Publications by authors named "Partha Pratim Das"

47 Publications

Characterizing miRNA and mse-tsRNA in fertile and subfertile yak bull spermatozoa from Arunachal Pradesh.

J Genet 2020 ;99

Gauhati University, Guwahati 781 014, India.

Male fertility in farm animals is considered as an important economic trait. The phenomenon of spermatogenesis plays a dynamic functional role in determining the viability of sperm and thereby can impact on fertility-driven complications. The process of spermatogenesis is controlled by numerous molecular factors and requires a precisely regulated pattern of gene expression. The role of small noncoding RNAs in altering gene expression has been extensively studied. However, limited information is available apropos their role in yak spermatogenesis. The present study aimed to evaluate the assessment of some significant microRNAs and their expression pattern in the body tissues and sperm of fertile and subfertile yak from Arunachal Pradesh besides identified a novel class of sperm enriched small RNA 'mature-sperm-enriched small RNA' (mse-tsRNA) in Yak spermatozoa. The RNAwas extracted from tissue and sperm using 27 gauge needles and subsequently reverse transcribed into small RNA cDNAs. The PCR positive sperm-predominant miRNAs were validated by quantitative reverse transcriptase PCR (qRT-PCR) for their expression in fertile and subfertile yak. Of the 22 microRNAs, the miRNA19a, miRNA142 and miRNA143 showed higher expression in the subfertile yak, whereas expression of miRNA7d, miRNA23a and miRNA23b were found elevated in the fertile animal. The presence of these small noncoding RNAs in yak sperm and testis indicated the legitimate involvement of their role in yak bull fertility.
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January 2020

Smart Self-Sensing Composite: Piezoelectric and Magnetostrictive FEA Modeling and Experimental Characterization Using Wireless Detection Systems.

Sensors (Basel) 2020 Dec 3;20(23). Epub 2020 Dec 3.

Department of Mechanical and Aerospace Engineering, University of Texas at Arlington, Arlington, TX 76019, USA.

This research work focuses on the development of a piezoelectric magnetostrictive smart composite with advanced sensing capability. The composite piezoelectric property is achieved from the dispersion of single-walled carbon nanotubes (SWCNTs) and the magnetostrictive property from Terfenol-D nanoparticles. Finite element analysis (FEA) is used to examine the feasibility of modelling the piezoelectric (change in electric field) and magnetostrictive (change in magnetic field) self-sensing responses in the presence of applied stress. The numerical work was coupled with a series of mechanical tests to characterize the piezoelectric response, magnetostriction response and mechanical strength. Tensile tests of the composite samples manufactured as is (virgin), samples with SWCNTs, samples with Terfenol-D nanoparticles and samples with both SWCNTs and Terfenol-D nanoparticles were conducted. It was observed that an increase in volume fraction of Terfenol-d nanoparticles increases the change in magnetization, therefore increasing voltage response up to the point of saturation. The optimum change in amplitude was observed with 0.35% volume fraction of Terfenol-D nanoparticles. A constant ratio of SWCNTs was maintained, and maximum change in electrical resistance was at 7.4%. Fracture toughness for the samples with all nanoparticles was explored, and the results showed improved resistance to crack propagation.
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http://dx.doi.org/10.3390/s20236906DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7729512PMC
December 2020

Study of the Microstructure of Amorphous Silica Nanostructures Using High-Resolution Electron Microscopy, Electron Energy Loss Spectroscopy, X-ray Powder Diffraction, and Electron Pair Distribution Function.

Materials (Basel) 2020 Oct 1;13(19). Epub 2020 Oct 1.

Institute of Technical Physics and Materials Science, Centre for Energy Research, 1121 Budapest, Hungary.

Silica has many industrial (i.e., glass formers) and scientific applications. The understanding and prediction of the interesting properties of such materials are dependent on the knowledge of detailed atomic structures. In this work, amorphous silica subjected to an accelerated alkali silica reaction (ASR) was recorded at different time intervals so as to follow the evolution of the structure by means of high-resolution transmission electron microscopy (HRTEM), electron energy loss spectroscopy (EELS), and electron pair distribution function (e-PDF), combined with X-ray powder diffraction (XRPD). An increase in the size of the amorphous silica nanostructures and nanopores was observed by HRTEM, which was accompanied by the possible formation of Si-OH surface species. All of the studied samples were found to be amorphous, as observed by HRTEM, a fact that was also confirmed by XRPD and e-PDF analysis. A broad diffuse peak observed in the XRPD pattern showed a shift toward higher angles following the higher reaction times of the ASR-treated material. A comparison of the EELS spectra revealed varying spectral features in the peak edges with different reaction times due to the interaction evolution between oxygen and the silicon and OH ions. Solid-state nuclear magnetic resonance (NMR) was also used to elucidate the silica nanostructures.
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http://dx.doi.org/10.3390/ma13194393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7579662PMC
October 2020

A saturating mutagenesis CRISPR-Cas9-mediated functional genomic screen identifies and regulatory elements of in murine ESCs.

J Biol Chem 2020 11 29;295(47):15797-15809. Epub 2020 Sep 29.

Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia

Regulatory elements (REs) consist of enhancers and promoters that occupy a significant portion of the noncoding genome and control gene expression programs either in or in Putative REs have been identified largely based on their regulatory features (co-occupancy of ESC-specific transcription factors, enhancer histone marks, and DNase hypersensitivity) in mouse embryonic stem cells (mESCs). However, less has been established regarding their regulatory functions in their native context. We deployed and regulatory elements scanning through saturating mutagenesis and sequencing (ctSCAN-SMS) to target elements within the ∼12-kb -region (REs; CREs) of the gene locus, as well as genome-wide 2,613 high-confidence REs (TREs), in mESCs. ctSCAN-SMS identified 10 CREs and 12 TREs as novel candidate REs of the gene in mESCs. Furthermore, deletions of these candidate REs confirmed that the majority of the REs are functionally active, and CREs are more active than TREs in controlling gene expression. A subset of active CREs and TREs physically interact with the promoter to varying degrees; specifically, a greater number of active CREs, compared with active TREs, physically interact with the promoter. Moreover, comparative genomics analysis reveals that a greater number of active CREs than active TREs are evolutionarily conserved between mice and primates, including humans. Taken together, our study demonstrates the reliability and robustness of ctSCAN-SMS screening to identify critical REs and investigate their roles in the regulation of transcriptional output of a target gene (in this case ) in their native context.
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http://dx.doi.org/10.1074/jbc.RA120.013772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7681025PMC
November 2020

Pressure-induced assemblies and structures of graphitic-carbon sheet encapsulated Au nanoparticles.

Nanoscale 2020 Aug;12(33):17462-17469

Department of Earth System Sciences, Yonsei University, Seoul 120749, Korea.

A novel strategy of using hydrostatic pressures to synthesize gold-carbon (Au-C) nanohybrid materials is explored. The stable face-centered-cubic (fcc) Au undergoes a structural phase transition to a mixture of primitive orthorhombic and cubic phases as the carbon phase acquires a highly ordered onion-like carbon (OLC) structure which encapsulates the Au nanoparticles, thereby exerting an additional pressure. Increasing the pressure results in a one dimensional (1-D) chain-like structure with the primitive cubic Au nanoparticles contained in an amorphous carbon matrix. The OLC structure allows the formation of quenchable Au nanoparticle phases with the primitive close packing and Au-C hybrids with new mesoscopic structures. Under pressure, we observe the formation of a hybrid material composed of a poorly conducting matrix made of amorphous carbon and conducting OLC-encapsulated Au nanoparticles. The electrical conductivity of this hybrid material under pressure reveals a percolation threshold. We present a new synthesis approach to explore the interplay between atomic and mesoscopic structures and the electrical conductivity of metal hybrid structures.
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http://dx.doi.org/10.1039/d0nr04443aDOI Listing
August 2020

Reliable Characterization of Organic & Pharmaceutical Compounds with High Resolution Monochromated EEL Spectroscopy.

Polymers (Basel) 2020 Jun 27;12(7). Epub 2020 Jun 27.

NanoMegas SPRL, Boulevard Edmond Machtens 79, B1080 Brussels, Belgium.

Organic and biological compounds (especially those related to the pharmaceutical industry) have always been of great interest for researchers due to their importance for the development of new drugs to diagnose, cure, treat or prevent disease. As many new API (active pharmaceutical ingredients) and their polymorphs are in nanocrystalline or in amorphous form blended with amorphous polymeric matrix (known as amorphous solid dispersion-ASD), their structural identification and characterization at nm scale with conventional X-Ray/Raman/IR techniques becomes difficult. During any API synthesis/production or in the formulated drug product, impurities must be identified and characterized. Electron energy loss spectroscopy (EELS) at high energy resolution by transmission electron microscope (TEM) is expected to be a promising technique to screen and identify the different (organic) compounds used in a typical pharmaceutical or biological system and to detect any impurities present, if any, during the synthesis or formulation process. In this work, we propose the use of monochromated TEM-EELS, to analyze selected peptides and organic compounds and their polymorphs. In order to validate EELS for fingerprinting (in low loss/optical region) and by further correlation with advanced DFT, simulations were utilized.
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http://dx.doi.org/10.3390/polym12071434DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7408036PMC
June 2020

De-Identification of Radiomics Data Retaining Longitudinal Temporal Information.

J Med Syst 2020 Apr 2;44(5):99. Epub 2020 Apr 2.

CSE, IIT Kharagpur, Kharagpur, India.

We propose a de-identification system which runs in a standalone mode. The system takes care of the de-identification of radiation oncology patient's clinical and annotated imaging data including RTSTRUCT, RTPLAN, and RTDOSE. The clinical data consists of diagnosis, stages, outcome, and treatment information of the patient. The imaging data could be the diagnostic, therapy planning, and verification images. Archival of the longitudinal radiation oncology verification images like cone beam CT scans along with the initial imaging and clinical data are preserved in the process. During the de-identification, the system keeps the reference of original data identity in encrypted form. These could be useful for the re-identification if necessary.
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http://dx.doi.org/10.1007/s10916-020-01563-0DOI Listing
April 2020

Crystallographic information data of natural occurring zaccariniite (RhNiAs) obtained by means of precession electron diffraction.

Data Brief 2019 Aug 2;25:104346. Epub 2019 Aug 2.

Department of Mineralogy, Petrology and Applied Geology, University of Barcelona, Marti i Franquès s/n, Barcelona, Catalunya, 08028, Spain.

The crystal structure of naturally occurring zaccariniite (RhNiAs) has been studied in Transmission Electron Microscopy (TEM) with variable angle Precession Electron Diffraction (PED) techniques. The analysis of the data has yielded tetragonal cell parameters of 3.86, 3.86, 6.77 Å and space group of P4/nmm for the basic structure, and its constituent atom positions for Ni, As and Rh were determined as well by ab-initio structure resolution method. The data is related to "Structural characterization and ab-initio resolution of natural occurring zaccariniite (RhNiAs) by means of Precession Electron Diffraction" (Roqué Rosell et al., 2019).
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http://dx.doi.org/10.1016/j.dib.2019.104346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6712965PMC
August 2019

High-Pressure Phase Transitions of Morphologically Distinct ZnSnO Nanostructures.

ACS Omega 2019 Jun 18;4(6):10539-10547. Epub 2019 Jun 18.

Department of Earth System Sciences, Yonsei University, Seoul 120749, Korea.

Many aspects of nanostructured materials at high pressures are still unexplored. We present here, high-pressure structural behavior of two ZnSnO nanomaterials with inverse spinel type, one a particle with size of ∼7 nm [zero dimensional (0-D)] and the other with a chain-like [one dimensional (1-D)] morphology. We performed in situ micro-Raman and synchrotron X-ray diffraction measurements and observed that the cation disordering of the 0-D nanoparticle is preserved up to ∼40 GPa, suppressing the reported martensitic phase transformation. On the other hand, an irreversible phase transition is observed from the 1-D nanomaterial into a new and dense high-pressure orthorhombic CaFeO-type structure at ∼40 GPa. The pressure-treated 0-D and 1-D nanomaterials have distinct diffuse reflectance and emission properties. In particular, a heterojunction between the inverse spinel and quenchable orthorhombic phases allows the use of 1-D ZnSnO nanomaterials as efficient photocatalysts as shown by the degradation of the textile pollutant methylene blue.
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http://dx.doi.org/10.1021/acsomega.9b01361DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6649287PMC
June 2019

Width dependence of the 0.5 × (2e/h) conductance plateau in InAs quantum point contacts in presence of lateral spin-orbit coupling.

Sci Rep 2019 Aug 21;9(1):12172. Epub 2019 Aug 21.

Department of Materials Science and Engineering, Kyushu Institute of Technology, Tobata-ku, Kitakyushu, 804-8550, Japan.

The evolution of the 0.5G (G = 2e/h) conductance plateau and the accompanying hysteresis loop in a series of asymmetrically biased InAs based quantum point contacts (QPCs) in the presence of lateral spin-orbit coupling (LSOC) is studied using a number of QPCs with varying lithographic channel width but fixed channel length. It is found that the size of the hysteresis loops is larger for QPCs of smaller aspect ratio (QPC channel width/length) and gradually disappears as their aspect ratio increases. The physical mechanisms responsible for a decrease in size of the hysteresis loops for QPCs with increasing aspect ratio are: (1) multimode transport in QPCs with larger channel width leading to spin-flip scattering events due to both remote impurities in the doping layer of the heterostructure and surface roughness and impurity (dangling bond) scattering on the sidewalls of the narrow portion of the QPC, and (2) an increase in carrier density resulting in a screening of the electron-electron interactions in the QPC channel. Both effects lead to a progressive disappearance of the net spin polarization in the QPC channel and an accompanying reduction in the size of the hysteresis loops as the lithographic width of the QPC channel increases.
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http://dx.doi.org/10.1038/s41598-019-48380-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6704071PMC
August 2019

Bacillus cereus-Attributable Primary Cutaneous Anthrax-Like Infection in Newborn Infants, India.

Emerg Infect Dis 2019 07;25(7):1261-1270

During March 13-June 23, 2018, anthrax-like cutaneous lesions attributed to the Bacillus cereus group of organisms developed in 12 newborns in India. We traced the source of infection to the healthcare kits used for newborn care. We used multilocus sequence typing to characterize the 19 selected strains from various sources in hospital settings, including the healthcare kits. This analysis revealed the existence of a genetically diverse population comprising mostly new sequence types. Phylogenetic analysis clustered most strains into the previously defined clade I, composed primarily of pathogenic bacilli. We suggest that the synergistic interaction of nonhemolytic enterotoxin and sphingomyelinase might have a role in the development of cutaneous lesions. The infection was controlled by removing the healthcare kits and by implementing an ideal housekeeping program. All the newborns recovered after treatment with ciprofloxacin and amikacin.
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http://dx.doi.org/10.3201/eid2507.181493DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590766PMC
July 2019

Identification and expression profiling of MSY genes of yak for bull fertility.

J Genet 2019 06;98(2)

Indian Council of Agricultural Research-National Research Centre on Yak, West Kameng, India.

Yak () is a unique bovine species and considered as lifeline of highlanders. The male subfertility in yak is a matter of concern that causes huge economic loses. The spermatogenesis and male reproduction machinery are critically governed by Y-linked genes which tend to acquire necessary information in the course of evolution. The Y-linked fertility genes are present in multiple copies with testis-limited expression. To understand this novel complexity, 12 male-specific region of Y chromosome (MSY) genes have been studied in the yak. Targeted genes are amplified in male and female genomic DNA and confirmed the male derived specificity. Moreover, testis and sperm-specific expressions of MSY genes are distinct among different tissues. The quantitative polymerase chain reaction results validate the expression pattern of these genes in various tissues with predominant expression intestis and sperm. The sequencing of resultant yak MSY genes gives significant result and shows similarity with cattle (), but few nucleotide mismatches define the proposition of infertile male in the F hybrid of cattle and yak. The identified MSY genes can be used to establish male-specific characteristics and to differentiate male and female yak genotypically. Further, these genes may act as valuable resources to understand the capacity of spermatogenesis, embryogenesis, cellular growth, azoospermia and malesubfertility in the yak.
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June 2019

TAF5L and TAF6L Maintain Self-Renewal of Embryonic Stem Cells via the MYC Regulatory Network.

Mol Cell 2019 06 17;74(6):1148-1163.e7. Epub 2019 Apr 17.

Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia. Electronic address:

Self-renewal and pluripotency of the embryonic stem cell (ESC) state are established and maintained by multiple regulatory networks that comprise transcription factors and epigenetic regulators. While much has been learned regarding transcription factors, the function of epigenetic regulators in these networks is less well defined. We conducted a CRISPR-Cas9-mediated loss-of-function genetic screen that identified two epigenetic regulators, TAF5L and TAF6L, components or co-activators of the GNAT-HAT complexes for the mouse ESC (mESC) state. Detailed molecular studies demonstrate that TAF5L/TAF6L transcriptionally activate c-Myc and Oct4 and their corresponding MYC and CORE regulatory networks. Besides, TAF5L/TAF6L predominantly regulate their target genes through H3K9ac deposition and c-MYC recruitment that eventually activate the MYC regulatory network for self-renewal of mESCs. Thus, our findings uncover a role of TAF5L/TAF6L in directing the MYC regulatory network that orchestrates gene expression programs to control self-renewal for the maintenance of mESC state.
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http://dx.doi.org/10.1016/j.molcel.2019.03.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6671628PMC
June 2019

Model Complexes for the Ni Site of Acetyl Coenzyme A Synthase/Carbon Monoxide (CO) Dehydrogenase: Structure, Electrochemistry, and CO Reactivity.

Inorg Chem 2018 Nov 19;57(21):13713-13727. Epub 2018 Oct 19.

Department of Chemistry , National Institute of Technology Durgapur , Mahatma Gandhi Avenue , Durgapur 713209 , India.

Aliphatic thiolato-S-bridged tri- and binuclear nickel(II) complexes have been synthesized and characterized as models for the Ni site of the A cluster of acetyl coenzyme A synthase (ACS)/carbon monooxide (CO) dehydrogenase. Reaction of the in situ formed NS donor ligands with [Ni(HO)](ClO) afforded the trinuclear complexes [Ni{(L)Ni}](ClO)·CHCN (1·CHCN) and [Ni{(L)Ni}](ClO)·5HO (2·5HO) following self-assembly. Complexes 1 and 2 react with [Ni(dppe)Cl] and dppe [dppe = 1,2-bis(diphenylphosphino)ethane] to afford the binuclear [Ni(dppe)Ni(L)](ClO)·2HO (3·2HO) and [Ni(dppe)Ni(L)](ClO)·0.75O(CH) [4·0.75O(CH)], respectively. The X-ray crystal structures of 1-4 revealed a central NiS moiety in 1 and 2 and a NiPS moiety in 3 and 4; both moieties have a square-planar environment around Ni and may mimic the properties of the Ni site of ACS. The electrochemical reduction of both terminal Ni ions of 1 and 2 occurs simultaneously, which is further confirmed by the isolation of [Ni{(L)Ni(NO)}](ClO) (5) and [Ni{(L)Ni(NO)}](ClO) (6) following reductive nitrosylation of 1 and 2. Complexes 5 and 6 exhibit ν at 1773 and 1789 cm, respectively. In the presence of O, both 5 and 6 transform to nitrite-bound monomers [(L)Ni(NO)](ClO) (7) and [(L)Ni(NO)](ClO) (8). The nature of the ligand modification is evident from the X-ray crystal structure of 7. To understand the origin of multiple reductive responses of 1-4, complex [(L)Ni](ClO) (9) is considered. The central NiS part of 1 is labile like the Ni site of ACS and can be replaced by phenanthroline. The treatment of CO to reduce 3 generates a 3-(CO) species, as confirmed by Fourier transform infrared (ν = 1997 and 2068 cm) and electron paramagnetic resonance ( g = 2.18, g = 2.13, g = 1.95, and A = 30-80 G) spectroscopy. The CO binding to Ni of 3 is relevant to the ACS activity.
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http://dx.doi.org/10.1021/acs.inorgchem.8b02276DOI Listing
November 2018

Cu(ii)-Bu-PHOX catalyzed enantioselective malonate addition onto 3-hydroxy 2-oxindoles: application in the synthesis of dimeric pyrroloindoline alkaloids.

Chem Commun (Camb) 2018 Jul;54(57):7963-7966

Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal - 462 066, Madhya Pradesh, India.

An efficient Cu(ii)-PHOX-catalyzed malonate addition onto 3-hydroxy 3-indolyl-2-oxindoles is envisioned to afford excellent enantioselectivities (up to >99% ee) in high chemical yields. Detailed characterization techniques including X-ray, NMR, CV and EPR experiments suggest that a Cu(ii)-complex is involved as an active species in this process. Applying this strategy, an advanced intermediate of cyclotryptamine alkaloids has been synthesized in few steps for a general approach to bis-cyclotryptamine alkaloids.
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http://dx.doi.org/10.1039/c8cc04338hDOI Listing
July 2018

Detection of p16 Promoter Hypermethylation by Methylation-Specific PCR.

Methods Mol Biol 2018 ;1726:111-122

Molecular Medicine Laboratory, Department of Biotechnology, Assam University, Silchar, Assam, India.

DNA methylation plays a decisive role in the regulation and control of gene expression. DNA methylation is a covalent modification, in which a methyl group is attached to the 5th carbon of the cytosine ring of a CpG dinucleotide that is located upstream from the promoter region of a gene. Promoter hypermethylation (gain of DNA methylation) of the p16 gene may cause silencing of gene expression and plays an important role in cancer. Therefore, detection of the methylation status of p16 gene is an important tool in epigenetic studies of various human cancers. The methylation-specific PCR (MSP) is the most commonly used technique for studying DNA methylation. This technique is based on bisulfite modification of DNA, which converts unmethylated cytosine (C) into uracil (U) and leaving methylated cytosine (C) unchanged. Here we describe the bisulfite modification of DNA samples and detection of promoter methylation of p16 gene from bisulfite-treated DNA using MSP. In MSP, modified DNA samples are subjected to PCR amplification using methylated and unmethylated specific primers for the p16 gene separately. The PCR amplified products are then analyzed in a 2.5-3% agarose gel containing ethidium bromide. The PCR amplified band generated by specific sets of primers is used to determine the methylation status of the p16 gene.
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http://dx.doi.org/10.1007/978-1-4939-7565-5_11DOI Listing
January 2019

Estimation of biofilm, proteinase & phospholipase production of the species isolated from the oropharyngeal samples in HIV-infected patients.

Indian J Med Res 2017 May;145(5):635-640

Department of Microbiology, Assam Medical College & Hospital, Dibrugarh, India.

Background & Objectives: Candida, the most common opportunistic infection in acquired immunodeficiency syndrome (AIDS), attributes its pathogenicity to its virulence factors, mainly the biofilms, the proteinases and the phospholipases. There is a significant interplay of these factors during the HIV infection. This study was aimed to estimate the biofilm, proteinase and phospholipase production in Candida species isolated from the oropharyngeal samples in the HIV-infected patients.

Methods: A total of 126 consecutive HIV-positive patients were screened for Candida growth using oropharyngeal swabs. Identification was done by Gram staining, germ tube test, chlamydospore identification, chromagar and biochemical tests on Vitek 2. Biofilm production was observed on Sabouraud's dextrose broth with glucose, phospholipase production in egg yolk agar medium and proteinase production in bovine serum albumin agar medium.

Results: Of a total of 126 patients, 53 (42.06%) showed Candida growth: Candida albicans (n=46, 86.8%) was most common followed by the non-albicans Candida (NAC) (n=7, 13.93%). Of a total 33 (62.3%) biofilm positive isolates, significant production was observed in the NAC species (P <0.05). C. albicans reported the highest phospholipase (n=37/41, 90.24%) and proteinase (n=37/43, 86%) activities in a total of 41 (77%) phospholipase positive and 43 (81.1%) proteinase positive isolates.

Interpretation & Conclusions: Although C. albicans was the most common Candida species identified in HIV positive patients, the emergence of NAC was of special concern. Virulence factors such as biofilms, proteinases and phospholipases were noted in both these groups. Further research is required for better understanding of the pathogenic role of Candida species so as to aid in therapeutic interventions.
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http://dx.doi.org/10.4103/ijmr.IJMR_1773_14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5644298PMC
May 2017

Use of Bacillus Subtilis PB6 as a potential antibiotic growth promoter replacement in improving performance of broiler birds.

Poult Sci 2017 Aug;96(8):2614-2622

West Bengal University of Animal and Fishery Sciences, India.

The intestinal gut health is one of the primary determinants of broiler growth and performance. Among the various enteric diseases, necrotic enteritis (NE) is an enterotoxemic disease caused by Clostridium perfringens, which can result in severe economic losses in poultry farming. Antibiotics like bacitracin methylene disalicylate (BMD) and avilamycin (AVL) are commonly used antibiotic growth promoters (AGP) in poultry feed to control necrotic enteritis in birds. Bacillus subtilis PB6 was reported to prevent necrotic enteritis and improve performance in birds. This paper investigated the influence of Bacillus subtilis PB6 in improving the performance of broiler birds in comparison with BMD and avilamycin. A 35 day trial was conducted with 240 day-old commercial broiler chicks (VenCobb 400), which were divided into four treatment groups, where each treatment group was composed of 6 replicates each containing 10 birds, for a total of 60 birds per treatment. The treatment groups included a negative control (no AGP), Bacillus subtilis PB6, BMD, and avilamycin. The parameters analyzed included body weight, feed conversion ratio (FCR), mortality, villus histomorphometry, and European efficiency factor (EEF). Bacillus subtilis PB6 significantly (P < 0.05) improved body weight and FCR (8 points) compared to the control. The group supplemented with B. subtilis PB6 or BMD had higher (P < 0.05) body weight compared to all other treatment groups. The supplementation of B. subtilis PB6 significantly improved the villus height (P < 0.05) compared to control and other AGP groups. The EEF was found to be the highest in the B. subtilis PB6 supplemented group at 35th day as compared to other treatment groups. The combined data from this study indicate that supplementation of B. subtilis PB6 improves overall performance of broilers compared to BMD and avilamycin, and can be used as potential AGP replacement in poultry farming.
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http://dx.doi.org/10.3382/ps/pex079DOI Listing
August 2017

Performance of colloidal CdS sensitized solar cells with ZnO nanorods/nanoparticles.

Beilstein J Nanotechnol 2017 23;8:210-221. Epub 2017 Jan 23.

Sensor and Actuator Division, CSIR - Central Glass and Ceramic Research Institute, Kolkata 700032, India; CSIR - Network Institute of Solar Energy (CSIR-NISE), New Delhi, India.

As an alternative photosensitizer in dye-sensitized solar cells, bovine serum albumin (BSA) (a nonhazardous protein) was used in the synthesis of colloidal CdS nanoparticles (NPs). This system has been employed to replace the commonly used N719 dye molecule. Various nanostructured forms of ZnO, namely, nanorod and nanoparticle-based photoanodes, have been sensitized with colloidal CdS NPs to evaluate their effective performance towards quantum dot sensitized solar cells (QDSSCs). A polysulphide (S )-based electrolyte and Cu S counter electrode were used for cell fabrication and testing. An interesting improvement in the performance of the device by imposing nanorods as a scattering layer on a particle layer has been observed. As a consequence, a maximum conversion efficiency of 1.06% with an open-circuit voltage () of 0.67 V was achieved for the ZnO nanorod/nanoparticle assembled structure. The introduction of ZnO nanorods over the nanoparticle led to a significant enhancement of the overall efficiency compared to the corresponding bare nanoparticles.
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http://dx.doi.org/10.3762/bjnano.8.23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5301656PMC
January 2017

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci.

Nat Genet 2017 Apr 20;49(4):625-634. Epub 2017 Feb 20.

Division of Hematology/Oncology, Boston Children's Hospital; Department of Pediatric Oncology, Dana-Farber Cancer Institute; Harvard Stem Cell Institute; and Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA.

Cas9-mediated, high-throughput, saturating in situ mutagenesis permits fine-mapping of function across genomic segments. Disease- and trait-associated variants identified in genome-wide association studies largely cluster at regulatory loci. Here we demonstrate the use of multiple designer nucleases and variant-aware library design to interrogate trait-associated regulatory DNA at high resolution. We developed a computational tool for the creation of saturating-mutagenesis libraries with single or multiple nucleases with incorporation of variants. We applied this methodology to the HBS1L-MYB intergenic region, which is associated with red-blood-cell traits, including fetal hemoglobin levels. This approach identified putative regulatory elements that control MYB expression. Analysis of genomic copy number highlighted potential false-positive regions, thus emphasizing the importance of off-target analysis in the design of saturating-mutagenesis experiments. Together, these data establish a widely applicable high-throughput and high-resolution methodology to identify minimal functional sequences within large disease- and trait-associated regions.
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http://dx.doi.org/10.1038/ng.3793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374001PMC
April 2017

Selective Binding of Genomic Escherichia coli DNA with ZnO Leads to White Light Emission: A New Aspect of Nano-Bio Interaction and Interface.

ACS Appl Mater Interfaces 2017 Jan 28;9(1):644-657. Epub 2016 Dec 28.

Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology , Kolkata-700032, India.

Here, we report for the first time, a novel and intriguing application of deoxyribonucleic acid (DNA) in the area of optics by demonstrating white light emission by tuning the emission of a nanomaterial, ZnO rods, exhibiting surface defects, in the presence of genomic Escherichia coli DNA with a comparatively high quantum efficiency. In order to understand the DNA specificity, we have also studied the interaction of ZnO with CT, and ML DNA, ss EC DNA, synthetic polynucleotides and different mononucleosides and bases. Further, in order to understand the effect of particle shape and defects present in ZnO, we have also extended our study with ZnO rods prepared at higher temperature exhibiting red emission and ZnO particles exhibiting yellow emission. Interestingly, none of the above studies resulted in white light emission from ZnO-DNA complex. Our studies unequivocally confirmed that the concentration and the nature of DNA and ZnO together plays a crucial role in obtaining CIE coordinates (0.33, 0.33) close to white light. The much enhanced melting temperature (T) of EC DNA and the energetics factors confirm enhanced hydrogen bonding of ZnO with EC DNA leading to a new emission band. Our experimental observations not only confirm the selective binding of ZnO to EC DNA but also open a new perspective for developing energy saving light emitting materials through nano-bio interactions.
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http://dx.doi.org/10.1021/acsami.6b11109DOI Listing
January 2017

Mixed valence copper-sulfur clusters of highest nuclearity: a Cu wheel and a Cu nanoball.

Chem Commun (Camb) 2017 Mar;53(23):3334-3337

Department of Chemistry, National Institute of Technology Durgapur, Durgapur 713 209, West Bengal, India.

Fully spin delocalized mixed valence copper-sulfur clusters, 1 and 2, supported by μ-sulfido and NS donor ligands are synthesized and characterized. Wheel shaped 1 consists of CuS units. The unprecedented nanoball 2 can be described as S@Cu(tetrahedron)@O(octahedron)@CuS(cage) consisting of both CuS and (μ-S)Cu units. The CuS and (μ-S)Cu units resemble biological Cu and Cu sites respectively.
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http://dx.doi.org/10.1039/c6cc08301cDOI Listing
March 2017

Recent Outbreaks of Diphtheria in Dibrugarh District, Assam, India.

J Clin Diagn Res 2016 Jul 1;10(7):DR01-3. Epub 2016 Jul 1.

Post Graduate Trainee, Department of Microbiology, Assam Medical College & Hospital , Assam, India .

Diphtheria is still a significant child health problem in countries with low immunization coverage. Reports of diphtheria in adult population are also increasing. Here we describe three recent outbreaks of diphtheria in Dibrugarh district, Assam in two consecutive years. The study was undertaken in Assam Medical College & Hospital, Dibrugarh after the diagnosis of two Diphtheria cases in the month of September and October 2015 and another in January 2016. Outbreak investigation was done after defining operational definition and throat swabs were collected from thirty three (33) individuals including three (3) index cases and thirty (30) close contacts. Diagnosis was done by clinical findings, direct microscopy, bacteriological culture and in-house designed multiplex Polymerase Chain Reaction (PCR) of the isolates for the expression of Corynebacterium diphtheriae specific rpoB gene and tox gene. Out of the 10 confirmed cases, 2 and 7 were in the first two outbreaks while only one in the third outbreak respectively. All the cases were of age > 10 years, unimmunized or partially immunized. The overall mortality was 20%. PCR results revealed all the culture positive isolates to be tox gene positive. Diphtheria is a resurgent problem in our region with a significant age shift towards adult.
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http://dx.doi.org/10.7860/JCDR/2016/20212.8144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5020183PMC
July 2016

Ultrafast Electron Diffraction Tomography for Structure Determination of the New Zeolite ITQ-58.

J Am Chem Soc 2016 08 8;138(32):10116-9. Epub 2016 Aug 8.

Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia , Piazza S. Silvestro 12, 56127 Pisa, Italy.

In this work a new ultrafast data collection strategy for electron diffraction tomography is presented that allows reducing data acquisition time by one order of magnitude. This methodology minimizes the radiation damage of beam-sensitive materials, such as microporous materials. This method, combined with the precession of the electron beam, provides high quality data enabling the determination of very complex structures. Most importantly, the implementation of this new electron diffraction methodology is easily affordable in any modern electron microscope. As a proof of concept, we have solved a new highly complex zeolitic structure named ITQ-58, with a very low symmetry (triclinic) and a large unit cell volume (1874.6 Å(3)), containing 16 silicon and 32 oxygen atoms in its asymmetric unit, which would be very difficult to solve with the state of the art techniques.
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http://dx.doi.org/10.1021/jacs.6b06394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5261824PMC
August 2016

Electron transfer mechanism of catalytic superoxide dismutation via Cu(ii/i) complexes: evidence of cupric-superoxo/-hydroperoxo species.

Dalton Trans 2016 Aug 7;45(29):11898-910. Epub 2016 Jul 7.

Department of Chemistry, National Institute of Technology Durgapur, Mahatma Gandhi Avenue, Durgapur 713209, West Bengal, India.

To understand the electron transfer mechanisms (outer versus inner sphere) of catalytic superoxide dismutation via a Cu(ii/i) redox couple such as occur in the enzyme copper-zinc superoxide dismutase, the Cu(ii/i) complexes [(L1)2Cu](ClO4)2·CH3CN, (1·CH3CN) and [(L1)2Cu](ClO4), (2) supported by a bis-N2Sthioether ligand, 2-pyridyl-N-(2'-methylthiophenyl)methyleneimine (L1) have been synthesized and structurally characterised. Both 1 and 2 display the same cyclic voltammogram (CV) featuring a quasireversible response at E1/2 = +0.33 V vs. SCE that falls in the SOD potential window of -0.04 V to +0.99 V. These complexes catalytically dismutate superoxide radicals at 298 K in aqueous medium (the IC50 for 1 is 2.15 μM). Electronic absorption spectra (233 K and 298 K), FTIR, ESI mass spectra, CV (233 K and 298 K) and DFT calculations collectively indicate formation of [(L1)2Cu(O2˙(-))](+), [(L1)2Cu(O2(2-))] and [(L1)2Cu(OOH(-))](+) species and help to elucidate the electron transfer mechanism for the SOD function of 1 and 2. Once O2˙(-) binds to Cu(II) (evident at 233 K), the first step of the catalytic cycle (Cu(II) + O2˙(-)→ Cu(I) + O2) does not follow but the second step (Cu(I) + O2˙(-) + 2H(+)→ H2O2 + Cu(II)) does follow. Therefore, the catalytic disproportionation of superoxide radicals via1 and 2 at 298 K indicates that the first and second steps of the catalytic cycle proceed through outer and inner sphere electron transfer mechanisms, respectively. Feasibility of the first step to occur in pure aprotic solvent (where 18-crown-6-ether is used to solubilise KO2) was tested and also supports the same notion of the electron transfer mechanisms as stated above.
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http://dx.doi.org/10.1039/c6dt02220kDOI Listing
August 2016

Species distribution & antifungal susceptibility pattern of oropharyngeal Candida isolates from human immunodeficiency virus infected individuals.

Indian J Med Res 2016 Apr;143(4):495-501

Regional Medical Research Centre (ICMR), Dibrugarh, India.

Background & Objectives: The changing spectrum of Candida species in causation of oropharyngeal candidiasis and their antifungal susceptibility pattern among the HIV infected individuals has made the identification to species level mandatory and detection of drug resistance necessary for patient care. The present study was carried out to determine the species distribution and antifungal susceptibility profile of oral Candida isolates colonizing or infecting both HIV seropositive and seronegative individuals.

Methods: A case-control study was conducted including 141 consecutive, non-repeat HIV-seropositive individuals and an equal number of sex and age matched HIV-seronegative control. Speciation of the oropharyngeal Candida isolates was done using standard yeast identification protocol. Antifungal susceptibility testing was done by the disk-diffusion method as well as by Fungitest method.

Results: From the 59 culture positive HIV seropositive cases, 61 Candida isolates were recovered; Candidaalbicans (n=47, 77.0%), C. dubliniensis (n=9, 14.7%), C. parapsilosis (n=2, 3.2%), C. glabrata (n=2, 3.2%), and C. famata (n=1, 1.6%). Candida colonization in HIV-seropositive individuals was significantly higher than that of HIV-seronegative (control) group. Antifungal susceptibility testing revealed (n=6, 9.3%) C. albicans isolates resistant to voriconazole and fluconazole by disk-diffusion method whereas no resistance was seen by Fungitest method.

Interpretation & Conclusions: C. albicans was the commonest Candida species infecting or colonizing HIV seropositive individuals. Oropharyngeal Candida isolates had high level susceptibility to all the major antifungals commonly in use. Increased level of immunosuppression in HIV-seropositives and drug resistance of non-albicans Candida species makes identification and susceptibility testing of Candida species necessary in different geographical areas of the country.
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http://dx.doi.org/10.4103/0971-5916.184288DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4928557PMC
April 2016

Paragonimiasis in a Child from Assam, India.

J Clin Diagn Res 2016 Apr 1;10(4):DD06-7. Epub 2016 Apr 1.

Associate Professor, Department of Microbiology, Assam Medical College & Hospital , Dibrugarh, Assam, India .

Paragonimiasis or lung fluke infection is one of the neglected tropical parasitic disease which is found worldwide. Several endemic foci have been discovered in the Northeast India. Pulmonary paragonimiasis presenting with haemoptysis is generally mistaken for pulmonary tuberculosis. Herein, we present a case of pulmonary paragonimiasis, which initially presented with haemoptysis and remained undiagnosed for two years. The patient was treated with Praziquantel 25mg/kg thrice daily for two days along with the supportive care. Subsequently, on follow up after three months the patient had improved with no fever and cough.
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http://dx.doi.org/10.7860/JCDR/2016/18160.7616DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866105PMC
April 2016

Enhanced stability of Zn2SnO4 with N719, N3 and eosin Y dye molecules for DSSC application.

Phys Chem Chem Phys 2016 Jan 23;18(3):1429-38. Epub 2015 Oct 23.

Sensor and Actuator Division, CSIR-Central Glass and Ceramic Research Institute, Kolkata 700032, India.

In view of the increased prospects of Zn2SnO4 as an alternative photoanode for dye sensitized solar cells (DSSCs), we synthesized phase pure Zn2SnO4 nanostructures by a cost effective sonochemical technique. In order to establish the stability of this alternative photoanode in DSSCs, we further explored the interaction of the synthesized Zn2SnO4 with commonly used photosensitizers in DSSCs, such as N3, N719 and eosin Y. Based on the time dependent optical studies we could establish the prominence of anchoring groups in controlling the dye loading. Optical studies confirmed an enhanced stable interaction of Zn2SnO4 with all the studied sensitizers which could be beneficial in designing DSSC devices in future. In addition, we also established contact angle measurement as an indirect tool to understand the surface characteristics and thereby optimize the dye loading and stability of the photoanode surface. With the help of contact angle data, we could unequivocally establish the stability of the Zn2SnO4 photoanode surface modified with N3 and N719 dye molecules. Our studies further suggest the enhanced and superior stability of the prepared Zn2SnO4 compared to ZnO in different chemical environments. The quenching of the fluorescence and the abrupt decrease in the contact angle owing to an increase in the surface roughness further strengthen the above conclusion. To our best knowledge, this probably is the first report on the synthesis of Zn2SnO4 by a sonochemical process and its interaction with various photosensitizers. An exceptionally high open circuit voltage of >0.8 V was observed for all the devices fabricated with the synthesized ZTO as a photoanode. Our studies could pave way to future developments in the area of DSSCs using Zn2SnO4 as a photoanode.
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http://dx.doi.org/10.1039/c5cp04716aDOI Listing
January 2016

PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells.

Cell Rep 2015 Sep 20;12(9):1456-70. Epub 2015 Aug 20.

Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute (DFCI), Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute (HHMI), Boston, MA 02115, USA. Electronic address:

Polycomb Repressive Complex 2 (PRC2) function and DNA methylation (DNAme) are typically correlated with gene repression. Here, we show that PRC2 is required to maintain expression of maternal microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) from the Gtl2-Rian-Mirg locus, which is essential for full pluripotency of iPSCs. In the absence of PRC2, the entire locus becomes transcriptionally repressed due to gain of DNAme at the intergenic differentially methylated regions (IG-DMRs). Furthermore, we demonstrate that the IG-DMR serves as an enhancer of the maternal Gtl2-Rian-Mirg locus. Further analysis reveals that PRC2 interacts physically with Dnmt3 methyltransferases and reduces recruitment to and subsequent DNAme at the IG-DMR, thereby allowing for proper expression of the maternal Gtl2-Rian-Mirg locus. Our observations are consistent with a mechanism through which PRC2 counteracts the action of Dnmt3 methyltransferases at an imprinted locus required for full pluripotency.
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http://dx.doi.org/10.1016/j.celrep.2015.07.053DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5384103PMC
September 2015