payments and also holds stocks in the company. The author has no other competing interests to declare, US US held grants from Bayer Healthcare and Aileron Therapauetics, and received consultancy fees from Aileron Therapeutics, Stelexis Therapeutics, Pieris Pharmaceuticals and Trillium Therapeutics. US is Director at Stelexis Therapeutics and holds stocks in the company. The author has no other competing interests to declare, DS DS received consultancy fees from Kurome Therapeutics, Treeline Biosciences, Tolero Therapeutics, and Captor Therapeutics. DS also owns stocks in Kurome Therapeutics. The author has no other competing interests to declare, AV AV has received research funding from GlaxoSmithKline, BMS, Jannsen, Incyte, MedPacto, Celgene, Novartis, Curis, Prelude and Eli Lilly and Company, has received compensation as a scientific advisor to Novartis, Stelexis Therapeutics, Acceleron Pharma, and Celgene, and has equity ownership in Throws Exception and Stelexis Therapeutics, (© 2022, Choudhary, Pellagatti et al.)
- Published
- 2022
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146. Biomass-Based Silicon and Carbon for Lithium-Ion Battery Anodes.
- Author
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Muraleedharan Pillai M, Kalidas N, Zhao X, and Lehto VP
- Abstract
Lithium-ion batteries (LIBs) are the most preferred energy storage devices today for many high-performance applications. Recently, concerns about global warming and climate change have increased the need and requirements for LIBs used in electric vehicles, and thus more advanced technologies and materials are urgently needed. Among the anode materials under development, silicon (Si) has been considered the most promising anode candidate for the next generation LIBs to replace the widely used graphite. Si cannot be used as such as the electrode of LIB, and thus, carbon is commonly used to realize the applicability of Si in LIBs. Typically, this means forming a-Si/carbon composite (Si/C). One of the main challenges in the industrial development of high-performance LIBs is to exploit low-cost, environmentally benign, sustainable, and renewable chemicals and materials. In this regard, bio-based Si and carbon are favorable to address the challenge assuming that the performance of the LIB anode is not compromised. The present review paper focuses on the development of Si and carbon anodes derived from various types of biogenic sources, particularly from plant-derived biomass resources. An overview of the biomass precursors, process/extraction methods for producing Si and carbon, the critical physicochemical properties influencing the lithium storage in LIBs, and how they affect the electrochemical performance are highlighted. The review paper also discusses the current research challenges and prospects of biomass-derived materials in developing advanced battery materials., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Muraleedharan Pillai, Kalidas, Zhao and Lehto.)
- Published
- 2022
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147. Integrative genome-wide analysis reveals EIF3A as a key downstream regulator of translational repressor protein Musashi 2 (MSI2).
- Author
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Karmakar S, Ramirez O, Paul KV, Gupta AK, Kumari V, Botti V, de Los Mozos IR, Neuenkirchen N, Ross RJ, Karanicolas J, Neugebauer KM, and Pillai MM
- Abstract
Musashi 2 (MSI2) is an RNA binding protein (RBP) that regulates asymmetric cell division and cell fate decisions in normal and cancer stem cells. MSI2 appears to repress translation by binding to 3' untranslated regions (3'UTRs) of mRNA, but the identity of functional targets remains unknown. Here, we used individual nucleotide resolution cross-linking and immunoprecipitation (iCLIP) to identify direct RNA binding partners of MSI2 and integrated these data with polysome profiling to obtain insights into MSI2 function. iCLIP revealed specific MSI2 binding to thousands of mRNAs largely in 3'UTRs, but translational differences were restricted to a small fraction of these transcripts, indicating that MSI2 regulation is not triggered by simple binding. Instead, the functional targets identified here were bound at higher density and contain more 'UAG' motifs compared to targets bound nonproductively. To further distinguish direct and indirect targets, MSI2 was acutely depleted. Surprisingly, only 50 transcripts were found to undergo translational induction on acute loss. Using complementary approaches, we determined eukaryotic translation initiation factor 3A (EIF3A) to be an immediate, direct target. We propose that MSI2 downregulation of EIF3A amplifies these effects on translation. Our results also underscore the challenges in defining functional targets of RBPs since mere binding does not imply a discernible functional interaction., (© The Author(s) 2022. Published by Oxford University Press on behalf of NAR Cancer.)
- Published
- 2022
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148. The Development and Use of Scalable Systems for Studying Aberrant Splicing in SF3B1-Mutant CLL.
- Author
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Murthy T, Paul KV, Minella AC, and Pillai MM
- Subjects
- Animals, CRISPR-Cas Systems genetics, Cell Culture Techniques instrumentation, Cell Culture Techniques methods, Cell Line, Computational Biology instrumentation, Datasets as Topic, Gene Editing instrumentation, Gene Editing methods, High-Throughput Nucleotide Sequencing instrumentation, High-Throughput Nucleotide Sequencing methods, Humans, Induced Pluripotent Stem Cells, Leukemia, Lymphocytic, Chronic, B-Cell blood, Leukemia, Lymphocytic, Chronic, B-Cell pathology, Mice, Mouse Embryonic Stem Cells, Mutation, Protein Domains genetics, RNA Splice Sites genetics, RNA Splicing genetics, Sequence Analysis, RNA instrumentation, Software, Computational Biology methods, Leukemia, Lymphocytic, Chronic, B-Cell genetics, Phosphoproteins genetics, RNA Splicing Factors genetics, Sequence Analysis, RNA methods
- Abstract
Mutational landscape of CLL is now known to include recurrent non-synonymous mutations in SF3B1, a core splicing factor. About 5-10% of newly diagnosed CLL harbor these mutations which are typically limited to HEAT domains in the carboxyl-terminus of the protein. Importantly, the mutations are not specific to CLL but also present in several unrelated clonal disorders. Analysis of patient samples and cell lines has shown the primary splicing aberration in SF3B1-mutant cells to the use of novel or "cryptic" 3' splice sites (3SS). Advances in genome-editing and next-generation sequencing (NGS) have allowed development of isogenic models and detailed analysis of changes to the transcriptome with relative ease. In this manuscript, we focus on two relevant methods to study splicing factor mutations in CLL: development of isogenic scalable cell lines and informatics analysis of RNA-Seq datasets.
- Published
- 2019
- Full Text
- View/download PDF
149. E2F-2 Promotes Nuclear Condensation and Enucleation of Terminally Differentiated Erythroblasts.
- Author
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Swartz KL, Wood SN, Murthy T, Ramirez O, Qin G, Pillai MM, Rao S, and Minella AC
- Subjects
- Animals, Cell Cycle, Cell Differentiation, Cyclin E metabolism, Erythroblasts metabolism, Gene Deletion, Gene Expression Profiling, Gene Expression Regulation, Intracellular Signaling Peptides and Proteins genetics, Mice, Phosphorylation, Protein Serine-Threonine Kinases genetics, Retinoblastoma Protein metabolism, Cell Nucleus metabolism, E2F2 Transcription Factor genetics, E2F2 Transcription Factor metabolism, Erythroblasts cytology, Erythropoiesis
- Abstract
E2F-2 is a retinoblastoma (Rb)-regulated transcription factor induced during terminal erythroid maturation. Cyclin E-mediated Rb hyperphosphorylation induces E2F transcriptional activator functions. We previously reported that deregulated cyclin E activity causes defective terminal maturation of nucleated erythroblasts in vivo Here, we found that these defects are normalized by E2F-2 deletion; however, anemia in mice with deregulated cyclin E is not improved by E2F-2-loss, which itself causes reduced peripheral red blood cell (RBC) counts without altering relative abundances of erythroblast subpopulations. To determine how E2F-2 regulates RBC production, we comprehensively studied erythropoiesis using knockout mice and hematopoietic progenitors. We found that efficient stress erythropoiesis in vivo requires E2F-2, and we also identified an unappreciated role for E2F-2 in erythroblast enucleation. In particular, E2F-2 deletion impairs nuclear condensation, a morphological feature of maturing erythroblasts. Transcriptome profiling of E2F-2-null, mature erythroblasts demonstrated widespread changes in gene expression. Notably, we identified citron Rho-interacting kinase (CRIK), which has known functions in mitosis and cytokinesis, as induced in erythroblasts in an E2F-2-dependent manner, and we found that CRIK activity promotes efficient erythroblast enucleation and nuclear condensation. Together, our data reveal novel, lineage-specific functions for E2F-2 and suggest that some mitotic kinases have specialized roles supporting enucleation of maturing erythroblasts., (Copyright © 2016 American Society for Microbiology.)
- Published
- 2016
- Full Text
- View/download PDF
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