Browsing by Author "Ince, Ikbal Agah"

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Arthrobacter pityocampae sp nov., isolated from Thaumetopoea pityocampa (Lep., Thaumetopoeidae)
(MICROBIOLOGY SOC, 2014-01-01) Ince, Ikbal Agah; Demirbag, Zihni; Kati, Hatice
A bacterium (strain Tp2(T)) was isolated from a caterpillar of the pine processionary moth, Thaumetopoea pityocampa (Den. \& Schiff.) (Lepidoptera: Thaumetopoeidae), a destructive pine forest pest. The bacterium is a Gram-stain-positive, red-pigmented coccus, oxidase-negative, nitrate-reducing, non-motile and non-spore-forming. Strain Tp2(T) was subjected to a taxonomic study using polyphasic approach that included morphological and biochemical characterizations, 16S rRNA gene sequence analysis, DNA DNA hybridization, DNA G + C content analysis, comparative fatty acid profiles, and analyses of quinones and polar lipids. The 16S rRNA gene sequence of strain Tp2(T) revealed that Arthrobacter agilis DSM 20550(T) was the closest known strain (98\% 16S rRNA gene sequence similarity). DNA DNA hybridization of A. agilis DSM 20550(T) and strain Tp2(T) resulted in a DNA DNA relatedness value of 11.9\% (20.2\% reciprocal). The DNA base composition of strain Tp2(T) was 69.5 mol\%, which is consistent with the other recognized members of Actinobacteria that have a high G+C content in their genome. The polar lipid pattern of strain Tp2(T) consisted of diphosphatidylglycerol (major), phosphatidylglycerol and phosphatidylinositol and unknown glycolipids. The cellular fatty acids were anteiso C-15:0 and anteiso 0170 and the major menaquinone was MK-9(II-H-2). The peptidoglycan type was A3 alpha with an L-Lys L-Thr L-Ala(3) interpeptide bridge. The above-mentioned characterization qualifies strain Tp2(T) as genotypically and phenotypically distinct from closely related species of the genus Arthrobacter with validly published names. Strain Tp2(T) is therefore proposed to represent a novel species of the genus Arthrobacter, described as Arthrobacter pityocampae sp. nov. The type strain is Tp2(T) (=DSM 21719(T)=NCCB 100254(T)).
Bio-molecule functionalized rapid one-pot green synthesis of silver nanoparticles and their efficacy toward the multidrug resistant (MDR) gut bacteria of silkworms (Bombyx mori)
(ROYAL SOC CHEMISTRY, 2020-01-01) Some, Sudip; Sarkar, Biraj; Biswas, Kinkar; Jana, Tushar Kanti; Bhattacharjya, Debjoy; Dam, Paulami; Mondal, Rittick; Kumar, Anoop; Deb, Apurba Kanti; Sadat, Abdul; Saha, Soumen; Kati, Ahmet; Ocsoy, Ismail; Franco, Octavio L.; Mandal, Amitava; Mandal, Sukhendu; Mandal, Amit Kumar; Ince, Ikbal Agah
The present study aimed to synthesise bio-molecule functionalized silver nanoparticles (AgNPs) using leaf extract from mulberry variety S-1635 (Morus albaL.) and to explore its antibacterial efficacy against multidrug resistant (MDR) gut bacteria isolated from natural infection observed from silkworm larvae in rearing conditions. AgNPs formation was established by surface plasmon resonance at 480 nm. The crystallinity of the synthesised AgNPs was checked by HR-TEM and XRD analysis. SEM and TEM characterisation further exhibited the spherical, monodispersed, well scattered nature of the AgNPs with an average particle size of 11.8 nm +/- 2.8. The presence of (111), (200), (220) and (311) planes in Bragg's reflections confirmed the face-cantered-cubic crystalline silver. EDX analysis confirmed the presence of elemental silver. FT-IR spectra revealed functional groups were responsible for the reduction of silver ions. The zeta potential value of -17.3 mV and -25.6 mV was recorded in MH and DMEM/F-12 media, respectively. The LC-QTOF/MS and HRMS spectra disclosed the presence of bioactive compounds like flavonoid, gallic acid, and stigmasterol, which are probably involved in the reduction and functionalization of AgNPs. The antibacterial efficacy of bio-molecule functionalized AgNPs and the naked AgNPs was tested on Gram-positive and Gram-negative bacteria isolated from silkworms and characterized by using 16S rDNA andgyrBgenes. The cytotoxicity of AgNPs was tested on WRL-68, HEK-293, ACHN, and HUH-7 cell lines using MTT assay. This study provides an insight into the application of bio-molecule functionalized AgNPs for combating various silkworm pathogens which severely affect the agro-rural economy of developing countries.
Comparative Analysis of Salivary Gland Proteomes of Two Glossina Species that Exhibit Differential Hytrosavirus Pathologies
(FRONTIERS MEDIA SA, 2016-01-01) Kariithi, Henry M.; Ince, Ikbal Agah; Boeren, Sjef; Murungi, Edwin K.; Meki, Irene K.; Otieno, Everlyne A.; Nyanjom, Steven R. G.; van Oers, Monique M.; Vlak, Just M.; Abd-Alla, Adly M. M.
Glossina pallidipes salivary gland hypertrophy virus (GpSGHV
Comprehensive annotation of Glossina pallidipes salivary gland hypertrophy virus from Ethiopian tsetse flies: a proteogenomics approach
(MICROBIOLOGY SOC, 2016-01-01) Abd-Alla, Adly M. M.; Kariithi, Henry M.; Cousserans, Franc Ois; Parker, Nicolas J.; Ince, Ikbal Agah; Scully, Erin D.; Boeren, Sjef; Geib, Scott M.; Mekonnen, Solomon; Vlak, Just M.; Parker, Andrew G.; Vreysen, Marc J. B.; Bergoin, Max
Glossina pallidipes salivary gland hypertrophy virus (GpSGHV
Effect of feed supplementation with biosynthesized silver nanoparticles using leaf extract of Morus indica L. V1 on Bombyx mori L. (Lepidoptera: Bombycidae)
(NATURE PORTFOLIO, 2019-01-01) Some, Sudip; Bulut, Onur; Biswas, Kinkar; Kumar, Anoop; Roy, Anupam; Sen, Ipsita Kumar; Mandal, Amitava; Franco, Octavio L.; Ince, Ikbal Agah; Neog, Kartik; Das, Sandip; Pradhan, Sayantan; Dutta, Subhadeep; Bhattacharjya, Debjoy; Saha, Soumen; Das Mohapatra, Pradeep K.; Bhuimali, Anil; Unni, B. G.; Kati, Ahmet; Mandal, Amit Kumar; Yilmaz, M. Deniz; Ocsoy, Ismail
Herein, we report the synthesis of silver nanoparticles (AgNPs) by a green route using the aqueous leaf extract of Morus indica L. V1. The synthesized AgNPs exhibited maximum UV-Vis absorbance at 460 nm due to surface plasmon resonance. The average diameter (similar to 54 nm) of AgNPs was measured from HR-TEM analysis. EDX spectra also supported the formation of AgNPs, and negative zeta potential value (-14 mV) suggested its stability. Moreover, a shift in the carbonyl stretching (from 1639 cm(-1) to 1630 cm(-1)) was noted in the FT-IR spectra of leaf extract after AgNPs synthesis which confirm the role of natural products present in leaves for the conversion of silver ions to AgNPs. The four bright circular rings (111), (200), (220) and (311) observed in the selected area electron diffraction pattern are the characteristic reflections of face centered cubic crystalline silver. LC-MS/MS study revealed the presence of phytochemicals in the leaf extract which is responsible for the reduction of silver ions. MTT assay was performed to investigate the cytotoxicity of AgNPs against two human cell lines, namely HepG2 and WRL-68. The antibacterial study revealed that MIC value of the synthesized AgNPs was 80 mu g/ml against Escherichia coli K12 and Staphylococcus aureus (MTCC 96). Finally, the synthesized AgNPs at 10 mu g/ml dosages showed beneficial effects on the survivability, body weights of the Bombyx mori L. larvae, pupae, cocoons and shells weights via enhancing the feed efficacy.
Enhancing vector refractoriness to trypanosome infection: achievements, challenges and perspectives
(BMC, 2018-01-01) Kariithi, Henry M.; Meki, Irene K.; Schneider, Daniela I.; De Vooght, Linda; Khamis, Fathiya M.; Geiger, Anne; Demirbas-Uzel, Guler; Vlak, Just M.; Ince, Ikbal Agah; Kelm, Sorge; Njiokou, Flobert; Wamwiri, Florence N.; Malele, Imna I.; Weiss, Brian L.; Abd-Alla, Adly M. M.
With the absence of effective prophylactic vaccines and drugs against African trypanosomosis, control of this group of zoonotic neglected tropical diseases depends the control of the tsetse fly vector. When applied in an area-wide insect pest management approach, the sterile insect technique (SIT) is effective in eliminating single tsetse species from isolated populations. The need to enhance the effectiveness of SIT led to the concept of investigating tsetse-trypanosome interactions by a consortium of researchers in a five-year (2013-2018) Coordinated Research Project (CRP) organized by the Joint Division of FAO/IAEA. The goal of this CRP was to elucidate tsetse-symbiome-pathogen molecular interactions to improve SIT and SIT-compatible interventions for trypanosomoses control by enhancing vector refractoriness. This would allow extension of SIT into areas with potential disease transmission. This paper highlights the CRP's major achievements and discusses the science-based perspectives for successful mitigation or eradication of African trypanosomosis.
Genomic Clues of a Multidrug-Resistant Bacterium from Cultured Domestic Silkworm (Bombyx mori L.)
(AMER SOC MICROBIOLOGY, 2022-01-01) Mandal, Amit Kumar; Sarkar, Biraj; Mandal, Hrisikesh; Chakraborty, Arka Pratim; Das Mohapatra, Pradeep Kumar; Dam, Paulami; Mondal, Rittick; Some, Sudip; Sadat, Abdul; Ghati, Amit; Neog, Kartik; Mandal, Sukhendu; Ince, Ikbal Agah
Enterobacter sp. strain ASE was isolated from the gut of an infected domestic silkworm (Bombyx mori L
Hairpin structures with conserved sequence motifs determine the 3 ` ends of non-polyadenylated invertebrate iridovirus transcripts
(ACADEMIC PRESS INC ELSEVIER SCIENCE, 2017-01-01) Ince, Ikbal Agah; Pijlman, Gorben P.; Vlak, Just M.; van Oers, Monique M.
Previously, we observed that the transcripts of Invertebrate iridescent virus 6 (IIV6) are not polyadenylated, in line with the absence of canonical poly(A) motifs (AATAAA) downstream of the open reading frames (ORFs) in the genome. Here, we determined the 3' ends of the transcripts of fifty-four IIV6 virion protein genes in infected Drosophila Schneider 2 (52) cells. By using ligation-based amplification of cDNA ends (LACE) it was shown that the IIV6 mRNAs often ended with a CAUUA motif. In silico analysis showed that the 3'-untranslated regions of IIV6 genes have the ability to form hairpin structures (22-56 nt in length) and that for about half of all IIV6 genes these 3' sequences contained complementary TAATG and CATTA motifs. We also show that a hairpin in the 3' flanking region with conserved sequence motifs is a conserved feature in invertebrate-infecting iridoviruses (genus Iridovirus and Chloriridovirus).
Insecticide-releasing LLDPE films as greenhouse cover materials
(ELSEVIER, 2019-01-01) Seven, Senem Avaz; Tastan, Omer Faruk; Tas, Cuneyt Erdinc; Unal, Hayriye; Ince, Ikbal Agah; Menceloglu, Yusuf Ziya
The use of chemical pesticides is limited by several public health concerns regarding their toxicity levels and indiscriminate use. Nevertheless, they are still vital components of agricultural industry since no other competitive equivalents to chemical pesticides still exist in terms of efficiency. This study describes the preparation and biological assessment of an insecticide releasing plastic film for agricultural covering purposes. The formulation was prepared by incorporation of deltamethrin loaded, nano-sized halloysite nanotubes into polymeric films. Thermal, morphological, and mechanical properties of films were characterized by Differential Scanning Calorimetry (DSC), Scanning Electron Microscopy (SEM) and Universal Testing Machine UTM. Sustained release profiles of the films were evaluated by Thermogravimetric Analysis (TGA). Results reveal that deltamethrin was successfully loaded into halloysite nanotubes and nanotube incorporation enhances the elastic modulus of linear-low density polyethylene (LLDPE) films. In addition, films exhibit sustained release function of the active agent for 60 days. Bioassays of the nanocomposite films with varying deltamethrin doses tested on grasshoppers showed that the LD(50 )values of the films are 1.85x10(-5) g/cm(2). Insecticidal activities of films were tested in greenhouse on Medicago Saliva plants contaminated with thrips and aphid. Nanocomposites are observed to repel mature aphids and kill young aphids and thrips.
Invertebrate Iridoviruses: A Glance over the Last Decade
(MDPI, 2018-01-01) Ince, Ikbal Agah; Ozcan, Orhan; Ilter-Akulke, Ayca Zeynep; Scully, Erin D.; Ozgen, Arzu
Members of the family Iridoviridae (iridovirids) are large dsDNA viruses that infect both invertebrate and vertebrate ectotherms and whose symptoms range in severity from minor reductions in host fitness to systemic disease and large-scale mortality. Several characteristics have been useful for classifying iridoviruses
Study of epidemiological behaviour of malaria and its control in the Purulia district of West Bengal, India (2016-2020)
(NATURE PORTFOLIO, 2022-01-01) Pradhan, Sayantan; Hore, Samrat; Maji, Suman Kumar; Manna, Simi; Maity, Abhijit; Kundu, Pratip Kumar; Maity, Krishna; Roy, Stabak; Mitra, Saptarshi; Dam, Paulami; Mondal, Rittick; Ghorai, Suvankar; Jawed, Junaid Jibran; Dutta, Subhadeep; Das, Sandip; Mandal, Sukhendu; Mandal, Sanjib; Kati, Ahmet; Sinha, Sangram; Maity, Amit Bikram; Dolai, Tuphan Kanti; Mandal, Amit Kumar; Ince, Ikbal Agah
Purulia is a malaria-prone district in West Bengal, India, with approximately half of the blocks defined as malaria endemic. We analyzed the malaria case in each block of the Purulia district from January 1, 2016, to December 31, 2020. As per the API, 20 blocks of Purulia were assigned to four different categories (0-3) and mapped using ArcGIS software. An exponential decay model was fitted to forecast the trend of malaria cases for each block of Purulia (2021-2025). There was a sharp decrease in total malaria cases and API from 2016 to 2020 due to the mass distribution of LLINs. The majority of cases (72.63\%) were found in >= 15-year age group. Males were more prone to malaria (60.09\%). Malaria was highly prevalent among Scheduled Tribes (48.44\%). Six blocks were reported in Category 3 (high risk) and none in Category 0 (no risk) in 2016, while no blocks were determined to be in Category 3, and three blocks were in Category 0 in 2020. The exponential decay model prediction is oriented towards gaining malaria-free status in thirteen blocks of Purulia by 2025. This study will incite the government to uphold and strengthen the current efforts to meet the malaria elimination goals.
Temporal proteomic analysis and label-free quantification of viral proteins of an invertebrate iridovirus
(MICROBIOLOGY SOC, 2015-01-01) Ince, Ikbal Agah; Boeren, Sjef; van Oers, Monique M.; Vlak, Just M.
Invertebrate iridescent virus 6 (IIV-6) is a nucleocytoplasmic virus with a similar to 212 kb linear dsDNA genome that encodes 215 putative ORFs. The IIV-6 virion-associated proteins consist of at least 54 virally encoded proteins. One of our previous findings showed that most of these proteins are encoded by genes from the early transcriptional class. This indicated that these structural proteins may not only function in the formation of the virion, but also in the initial stage of viral infection. In the current study, we followed the protein expression profile of IIV-6 over time in Drosophila S2 cells by label-free quantification using a proteomic approach. A total of 95 virally encoded proteins were detected in infected cells, of which 37 were virion proteins. The expressed IIV-6 virion proteins could be categorized into three main clusters based on their expression profiles: proteins with stably low expression levels during infection, proteins with exponentially increasing expression levels during infection and proteins that were initially highly abundant, but showed slightly reduced levels after 48 h post-infection. We thus provided novel information on the kinetics of virion and infected cell-specific protein levels that assists in our understanding of gene regulation in this lesser-known DNA virus model.