Publications by authors named "Arpita Bhattacharya"

32 Publications

Effects of Oxytocin on Emotion Recognition in Schizophrenia: A Randomized Double-Blind Pilot Study.

J Clin Psychopharmacol 2021 Mar-Apr 01;41(2):103-113

Atlanta Veterans Affairs Health Care System, Decatur.

Background: Schizophrenia (SCZ) is a neurodevelopmental disorder that leads to poor social function. Oxytocin (OXT), a neuropeptide involved in social cognition, is a potential therapeutic agent for alleviating social dysfunction. Therefore, we investigated the effects of intranasal oxytocin (IN-OXT) on emotional processes in experimental interactive social contexts in individuals with SCZ.

Methods: In a male-only parallel randomized placebo-controlled double-blind trial, we investigated the effects of IN-OXT (24 IU) on visual fixation on pictures of faces and emotion recognition in an interactive ball-tossing game that probed processing of social and nonsocial stimuli.

Results: Intranasal oxytocin enhanced the recognition of emotions during an emotion-based ball-tossing game. This improvement was specific to the game that included social cue processing. Intranasal oxytocin did not affect eye gaze duration or gaze dwell time on faces in these patients.

Conclusions: An acute low dose of IN-OXT had a modest effect on social cue processing and was limited to emotion recognition. Higher doses and long-term trials targeting emotional processing in SCZ may lead to improved social function.
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http://dx.doi.org/10.1097/JCP.0000000000001367DOI Listing
February 2021

Langerhans cell histiocytosis in children: A retrospective case series of 126 cases.

Pediatr Dermatol 2020 Nov 27;37(6):1085-1089. Epub 2020 Sep 27.

Department of Pediatric Medicine, Institute of Child Health, Kolkata, India.

Background/objectives: Langerhans cell histiocytosis (LCH), a rare neoplasm of hematopoietic myeloid precursor cells, is clinically characterized by spontaneously resolving lesions to a progressive life-threatening multisystem disorder. Diagnosing LCH in children is challenging as it mimics other skin disorders. This study describes the varied clinical presentation and disease course in children less than 18 years diagnosed with LCH.

Methods: We performed a retrospective observational study of all cases diagnosed with LCH presenting to a children's hospital in the last 26 years. Data on history, cutaneous and systemic examination, and laboratory evaluation performed, were recorded.

Results: A total of 126 children diagnosed with LCH were included in the study. There were 68% cases limited only to skin, and 32% children with multisystem involvement at the initial presentation. Scaly papules were the most common morphologic finding in skin. The skeletal system was the second most common organ system to be affected. Failure to thrive was a common symptom. Progression of skin to systemic involvement was seen in 27.9%. In 76.7%, skin lesions cleared over a period of 2 to 4 years. Complete remission was seen in 56.9% of children over a period of 3 to 7 years, while 8.1% children died of complicationsand 31.8% were lost to follow-up.

Conclusions: Long-term follow-up in this study has shown cutaneous LCH without systemic involvement has a good prognosis. Skin involvement,along with failure to thrive, was the most common clinical presentation in our study. The skeletal system was the second most common organ system involved.
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http://dx.doi.org/10.1111/pde.14389DOI Listing
November 2020

Relationship of prolonged acoustic startle latency to diagnosis and biotype in the bipolar-schizophrenia network on intermediate phenotypes (B-SNIP) cohort.

Schizophr Res 2020 02 30;216:357-366. Epub 2019 Nov 30.

Atlanta Veterans Affairs Medical Center, Decatur, GA, 30033, USA; Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30329, USA. Electronic address:

Background: Latency of the acoustic startle reflex is the time from presentation of the startling stimulus until the response and provides an index of neural processing speed. Latency is prolonged in schizophrenia, is 90% heritable, and predicts conversion to schizophrenia in a high-risk population. The Bipolar-Schizophrenia Network for Intermediate Phenotypes (B-SNIP) consortium investigates neurobiological features found in psychotic disorders spanning diagnostic criteria for schizophrenia (SCZ), schizoaffective disorder (SAD), and psychotic bipolar disorder (BP). We investigated whether differences in startle latency and prepulse inhibition (PPI) occur in probands, their first-degree relatives, and neurobiologically defined subgroups of the probands (Biotypes).

Methods: 1143 subjects were included from the B-SNIP cohort: 143 with SCZ, 178 SCZ relatives (SCZ-Fam), 123 with SAD, 152 SAD relatives (SAD-Fam), 138 BP, 183 BP relatives (BP-Fam), and 226 controls (CON). A Biopac system recorded the eyeblink component of the startle reflex during startle testing.

Results: Latency differed by diagnosis (F(3,620) = 5.10, p = 0.002): SCZ, SAD, and BP probands had slower latency than CON, with relatives intermediate. Biotypes 1 and 2 had slower latency than CON (p < 0.031) but Biotype 3 did not differ from CON. PPI did not separate CON from other subjects when analyzed by diagnoses nor when analyzed by biotype. Biotype 1 relatives had slower latency (F(3,663) = 3.49, p = 0.016) and more impaired PPI than Biotype 2 and 3 relatives (F(3,663) = 2.77, p = 0.041).

Conclusion: Startle latency is prolonged in psychotic disorders that cross traditional diagnostic categories. These data suggest a genetic difference between biotypes that span across clinically defined diagnoses.
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http://dx.doi.org/10.1016/j.schres.2019.11.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7239737PMC
February 2020

Supplementation of Trichoderma improves the alteration of nutrient allocation and transporter genes expression in rice under nutrient deficiencies.

Plant Physiol Biochem 2019 Oct 11;143:351-363. Epub 2019 Sep 11.

Division of Microbial Technology, Council of Scientific and Industrial Research- National Botanical Research Institute, Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India. Electronic address:

Nutrients are the finite natural resources that are essential for productivity and development of rice and its deficiency causes compromised yield along with reduced immunity against several biotic and abiotic stresses. In this study, the potential of Trichoderma reesei has been investigated as a biofertilizer (BF) to ameliorate nutrient stress in different rice cultivars at physiological, biochemical and molecular levels. The results indicated that cultivar Heena is much more compatible with BF as compared to cultivar Kiran at 50% nutrient limiting condition. Enhancement in physiological attributes and photosynthetic pigments were observed in BF treated Heena seedlings. The localization of biofertilizer in treated roots was further validated by scanning electron micrographs. This result correlated well with the higher levels of Indole acetic acid and Gibberellic acid in biofertilizer treated rice. Similarly, the uptake of micro-nutrients such as Fe, Co, Cu and Mo was found to be 1.4-1.9 fold higher respectively in BF treated Heena seedlings under 50% nutrient deficient condition. Furthermore, different stress ameliorating enzymes Guaiacol peroxidase, Super oxide dismutase, Total Phenolic Content, Phenol Peroxidase, Phenylalanine ammonia lyase and Ascorbate peroxidase in Heena seedlings were also increased by 1.8, 1.4, 1.2, 2.4, 1.2, and 8.3-fold respectively, at 50% nutrient deficient condition. The up-regulation of different micro and macro-nutrients allocation and accumulation; metal tolerance related; auxin synthesis genes in BF treated Heena as compared to 50% nutrient deficient condition was further supported by our findings that the application of biofertilizer efficiently ameliorated the deficiency of nutrients in rice.
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http://dx.doi.org/10.1016/j.plaphy.2019.09.015DOI Listing
October 2019

Engaging Teenagers in Asynchronous Online Groups to Design for Stress Management.

Proc 18th ACM Int Conf Interact Des Child (2019) 2019 Jun;2019:26-37

University of Washington | DUB group, Seattle, USA.

Teenagers have unique needs for mental wellbeing that can be supported by interactive technologies. Teens also have valuable input in the design of technology, so designers and researchers must seek new methods for involving them in the design process. We enrolled 23 unacquainted teenagers in an Asynchronous Remote Communities (ARC) study consisting of two private online groups. Teens participated in 10 weekly design activities on stress management across three months. We found that teens sought support from technology tailored to their perception of control in stressful contexts, developing sense of self, and varying social needs, including asking for no intervention from others. Teens appreciated that the ARC design experience allowed for flexibility in participation and supported selective disclosure. However, there were limited interactions between teenagers online. Reflecting on our study, we provide design implications for tools to support teenager mental health and discuss how the ARC method can be adapted for designing with teenagers.
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http://dx.doi.org/10.1145/3311927.3323140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7500255PMC
June 2019

Role of silica coated magnetic nanoparticle on cell flocculation, lipid extraction and linoleic acid production from .

Nat Prod Res 2020 Oct 11;34(19):2852-2856. Epub 2019 May 11.

Amity Institute of Biotechnology, Amity University , Uttar Pradesh, Sector-125, Noida , Uttar Pradesh , India.

In the present work, it has been observed that magnetic (FeO) - silica core- shell nanoparticles helps in flocculation of cells with simultaneous production of linoleic acid. The mean particle size in Dynamic light scattering (DLS) of the silica coated magnetic nanoparticle was estimated 444.7 nm. The characterization of nanoparticles was also performed by X-ray diffraction technique (XRD). Apart from flocculation, it has been observed that in presence of magnetic silica core- shell nanoparticles the amount of lipid obtained was four times than that of control. On the contrary, in presence of these nanoparticles, linoleic acid (18:2) has been produced in cells almost by 80% whereas, it has been noticed only 8.73% in control. This is the first report where the linoleic acid has been obtained as major component of microalgal fatty acid methyl esters (FAME) having important application in nutraceuticals and pharmaceutical sectors.
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http://dx.doi.org/10.1080/14786419.2019.1593164DOI Listing
October 2020

Development of coating formulation with silica-titania core-shell nanoparticles against pathogenic fungus.

R Soc Open Sci 2018 Aug 15;5(8):180633. Epub 2018 Aug 15.

Amity Institute of Nanotechnology, Amity University, Noida, Uttar Pradesh 201303, India.

In the present study, we developed an antifungal coating formulation using silica, titania and silica-titania core-shell nanoparticles individually. The idea behind the synthesis of core-shell nanoparticles was to use the mechanical strength of silica and the antimicrobial property of TiO together. These nanoparticles were characterized by dynamic light scattering, transmission electron microscopy, scanning electron microscopy, EDX, FTIR and X-ray diffraction. Silica nanoparticles of 92 nm were prepared by the sol-gel process, while TiO nanoparticles and nano-core-shells were prepared through the peptization process with a size of 77 and 144 nm separately. The antifungal effect of the prepared nanoparticles was observed in potato dextrose agar media using the concentration of nanoparticles at 1 wt%. These nanoparticles were incorporated in two types of binder, polyurethane and polyacrylic, with the same concentration of nanoparticles. Coatings were applied on tiles, dried and tested against pathogenic fungus, and fungus growth reduction was observed up to 7-10 days. Coatings developed with TiO nanoparticles have shown good growth reduction of pathogenic fungus, but coatings formulated with silica-titania core-shell nanoparticles killed the fungus fusarium completely and have shown around 90% growth reduction for acremonium species also.
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http://dx.doi.org/10.1098/rsos.180633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6124124PMC
August 2018

Bacterial endophytes modulates the withanolide biosynthetic pathway and physiological performance in Withania somnifera under biotic stress.

Microbiol Res 2018 Jul - Aug;212-213:17-28. Epub 2018 Apr 22.

Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, 226001, India. Electronic address:

Despite the vast exploration of endophytic microbes for growth enhancement in various crops, knowledge about their impact on the production of therapeutically important secondary metabolites is scarce. In the current investigation, chitinolytic bacterial endophytes were isolated from selected medicinal plants and assessed for their mycolytic as well as plant growth promoting potentials. Among them the two most efficient bacterial endophytes namely Bacillus amyloliquefaciens (MPE20) and Pseudomonas fluorescens (MPE115) individually as well as in combination were able to modulate withanolide biosynthetic pathway and tolerance against Alternaria alternata in Withania somnifera. Interestingly, the expression level of withanolide biosynthetic pathway genes (3-hydroxy-3-methylglutaryl co-enzyme A reductase, 1-deoxy-D-xylulose-5-phosphate reductase, farnesyl di-phosphate synthase, squalene synthase, cytochrome p450, sterol desaturase, sterol Δ-7 reductase and sterol glycosyl transferases) were upregulated in plants treated with the microbial consortium under A. alternata stress. In addition, application of microbes not only augmented withaferin A, withanolide A and withanolide B content (1.52-1.96, 3.32-5.96 and 12.49-21.47 fold, respectively) during A. alternata pathogenicity but also strengthened host resistance via improvement in the photochemical efficiency, normalizing the oxidized and non-oxidized fraction, accelerating photochemical and non-photochemical quantum yield, and electron transport rate. Moreover, reduction in the passively dissipated energy of PSI and PSII in microbial combination treated plants corroborate well with the above findings. Altogether, the above finding highlights novel insights into the underlying mechanisms in application of endophytes and emphasizes their capability to accelerate biosynthesis of withanolides in W. somnifera under biotic stress caused by A. alternata.
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http://dx.doi.org/10.1016/j.micres.2018.04.006DOI Listing
October 2018

Endophyte-Mediated Modulation of Defense-Related Genes and Systemic Resistance in Withania somnifera (L.) Dunal under Alternaria alternata Stress.

Appl Environ Microbiol 2018 04 2;84(8). Epub 2018 Apr 2.

Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, India.

Endophytes have been explored and found to perform an important role in plant health. However, their effects on the host physiological function and disease management remain elusive. The present study aimed to assess the potential effects of endophytes, singly as well as in combination, in (L.) Dunal, on various physiological parameters and systemic defense mechanisms against Seeds primed with the endophytic bacteria and individually and in combination demonstrated an enhanced vigor index and germination rate. Interestingly, plants treated with the two-microbe combination showed the lowest plant mortality rate (28%) under stress. Physiological profiling of treated plants showed improved photosynthesis, respiration, transpiration, and stomatal conductance under pathogenic stress. Additionally, these endophytes not only augmented defense enzymes and antioxidant activity in treated plants but also enhanced the expression of salicylic acid- and jasmonic acid-responsive genes in the stressed plants. Reductions in reactive oxygen species (ROS) and reactive nitrogen species (RNS) along with enhanced callose deposition in host plant leaves corroborated well with the above findings. Altogether, the study provides novel insights into the underlying mechanisms behind the tripartite interaction of endophyte-- and underscores their ability to boost plant health under pathogen stress. is well known for producing several medicinally important secondary metabolites. These secondary metabolites are required by various pharmaceutical sectors to produce life-saving drugs. However, the cultivation of faces severe challenge from leaf spot disease caused by To keep pace with the rising demand for this plant and considering its capacity for cultivation under field conditions, the present study was undertaken to develop approaches to enhance production of through intervention using endophytes. Application of bacterial endophytes not only suppresses the pathogenicity of but also mitigates excessive ROS/RNS generation via enhanced physiological processes and antioxidant machinery. Expression profiling of plant defense-related genes further validates the efficacy of bacterial endophytes against leaf spot disease.
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http://dx.doi.org/10.1128/AEM.02845-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5881058PMC
April 2018

Understanding pivotal experiences in behavior change for the design of technologies for personal wellbeing.

J Biomed Inform 2018 03 11;79:129-142. Epub 2018 Jan 11.

Human Centered Design and Engineering, DUB Group, University of Washington, Seattle, USA. Electronic address:

Most health technologies are designed to support people who have already decided to work toward better health. Thus, there remains an opportunity to design technologies to help motivate people who have not yet decided to make a change. Understanding the experiences of people who have already started to make a health behavior change and how they made a pivotal decision can be useful in understanding how to design such tools. In this paper, we describe results from data collected in 2 phases. Phase 1 consisted of 127 surveys and 13 interviews with adults who have already accomplished behavior change(s). Phase 2 consisted of 117 surveys and 12 interviews with adults who have either already accomplished their behavior change(s) or are currently working toward them. We identified four factors that lead to pivotal experiences: (1) prolonged discontent and desire to change, (2) significant changes that increase fear or hope of future, (3) increased understanding of one's behavior and personal data, and (4) social accountability. We also describe a design space for designing technology-based interventions for encouraging people to decide to make a change to improve their health. Based on feedback from participants, we discuss opportunities for further exploration of the design space for people who are not yet motivated to change and for ethical considerations for this type of intervention.
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http://dx.doi.org/10.1016/j.jbi.2018.01.002DOI Listing
March 2018

Protective role of biosynthesized silver nanoparticles against early blight disease in Solanum lycopersicum.

Plant Physiol Biochem 2017 Dec 10;121:216-225. Epub 2017 Nov 10.

Department of Plant Microbe Interactions, CSIR-NBRI, Lucknow, 226001, U.P, India.

Tomato suffers a huge loss every year because of early blight disease. This study focuses on efficient inhibition of Alternaria solani, the causative agent of early blight disease in tomato in vitro and in vivo. Foliar spray of 5 μg/mL of biosynthesized silver nanoparticles in A. solani infected plants resulted in significant increase of 32.58% in fresh weight and 23.52% in total chlorophyll content of tomato as compared to A. solani infected plants. A decrease of 48.57, 30, 39.59 and 28.57% was observed in fungal spore count, lipid peroxidation, proline content and superoxide dismutase respectively in infected tomato plants after treatment with synthesized silver nanoparticles as compared to A. solani infected plants. No significant variation in terms of soil pH, cultured population, carbon source utilization pattern and soil enzymes including dehydrogenase, urease, protenase and β-glucosidase was observed after foliar spray of nanoparticles. It was revealed that direct killing of pathogens, increased photosynthetic efficiencies, increased plant resistance and decrease in stress parameters and stress enzymes are the mechanisms employed by plants and nanoparticles simultaneously to combat the biotic stress. Biosynthesized silver nanoparticles bear the potential to revolutionize plant disease management, though the molecular aspects of increased resistance must be looked upon.
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http://dx.doi.org/10.1016/j.plaphy.2017.11.004DOI Listing
December 2017

Lessons from Practice: Designing Tools to Facilitate Individualized Support for Quitting Smoking.

ACM Trans Comput Hum Interact 2017 ;2017:3057-3070

Human Centered Design and Engineering, DUB Group, University of Washington, Seattle, USA.

Many health care providers, with a variety of trainings, counsel clients on quitting smoking on a day-to-day basis. In their clinical practice, they draw from and adapt guidelines and research-based strategies to fit individual client situations and challenges. Designers of technologies to support quitting smoking can learn from these real world practices to create tools that better adapt to individual differences. We present findings from interviews with 28 providers with diverse experiences in smoking cessation counselling. Through analysis of their individualization strategies, challenges, and perceptions of technology, we find that providers: (1) individualize context appropriate coping strategies by involving clients in brainstorming, (2) emphasize the need to support nicotine withdrawal in clients, (3) mitigate social triggers and mediate social support for clients, and (4) need to navigate dependencies with other providers for managing medications and comorbid health conditions of clients. With this empirical understanding, we extend the discussion on the design of technology to support quitting smoking, highlight current barriers to individualization, and suggest future opportunities to address these barriers.
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http://dx.doi.org/10.1145/3025453.3025725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5675113PMC
January 2017

Mixed-phenotypic acute leukemia series from tertiary care center.

Indian J Pathol Microbiol 2017 Jan-Mar;60(1):43-49

Department of Laboratory Haematology and Molecular Genetics, Tata Medical Centre, Kolkata, West Bengal, India.

Introduction: Mixed-phenotype acute leukemias (MPALs) are a heterogeneous group of rare leukemias constituting approximately 2%-5% of all leukemias, in which assigning a single lineage of origin is not possible. They are diagnosed by either the presence of antigens of more than one lineage or by the presence of dual population of blasts belonging to two or more lineages. We highlight the clinicopathological, immunophenotype, and genetic data of a cohort (n = 14) of patients diagnosed and treated at our center.

Materials And Methods: We retrospectively analyzed consecutive cases of MPAL diagnosed in our flow cytometry laboratory from May 2012 to August 2015. These cases were diagnosed based on immunophenotyping of peripheral blood/bone marrow aspirates and morphology/genetics wherever available as per the World Health Organization (WHO) 2008 guideline.

Results: Among 628 consecutive acute leukemia (AL) cases diagnosed and evaluated during this period, we identified 14 (2.2%) patients with MPAL fulfilling WHO 2008/EGIL criteria for immunological characterizing of AL criteria. Majority of these were males (n = 8, male:female ratio 1.3:1) and adults (n = 11, 78.5%). The median age of this cohort was 41 years (range 2-80). These cases were further classified as: B/myeloid (n = 9), T/myeloid (n = 4), and B/T MPAL (n = 1). Cytogenetics was available in 12 out of 14 cases, out of which, three cases had normal karyotype, three with t(9;22)(q34;q11), and two cases with complex karyotype. We also came across a rare case of B + T lymphoid MPAL who had mixed-lineage leukemia gene t(v; 11q23) rearrangement.

Conclusion: MPAL is a complex entity with heterogeneous clinical, immunophenotypic, cytogenetic, and molecular features. Multiparametric flowcytometry by using comprehensive antibody panels is a valuable tool for diagnosis. Subsequent cytogenetic and molecular analysis for further prognostic stratification and treatment modalities are important.
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http://dx.doi.org/10.4103/0377-4929.200057DOI Listing
March 2017

A Possible Role of the Full-Length Nascent Protein in Post-Translational Ribosome Recycling.

PLoS One 2017 18;12(1):e0170333. Epub 2017 Jan 18.

Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata, India.

Each cycle of translation initiation in bacterial cell requires free 50S and 30S ribosomal subunits originating from the post-translational dissociation of 70S ribosome from the previous cycle. Literature shows stable dissociation of 70S from model post-termination complexes by the concerted action of Ribosome Recycling Factor (RRF) and Elongation Factor G (EF-G) that interact with the rRNA bridge B2a/B2b joining 50S to 30S. In such experimental models, the role of full-length nascent protein was never considered seriously. We observed relatively slow release of full-length nascent protein from 50Sof post translation ribosome, and in that process, its toe prints on the rRNA in vivo and in in vitro translation with E.coli S30 extract. We reported earlier that a number of chemically unfolded proteins like bovine carbonic anhydrase (BCA), lactate dehydrogenase (LDH), malate dehydrogenase (MDH), lysozyme, ovalbumin etc., when added to free 70Sin lieu of the full length nascent proteins, also interact with identical RNA regions of the 23S rRNA. Interestingly the rRNA nucleotides that slow down release of the C-terminus of full-length unfolded protein were found in close proximity to the B2a/B2b bridge. It indicated a potentially important chemical reaction conserved throughout the evolution. Here we set out to probe that conserved role of unfolded protein conformation in splitting the free or post-termination 70S. How both the RRF-EFG dependent and the plausible nascent protein-EFG dependent ribosome recycling pathways might be relevant in bacteria is discussed here.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170333PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5242463PMC
August 2017

Biopolymer matrix for nano-encapsulation of urease - A model protein and its application in urea detection.

J Colloid Interface Sci 2017 Mar 9;490:452-461. Epub 2016 Nov 9.

Amity Institute of Biotechnology, AUUP, Noida 201301, India. Electronic address:

Alginate microparticles and nanoparticles crosslinked with Ca ions are frequently employed in biomedical applications. Here we use microemulsion polymerization to prepare alginate nanoparticles (nanogels) using different crosslinking ions (Ca, Sr, Ba) to encapsulate a model protein, urease enzyme (jackbeans). With alginate concentrations of 0.2wt% in the aqueous phase, emulsion droplets showed good stability and narrow, monomodal distributions with radii ∼65±10nm. The size of the nanogel varies with the crosslinking cation and its affinity for the mannuronate and guluronate units in the linear alginate chain. The nanogels were further characterized using dynamic light scattering, scanning electron microscopy, energy dispersive X-ray spectrometry and zeta potential. This work demonstrates the potential application of Ba-alginate as an alternative matrix for nano-encapsulation of proteins and its use for biomedical applications.
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http://dx.doi.org/10.1016/j.jcis.2016.11.030DOI Listing
March 2017

Tailoring shape and size of biogenic silver nanoparticles to enhance antimicrobial efficacy against MDR bacteria.

Microb Pathog 2017 Apr 23;105:346-355. Epub 2016 Nov 23.

CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226 001, India.

Spherical, rectangular, penta, and hexagonal silver nanoparticles of different dimensions were biosynthesized in an eco-friendly manner by biocontrol agent, Trichoderma viride by manipulating physical parameters, pH, temperature, and reaction time. The particles were characterized by UV-vis spectroscopy; Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM) and Fourier Transform Infra-red Spectroscopy (FTIR). Shape and size dependent antimicrobial activity of nanoparticles against human pathogens was observed. Maximum inhibition was found with spherical nanoparticles (2-5 nm) showing 40, 51, 43, 53.9 and 55.8% against Shigella sonnei, Escherichia coli, Serratia marcescens, Staphylococcus. aureus and Pseudomonas aeruginosa respectively, where as pentagonal and hexagonal nanoparticles (50-100 nm) demonstrated 32, 41, 31, 42.84 and 42.80% of inhibition as compared to control. Nanoparticles of different geometry and dimension established enhanced antagonistic activity against pathogens with all the tested antibiotics. Excellent antimicrobial efficacy was obtained with spherical nanoparticles of 2-5 nm with ampicillin and penicillin. Shape and size played major role in enhancing antimicrobial potential of silver nanoparticles, both singly and synergistically with antibiotics which can be exploited to combat the spread of multidrug resistant pathogens.
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http://dx.doi.org/10.1016/j.micpath.2016.11.012DOI Listing
April 2017

A Comprehensive Characterization of Simple Sequence Repeats in the Sequenced Trichoderma Genomes Provides Valuable Resources for Marker Development.

Front Microbiol 2016 27;7:575. Epub 2016 Apr 27.

Division of Plant Microbe Interaction, Council of Scientific and Industrial Research-National Botanical Research Institute Lucknow, India.

Members of genus Trichoderma are known worldwide for mycoparasitism. To gain a better insight into the organization and evolution of their genomes, we used an in silico approach to compare the occurrence, relative abundance and density of SSRs in Trichoderma atroviride, T. harzianum, T. reesei, and T. virens. Our analysis revealed that in all the four genome sequences studied, the occurrence, relative abundance, and density of microsatellites varied and was not influenced by genome sizes. The relative abundance and density of SSRs positively correlated with the G + C content of their genomes. The maximum frequency of SSRs was observed in the smallest genome of T. reesei whereas it was least in second smallest genome of T. atroviride. Among different classes of repeats, the tri-nucleotide repeats were abundant in all the genomes and accounts for ∼38%, whereas hexa-nuceotide repeats were the least (∼10.2%). Further evaluation of the conservation of motifs in the transcript sequences shows a 49.5% conservation among all the motifs. In order to study polymorphism in Trichoderma isolates, 12 polymorphic SSR markers were developed. Of the 12 markers, 6 markers are from T. atroviride and remaining 6 belong to T. harzianum. SSR markers were found to be more polymorphic from T. atroviride with an average polymorphism information content value of 0.745 in comparison with T. harzianum (0.615). Twelve polymorphic markers obtained in this study clearly demonstrate the utility of newly developed SSR markers in establishing genetic relationships among different isolates of Trichoderma.
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http://dx.doi.org/10.3389/fmicb.2016.00575DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846858PMC
May 2016

Nonsense suppression in archaea.

Proc Natl Acad Sci U S A 2015 May 27;112(19):6015-20. Epub 2015 Apr 27.

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139

Bacterial strains carrying nonsense suppressor tRNA genes played a crucial role in early work on bacterial and bacterial viral genetics. In eukaryotes as well, suppressor tRNAs have played important roles in the genetic analysis of yeast and worms. Surprisingly, little is known about genetic suppression in archaea, and there has been no characterization of suppressor tRNAs or identification of nonsense mutations in any of the archaeal genes. Here, we show, using the β-gal gene as a reporter, that amber, ochre, and opal suppressors derived from the serine and tyrosine tRNAs of the archaeon Haloferax volcanii are active in suppression of their corresponding stop codons. Using a promoter for tRNA expression regulated by tryptophan, we also show inducible and regulatable suppression of all three stop codons in H. volcanii. Additionally, transformation of a ΔpyrE2 H. volcanii strain with plasmids carrying the genes for a pyrE2 amber mutant and the serine amber suppressor tRNA yielded transformants that grow on agar plates lacking uracil. Thus, an auxotrophic amber mutation in the pyrE2 gene can be complemented by expression of the amber suppressor tRNA. These results pave the way for generating archaeal strains carrying inducible suppressor tRNA genes on the chromosome and their use in archaeal and archaeviral genetics. We also provide possible explanations for why suppressor tRNAs have not been identified in archaea.
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http://dx.doi.org/10.1073/pnas.1501558112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4434778PMC
May 2015

Identical RNA-protein interactions in vivo and in vitro and a scheme of folding the newly synthesized proteins by ribosomes.

J Biol Chem 2012 Oct 29;287(44):37508-21. Epub 2012 Aug 29.

Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, 92-A.P.C. Road, Kolkata 700 009, India.

A distinct three-dimensional shape of rRNA inside the ribosome is required for the peptidyl transfer activity of its peptidyltransferase center (PTC). In contrast, even the in vitro transcribed PTC RNA interacts with unfolded protein(s) at about five sites to let them attain their native states. We found that the same set of conserved nucleotides in the PTC interact identically with nascent and chemically unfolded proteins in vivo and in vitro, respectively. The time course of this interaction, difficult to follow in vivo, was observed in vitro. It suggested nucleation of folding of cytosolic globular proteins vectorially from hydrophilic N to hydrophobic C termini, consistent with our discovery of a regular arrangement of cumulative hydrophobic indices of the peptide segments of cytosolic proteins from N to C termini. Based on this observation, we propose a model here for the nucleation of folding of the nascent protein chain by the PTC.
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http://dx.doi.org/10.1074/jbc.M112.396127DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3481345PMC
October 2012

Involvement of mitochondrial ribosomal proteins in ribosomal RNA-mediated protein folding.

J Biol Chem 2011 Dec 21;286(51):43771-43781. Epub 2011 Oct 21.

Department of Biophysics, Molecular Biology and Bioinformatics, University College of Science, University of Calcutta, Kolkata 700009, India; Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, Nadia 741252, India. Electronic address:

The peptidyl transferase center of the domain V of large ribosomal RNA in the prokaryotic and eukaryotic cytosolic ribosomes acts as general protein folding modulator. We showed earlier that one part of the domain V (RNA1 containing the peptidyl transferase loop) binds unfolded protein and directs it to a folding competent state (FCS) that is released by the other part (RNA2) to attain the folded native state by itself. Here we show that the peptidyl transferase loop of the mitochondrial ribosome releases unfolded proteins in FCS extremely slowly despite its lack of the rRNA segment analogous to RNA2. The release of FCS can be hastened by the equivalent activity of RNA2 or the large subunit proteins of the mitochondrial ribosome. The RNA2 or large subunit proteins probably introduce some allosteric change in the peptidyl transferase loop to enable it to release proteins in FCS.
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http://dx.doi.org/10.1074/jbc.M111.263574DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243548PMC
December 2011

Eukaryotic cells producing ribosomes deficient in Rpl1 are hypersensitive to defects in the ubiquitin-proteasome system.

PLoS One 2011 12;6(8):e23579. Epub 2011 Aug 12.

Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America.

It has recently become clear that the misassembly of ribosomes in eukaryotic cells can have deleterious effects that go far beyond a simple shortage of ribosomes. In this work we find that cells deficient in ribosomal protein L1 (Rpl1; Rpl10a in mammals) produce ribosomes lacking Rpl1 that are exported to the cytoplasm and that can be incorporated into polyribosomes. The presence of such defective ribosomes leads to slow growth and appears to render the cells hypersensitive to lesions in the ubiquitin-proteasome system. Several genes that were reasonable candidates for degradation of 60S subunits lacking Rpl1 fail to do so, suggesting that key players in the surveillance of ribosomal subunits remain to be found. Interestingly, in spite of rendering the cells hypersensitive to the proteasome inhibitor MG132, shortage of Rpl1 partially suppresses the stress-invoked temporary repression of ribosome synthesis caused by MG132.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0023579PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155557PMC
February 2012

Why Dom34 stimulates growth of cells with defects of 40S ribosomal subunit biosynthesis.

Mol Cell Biol 2010 Dec 27;30(23):5562-71. Epub 2010 Sep 27.

Department of Cell Biology, Albert Einstein College of Medicine, 1300 Morris Avenue, Bronx, NY 10461, USA.

A set of genome-wide screens for proteins whose absence exacerbates growth defects due to pseudo-haploinsufficiency of ribosomal proteins in Saccharomyces cerevisiae identified Dom34 as being particularly important for cell growth when there is a deficit of 40S ribosomal subunits. In contrast, strains with a deficit of 60S ribosomal proteins were largely insensitive to the loss of Dom34. The slow growth of cells lacking Dom34 and haploinsufficient for a protein of the 40S subunit is caused by a severe shortage of 40S subunits available for translation initiation due to a combination of three effects: (i) the natural deficiency of 40S subunits due to defective synthesis, (ii) the sequestration of 40S subunits due to the large accumulation of free 60S subunits, and (iii) the accumulation of ribosomes "stuck" in a distinct 80S form, insensitive to the Mg(2+) concentration, and at least temporarily unavailable for further translation. Our data suggest that these stuck ribosomes have neither mRNA nor tRNA. We postulate, based on our results and on previously published work, that the stuck ribosomes arise because of the lack of Dom34, which normally resolves a ribosome stalled due to insufficient tRNAs, to structural problems with its mRNA, or to a defect in the ribosome itself.
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http://dx.doi.org/10.1128/MCB.00618-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976434PMC
December 2010

Mechanism of ribosome assisted protein folding: a new insight into rRNA functions.

Biochem Biophys Res Commun 2009 Jun 3;384(2):137-40. Epub 2009 May 3.

Department of Biophysics, Molecular Biology and Genetics, University College of Science, Kolkata 700009, India.

The peptidyl transferase center (PTC), present in the domain V of 23S rRNA of bacteria can act as a general protein folding modulator. Any general function of a nucleic acid polymer (DNA or RNA) is always related to specific sequence/sequences. The ribosome mediated protein folding also involves a specific interaction between the nucleotides of peptidyl transferase center and the amino acids of an unfolded protein. In this article the mechanism of rRNA assisted protein folding and its significance in the light of high resolution crystal structure of ribosome are discussed.
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http://dx.doi.org/10.1016/j.bbrc.2009.04.106DOI Listing
June 2009

Reactive haemophagocytic lymphohistiocytosis.

Indian J Pediatr 2009 Jun 16;76(6):643-5. Epub 2009 Apr 16.

Institute of Child Health, Kolkata, India.

We present a series of five cases diagnosed and treated as reactive haemophagocytic lymphohistiocytosis (HLH) in three tertiary referral centers of Kolkata, within a time frame of 3 months. The initial presentations were very variable, the most prominent clinical feature being--acute renal failure in the first patient, convulsions in the second, encephalopathy the third, marked cervical lymphadenopathy in the fourth and polyserositis in the fifth. All had a history of prolonged fever preceding admission and hepatosplenomegaly on examination. Investigations revealed multi-organ involvement with pancytopenia; haemophagocytosis was eventually diagnosed by bone marrow examination. These cases highlight the diagnostic challenge posed by infection associated haemophagocytosis and the need for maintaining a high index of suspicion to promptly diagnose and treat this potentially life threatening condition.
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http://dx.doi.org/10.1007/s12098-009-0123-0DOI Listing
June 2009

Role of the ribosome in protein folding.

Biotechnol J 2008 Aug;3(8):999-1009

Department of Biophysics, Molecular Biology and Genetics, University College of Science, Kolkata, India.

In all organisms, the ribosome synthesizes and folds full length polypeptide chains into active three-dimensional conformations. The nascent protein goes through two major interactions, first with the ribosome which synthesizes the polypeptide chain and holds it for a considerable length of time, and then with the chaperones. Some of the chaperones are found in solution as well as associated to the ribosome. A number of in vitro and in vivo experiments revealed that the nascent protein folds through specific interactions of some amino acids with the nucleotides in the peptidyl transferase center (PTC) in the large ribosomal subunit. The mechanism of this folding differs from self-folding. In this article, we highlight the folding of nascent proteins on the ribosome and the influence of chaperones etc. on protein folding.
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http://dx.doi.org/10.1002/biot.200800098DOI Listing
August 2008

Tbf1 or not Tbf1?

Mol Cell 2008 Mar;29(5):537-8

Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.

In this issue of Molecular Cell, Hogues et al. (2008) demonstrate a wholesale shift in the key regulatory protein involved in ribosomal protein (RP) synthesis during the evolution of S. cerevisiae and, en passant, raise interesting questions about the relationship between RP genes and telomeres.
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http://dx.doi.org/10.1016/j.molcel.2008.02.008DOI Listing
March 2008

Protein folding by domain V of Escherichia coli 23S rRNA: specificity of RNA-protein interactions.

J Bacteriol 2008 May 29;190(9):3344-52. Epub 2008 Feb 29.

University College of Science, Department of Biophysics, Molecular Biology and Genetics, 92 A.P.C. Road, Kolkata-700009, India.

The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in Escherichia coli domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme. The amino acids that interact with these nucleotides are also found to be specific in the two cases tested: bovine carbonic anhydrase and lysozyme. They are either neutral or positively charged and are present in random coils on the surface of the crystal structure of both the proteins. In fact, two of these amino acid-nucleotide pairs are identical in the two cases. How these features might help the process of protein folding is discussed.
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http://dx.doi.org/10.1128/JB.01800-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2347393PMC
May 2008

In vitro protein folding by E. coli ribosome: unfolded protein splitting 70S to interact with 50S subunit.

Biochem Biophys Res Commun 2008 Feb 7;366(2):598-603. Epub 2007 Dec 7.

Department of Biophysics, Molecular Biology and Genetics, University College of Science, 92 A.P.C. Road, Kolkata 700009, India.

Folding of unfolded protein on Escherichia coli 70S ribosome is accompanied by rapid dissociation of the ribosome into 50S and 30S subunits. The dissociation rate of 70S ribosome with unfolded protein is much faster than that caused by combined effect of translation and polypeptide release factors known to be involved in the dissociation of ribosome into subunits. The protein then reaches a "folding competent" state on 50S and is released to take up native conformation by itself. Release before attaining the folding competent state or prevention of release by cross-linking it with ribosome, would not allow the protein to get back to its native conformation.
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http://dx.doi.org/10.1016/j.bbrc.2007.11.143DOI Listing
February 2008

Protein folding following synthesis in vitro and in vivo: association of newly synthesized protein with 50S subunit of E. coli ribosome.

Biochem Biophys Res Commun 2008 Feb 4;366(2):592-7. Epub 2007 Dec 4.

Department of Biophysics, Molecular Biology and Genetics, University College of Science, 92 A.P.C. Road, Kolkata 700009, India.

In the accompanying paper, it was shown that a protein, while reverting to native form from the unfolded state in vitro with the help of bacterial 70S ribosome, split the latter into its subunits (50S and 30S) and remains associated with the 50S subunit. Here, we follow the fate of nascent proteins both in case of in vivo and in vitro translation system. The newly synthesised protein was found to associate with the 50S subunit in both the cases.
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http://dx.doi.org/10.1016/j.bbrc.2007.11.142DOI Listing
February 2008