In-silico characterization and structure-based functional annotation of a hypothetical protein from Campylobacter jejuni involved in propionate catabolism

Mazumder, Lincon,Hasan, Mehedi,Rus’d, Ahmed Abu,Islam, Mohammad Ariful Korea Genome Organization 2021 Genomics & informatics Vol.19 No.4

Campylobacter jejuni is one of the most prevalent organisms associated with foodborne illness across the globe causing campylobacteriosis and gastritis. Many proteins of C. jejuni are still unidentified. The purpose of this study was to determine the structure and function of a non-annotated hypothetical protein (HP) from C. jejuni. A number of properties like physiochemical characteristics, 3D structure, and functional annotation of the HP (accession No. CAG2129885.1) were predicted using various bioinformatics tools followed by further validation and quality assessment. Moreover, the protein-protein interactions and active site were obtained from the STRING and CASTp server, respectively. The hypothesized protein possesses various characteristics including an acidic pH, thermal stability, water solubility, and cytoplasmic distribution. While alpha-helix and random coil structures are the most prominent structural components of this protein, most of it is formed of helices and coils. Along with expected quality, the 3D model has been found to be novel. This study has identified the potential role of the HP in 2-methylcitric acid cycle and propionate catabolism. Furthermore, protein-protein interactions revealed several significant functional partners. The in-silico characterization of this protein will assist to understand its molecular mechanism of action better. The methodology of this study would also serve as the basis for additional research into proteomic and genomic data for functional potential identification.

Hydroxycoumarin OT-55 kills CML cells alone or in synergy with imatinib or Synribo: Involvement of ER stress and DAMP release

Mazumder, Aloran,Lee, Jin-Young,Talhi, Oualid,Cerella, Claudia,Chateauvieux, Sé,bastien,Gaigneaux, Anthoula,Hong, Che Ry,Kang, Hyoung Jin,Lee, Youngjo,Kim, Kyu-Won,Kim, Dong-Wook,Shin, Hee-Young Elsevier 2018 Cancer letters Vol.438 No.-

<P><B>Abstract</B></P> <P>We synthetized and investigated the anti-leukemic potential of the novel cytostatic bis(4-hydroxycoumarin) derivative OT-55 which complied with the Lipinski's rule of 5 and induced differential toxicity in various chronic myeloid leukemia (CML) cell models. OT-55 triggered ER stress leading to canonical, caspase-dependent apoptosis and release of danger associated molecular patterns. Consequently, OT-55 promoted phagocytosis of OT-55-treated CML cells by both murine and human monocyte-derived macrophages. Moreover, OT-55 inhibited tumor necrosis factor α-induced activation of nuclear factor-кB and produced synergistic effects when used in combination with imatinib to inhibit colony formation <I>in vitro</I> and Bcr-Abl<SUP>+</SUP> patient blast xenograft growth in zebrafish. Furthermore, OT-55 synergized with omacetaxine in imatinib-resistant KBM-5 R cells to inhibit the expression of Mcl-1, triggering apoptosis. In imatinib-resistant K562 R cells, OT-55 triggered necrosis and blocked tumor formation in zebrafish in combination with omacetaxine.</P> <P><B>Highlights</B></P> <P> <UL> <LI> OT-55 inhibits cell proliferation and viability in CML. </LI> <LI> OT-55 induces ER stress, ecto-CRT, ecto-ERp57, ATP and HMGB1 elease leading to immunogenic cell death. </LI> <LI> OT-55-treated CML cells are phagocytosed by macrophages. </LI> <LI> OT-55 synergizes with imatinib in CML. </LI> <LI> OT-55 synergizes with Synribo in Bcr-Abl mutated CML. </LI> </UL> </P>

Investigation of the optical potentials for the 40Ca(α,t)41Sc reaction at 40 MeV

Mazumder U. K.,Somadder A.,Hoque E.,Das S. K. 한국물리학회 2022 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.80 No.7

The 40Ca(α,t)41Sc reaction has been studied at a 40 MeV incident energy. The angular distributions of the eight states of the reaction are analyzed using the full finite-range (FFR) distorted-wave Born approximation (DWBA) for both the bound and the unbound states of the 41Sc nucleus using the normal optical, Michel and molecular potentials. The spectroscopic factors that have been extracted for the three optical potentials are compared with the previous local zero-range (LZR) and local finite-range (LFR) calculations of the 40Ca(α,t)41Sc reaction for the normal optical potential. The χ2 values of all the potentials for different l transfers are calculated to estimate the quality of fits. The present analysis shows that the Michel and the molecular potentials fit the data more satisfactorily than the normal optical potential.

In situ CCVD synthesis of carbon nanotubes within zeolite crystal coated porous ceramic foam

MAZUMDER, Sangram,ZHAO, Wei,PARK, Jung Gyu,SARKAR, Naboneeta,KIM, Sukyoung,KIM, Ik Jin CERAMIC SOC OF JAPAN 2015 JOURNAL- CERAMIC SOCIETY JAPAN Vol.123 No.1438

<P>In this study, consolidated zeolite crystal coated porous ceramic foams containing a large quantity of carbon nanotubes (CNTs) within micro-metre sized pores were prepared. An alumina-silica porous ceramic body, having an average pore size of less than 100 mu m, was produced by the direct foaming technique. Well-shaped zeolite crystals having an average size of 180 nm were synthesized and homogeneously coated on the porous ceramic body by an in situ process. An Fe-supported zeolite/ceramic matrix, which is used for CNT synthesis, was prepared using ion-exchange by immersing the zeolite-coated porous ceramic body into FeCl2 aqueous solution. The CNTs were synthesized by a catalytic chemical vapour deposition (CCVD) process for four different reaction times. Both acicular-shaped and randomly bundled networks of multi-walled carbon nanotubes (MWCNTs) were synthesized using these different reaction times. Moreover, the yield of CNTs produced showed a tendency to increase with increasing reaction time. (C)2015 The Ceramic Society of Japan. All rights reserved.</P>

Evaluation of in vitro antioxidant activities of the methanol extracts of Glinus oppositifolius and Trianthema decandra

Mazumder, Upal Kanti,Gupta, Malaya,Haldar, Pallab Kanti,Kandar, Chandi Charan Kyung Hee Oriental Medicine Research Center 2007 Oriental pharmacy and experimental medicine Vol.7 No.3

Glinus oppositifolius and Trianthema decandra belonging to the Ficoidaceae family were commonly used by tribal peoples for the treatment of liver disorders and cancer. The preliminary phytochemical screening of those plants showed the presence of flavonoids, terpenoids, tannins and saponins. The aim of this study was to evaluate the in vitro antioxidant activities of the methanol extracts of Glinus oppositifolius (MEGO) and Trianthema decandra (METD). The antioxidative capacities of MEGO and METD were determined by the following four complementary assay; DPPH radical scavenging assay, superoxide anion generation by xanthine-xanthine Oxidase assay, hydroxyl radical scavenging assay and $Fe^{2+}$-ascorbate induced by lipid peroxidation assay. The $IC_{50}$ values of the both extracts were calculated from the inhibition curve. The $IC_{50}$ MEGO and METD in DPPH, superoxide anion, hydroxyl radical scavenging and lipid peroxidation assay are 1.85, 7.31, 13.95, 22.82 and 2.21, 9.78, 14.87, 19.76 ${\mu}g/ml$ respectively. Both the extracts exhibited a significant antioxidant effects.

Effect of Levels of Concentrate Supplement on Live Weight Gain and Carcass Characteristics in Sheep on Restricted Grazing

Mazumder, M.A.R.,Hossain, M.M.,Akhter, S. Asian Australasian Association of Animal Productio 1998 Animal Bioscience Vol.11 No.1

Sixteen local sheep (8 male + 8 female) of about six months old with average live weight 10.78 $({\pm}1.11)$ kg were allocated into four treatments. The treatments (T) are : $T_0$ = Restricted grazing without concentrate; $T_1$, $T_2$ and $T_3$ = Grazing + 100, 200 and 300 g concentrate per sheep daily. Live weight of grazing (7.30 hrs daily) sheep was recorded in each week. The uncastrated male sheep were slaughtered for carcass and non-carcass parameters. Statistically significant (p < 0.05) differences were observed in live weight gain (g/day) among the treatments ($T_0=15.71$; $T_1=22.66$; $T_2 =32.66$ and $T_3=40.47$). The dressing % were : ($T_0=32.75$, $T_1=38.50$, $T_2=36.90 $ and $T_3=37.75$). The warm carcass weight represented 37.21% of live weight. Significant (p < 0.01) correlation were observed for live weight with carcass weight (r = 0.99) and dressing % (r = 0.88). Concentrate supplement increase live weight gain in sheep on grazing. Live weight is a good indicator to assess carcass characteristics.

Natural scaffolds in anticancer therapy and precision medicine

Mazumder, Aloran,Cerella, Claudia,Diederich, Marc Elsevier 2018 BIOTECHNOLOGY ADVANCES Vol.36 No.6

<P>The diversity of natural compounds is essential for their mechanism of action. The source, structures and structure activity relationship of natural compounds contributed to the development of new classes of chemotherapy agents for over 40 years. The availability of combinatorial chemistry and high-throughput screening has fueled the challenge to identify novel compounds that mimic natures chemistry and to predict their macromolecular targets. Combining conventional and targeted therapies helped to successfully overcome drug resistance and prolong disease-free survival. Here, we aim to provide an overview of preclinical investigated natural compounds alone and in combination to further improve personalization of cancer treatment.</P>

SEM and ESEM techniques used for analysis of asphalt binder and mixture: A state of the art review

Mazumder, Mithil,Ahmed, Raju,Wajahat Ali, Ahmed,Lee, Soon-Jae Elsevier 2018 Construction and Building Materials Vol.186 No.-

<P><B>Abstract</B></P> <P>This paper reviews techniques and analyses performed on microstructure of the asphalt binder and mixture using Scanning Electron Microscopy (SEM) and Environmental Scanning Electron Microscopy (ESEM). An extensive insight on the SEM and ESEM principle and techniques, different sample preparation methods and instrument techniques for capturing the micromorphology of the binder and mixture have been presented. The difference between SEM and ESEM in terms of challenges and limitation regarding the analysis of bitumen has been explained. In depth discussions on the surface properties, fracture morphology, network structure, dispersion, phase morphology, structural and strength mechanism, adhesion, deform mechanism and the formation of fibril structures of asphalt binder and mixture have been provided. Recommendations and useful techniques are outlined for future research to obtain any correlation between the microstructure and physical/rheological properties of the asphalt binder/mixture.</P> <P><B>Highlights</B></P> <P> <UL> <LI> This paper reviews techniques and analyses performed on microstructure of the asphalt binder and mixture using Scanning Electron Microscopy (SEM) and Environmental Scanning Electron Microscopy (ESEM). </LI> <LI> The principle and techniques of SEM and ESEM, different sample preparation methods, used instrument techniques for different binder and mixture types, limitation of instrument and their effects on network structure, deformation mechanism, dispersion, phase and formation of fibril structures are discussed in this paper. </LI> </UL> </P>

Effect of Mg doping on the electrical properties of SnO2 nanoparticles

N. Mazumder,A. Bharati,S. Saha,D. Sen,K.K. Chattopadhyay 한국물리학회 2012 Current Applied Physics Vol.12 No.3

Sol-gel derived Mg doped tin oxide (Sn1-xMgxO2) nanocrystals were synthesized with x ranging between 0.5 and 7 at. %. Characteristic single phase tetragonal structure of pure and doped samples was obtained and doping saturation was inferred by X-ray diffraction analysis. Structural, morphological and phase informations were obtained by high resolution transmission electron microscope, field emission scanning electron microscope and X-ray photoelectron spectroscopy respectively whereas bonding information was obtained from Fourier transformed infrared spectroscopy. Measurement of different electrical parameters with frequency (200 Hze105 Hz) has been carried out at room temperature. Ultrahigh dielectric constant and metallic AC conductivity were observed for undoped tin oxide and the profiles reflected highly sensitive changes in the atomic and interfacial polarizability generated by doping concentrations. Relaxation spectra of tangent loss of any sample did not show any loss peak within the frequency range. Both the grain and grain boundary contributions are observed to increase as the doping concentration increased. Results of first principle calculation based on density functional theory indicated effective Fermi level (EF) suppression due to Mg doping which is responsible for the experimentally observed conductivity variation. AC conductivity was found to depend strongly on the doping concentration and the defect chemistry of the compound. Mg doped SnO2 may find applications as a low loss dielectric and high density energy storage material. Sol-gel derived Mg doped tin oxide (Sn1-xMgxO2) nanocrystals were synthesized with x ranging between 0.5 and 7 at. %. Characteristic single phase tetragonal structure of pure and doped samples was obtained and doping saturation was inferred by X-ray diffraction analysis. Structural, morphological and phase informations were obtained by high resolution transmission electron microscope, field emission scanning electron microscope and X-ray photoelectron spectroscopy respectively whereas bonding information was obtained from Fourier transformed infrared spectroscopy. Measurement of different electrical parameters with frequency (200 Hze105 Hz) has been carried out at room temperature. Ultrahigh dielectric constant and metallic AC conductivity were observed for undoped tin oxide and the profiles reflected highly sensitive changes in the atomic and interfacial polarizability generated by doping concentrations. Relaxation spectra of tangent loss of any sample did not show any loss peak within the frequency range. Both the grain and grain boundary contributions are observed to increase as the doping concentration increased. Results of first principle calculation based on density functional theory indicated effective Fermi level (EF) suppression due to Mg doping which is responsible for the experimentally observed conductivity variation. AC conductivity was found to depend strongly on the doping concentration and the defect chemistry of the compound. Mg doped SnO2 may find applications as a low loss dielectric and high density energy storage material.

Formulation of an ovarian cancer vaccine with the squalene-based AddaVax adjuvant inhibits the growth of murine epithelial ovarian carcinomas

Suparna Mazumder,Valerie Swank,Nina Dvorina,Justin M. Johnson,Vincent K. Tuohy 대한백신학회 2022 Clinical and Experimental Vaccine Research Vol.11 No.2

Purpose: Epithelial ovarian carcinoma (EOC) is the most lethal of all human gynecologic malignancies. We previously reported that vaccination of female mice with the extracellular domain of anti-Müllerian hormone receptor II (AMHR2-ED) in complete Freund’s adjuvant (CFA) generates AMHR2-ED specific immunoglobulin G (IgG) that provides prevention and therapy against murine EOCs. Although CFA is the “gold standard” adjuvant in animal studies, it is not approved for human use because it often induces painful granulomas and abscesses. Thus, the objective of this study is to identify an alternative adjuvant to CFA for use in our ovarian cancer vaccine clinical trials. Materials and Methods: Because it has been used successfully without serious adverse effects in numerous human clinical trials, we selected the IgG-inducing squalene-based adjuvant, AddaVaxTM, for evaluation of its ability to facilitate vaccine-induced prevention and treatment of EOC in mice. To this end, we immunized female C57BL/6 mice with recombinant mouse AMHR2-ED emulsified with either AddaVax or CFA as adjuvant and compared the results. Results: We found that formulation of the AMHR2-ED vaccine with AddaVax adjuvant induced high serum titers of IgG and significant inhibition of EOC growth with significantly enhanced overall survival of mice using both prevention and therapeutic protocols. These results were compared favorably with results obtained using CFA as an adjuvant in the AMHR2-ED vaccine. Conclusion: Our data indicate that the AMHR2-ED vaccine formulated with AddaVax may be used in human clinical trials and thereby serve as a novel and effective way to control human EOC.