Publications by authors named "Zihni Demirbag"

The envelope (env) protein of SARS-CoV-2, a pivotal component of the viral architecture, plays a multifaceted role in viral assembly, replication, pathogenesis, and ion channel activity. These features make it a significant target for understanding virus-host interactions and developing vaccines to combat COVID-19. Recent structural studies provide valuable insights into the conformational dynamics and membrane topology of the SARS-CoV-2 env protein, shedding light on its functional mechanisms.

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Invertebrate iridescent virus 6 (IIV6) is a nucleocytoplasmic insect virus and a member of the family Iridoviridae. The IIV6 genome consists of 212,482 bp of linear dsDNA with 215 non-overlapping and putative protein-encoding ORFs. The IIV6 118L ORF is conserved in all sequenced members of the Iridoviridae and encodes a 515 amino acid protein with three predicted transmembrane domains and several N-glycosylation/N-myristoylation sites.

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Amsacta moorei entomopoxvirus (AMEV) is a poxvirus that can only infect insects. This virus is an attractive research material because it is similar to smallpox virus. AMEV is one of many viruses that encode protein kinases that drive the host's cellular mechanisms, modifying immune responses to it, and regulating viral protein activity.

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The poultry red mite, Dermanyssus gallinae (Arachnida: Dermanyssidae) is a pest that causes significant economic loss in laying hens for which control methods are limited. In this study, the effects of 20 indigenous fungal strains on poultry red mites in chicken farms were investigated. All experiments were conducted under laboratory condition at 28 ± 1 °C and 80 ± 5% humidity.

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Article Synopsis
  • The study examines the complete genome sequences of three Lymantria dispar nucleopolyhedrovirus (LdMNPV) isolates from China, Japan, and Turkey, which target gypsy moth larvae.
  • Shotgun pyrosequencing was used to analyze the genomes, revealing differences in size, GC content, and the number of open reading frames (ORFs) among the isolates.
  • Phylogenetic analysis indicates distinct genetic clusters for the isolates, highlighting significant genomic differences between groups and their geographic relationships.
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As an alternative to chemical insecticides, gut bacteria of insects could be used to control insect pests. In this study, bacteria associated with Tuta absoluta, an invasive species that has developed resistance to chemical insecticides, were isolated, and their potential for pest control was investigated. We isolated 13 bacteria from larvae of the pest and identified the isolates on the basis of their morphological, physiological, biochemical, and molecular characteristics as Bacillus thuringiensis (Ta1-8), Staphylococcus petrasii (Ta9), Citrobacter freundii (Ta10), Chishuiella changwenlii (Ta11), Enterococcus casseliflavus (Ta12), and Pseudomonas tremae (Ta13).

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Invertebrate iridescent virus 6 (IIV6) is a nucleocytoplasmic virus with a ∼212 kb linear dsDNA genome that encodes 215 putative open reading frames (ORFs). Proteomic analysis has revealed that the IIV6 virion consists of 54 virally encoded proteins. Interactions among the structural proteins were investigated using the yeast two-hybrid system, revealing that the protein of 415R ORF interacts reciprocally with the potential envelope protein 118L and the major capsid protein 274L.

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Invertebrate iridescent virus 6 (IIV6) is the type species of the Iridovirus genus in the Betairidovirinae subfamily of the Iridoviridae family. Transcription of the 215 predicted IIV6 genes is temporally regulated, dividing the genes into three kinetic classes: immediate-early (IE), delayed-early (DE), and late (L). So far, the transcriptional class has been determined for a selection of virion protein genes and only for three genes the potential promoter regions have been analyzed in detail.

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The entire genome of Helicoverpa armigera single nucleopolyhedrovirus (HearNPV-TR) was sequenced, and compared to genomes of other existing isolates. HearNPV-TR genome is 130.691 base pairs with a 38.

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This study reports a new Helicoverpa armigera nucleopolyhedrovirus (NPV) isolated from Heliothis peltigera (Denis & Schiffermuller), collected in the vicinity of Adana, Turkey. Infection was confirmed by tissue polymerase chain reaction and sequence analysis. Results showed that dead H.

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The fall webworm (Hyphantria cunea) impacts a wide variety of crops and cultivated broadleaf plant species. The pest is native to North America, was introduced to Europe and has since spread further as far as central Asia. Despite several attempts to control its distribution, the pest continues to spread causing damage all over the world.

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In this study, microencapsulation by spray drying was performed to protect spores and crystals of an indigenous isolate of Se13 from environmental stress. The effects of wall material, inlet temperature, and outlet temperature on microencapsulation of -Se13 were investigated using Taguchi's orthogonal array. The most suitable wall material determined as maltodextrin DE10.

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The genome of Chilo iridescent virus (CIV) has two open reading frames (ORFs) with matrix metalloprotease (MMP) domains. The protein encoded by ORF 136R contains 178 amino acids with over 40% amino acid sequence identity to hypothetical metalloproteases of other viruses, and the protein 165R contains 264 amino acids with over 40% amino acid sequence identity to metalloproteases of a large group of organisms, primarily including a variety of Drosophila species. These proteins possess conserved zinc-binding motifs in their catalytic domains.

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The lackey moth, Malacosoma neustria (Linnaeus, 1758), a worldwide pest, causes extensive economic losses particularly on hazelnut, plum, oak, poplar, and willow trees. A baculovirus, Malacosoma neustria nucleopolyhedrovirus (ManeNPV-T2), has been isolated from the larvae collected in Turkey and appears to have a potential as a microbial control agent. In this study, we describe the complete genome sequence of ManeNPV-T2 and compare it to other sequenced baculovirus genomes.

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In order to find an effective and environmentally friendly biocontrol agent against Spodoptera exigua, we isolated and identified a total of 15 different bacterial species belonging to phyla Firmicutes, Proteobacteria and Bacteroidetes. According to the phenotypic, genotypic and phylogenetic properties, bacterial isolates were identified as Bacillus cereus (Se1), Lysinibacillus macroides (Se2), Pseudomonas geniculata (Se3), Paenibacillus tylopili (Se4), Staphylococcus succinus (Se5), Acinetobacter soli (Se6), Chryseobacterium indologenes (Se7), Bacillus toyonensis (Se8), Serratia marcescens (Se9), Paenibacillus amylolyticus (Se10), Paenibacillus xylanexedens (Se11), Enterobacter ludwigii (Se12), Bacillus thuringiensis (Se13), Bacillus thuringiensis (Se14) and Lysinibacillus fusiformis (Se15). Screening of bacterial isolates for insecticidal potential was conducted at 10 cfu ml bacterial concentration.

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Chilo iridescent virus (CIV), officially named invertebrate iridescent virus 6 (IIV6), is a nucleocytoplasmic virus with a ~212-kb linear dsDNA genome that encodes 215 putative open reading frames (ORFs). Proteomic analysis has revealed that the CIV virion consists of 54 virally encoded proteins. In this study, we identified the interactions between the structural proteins using the yeast two-hybrid system.

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Amsacta moorei entomopoxvirus (AMEV) infects certain lepidopteran and orthopteran insects and is the most studied member of the genus Betaentomopoxvirus. It has been considered as a potential vector for gene therapy, a vector to express exogenous proteins and a biological control agent. One of its open reading frames, amv248, encodes a putative glycosyltransferase and is the only known attachment protein conserved in AMEV and chordopoxviruses.

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Entomopoxviruses are an important group of viruses infecting only insects. They belong to Poxviridae which infect both invertebrates and vertebrates, including humans. Protein kinases are known to have roles at virus morphogenesis, host selectivity, the regulation of cell division and apoptosis in some vertebrate poxviruses.

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Amsacta moorei entomopoxvirus (AMEV), the most studied member of the genus Betaentomopoxvirus, was initially isolated from Red Hairy caterpillar larvae, Amsacta moorei. According to genome sequence and previous studies it was shown that amv248 encodes a putative glycosyltransferase that is the only conserved attachment protein in betaentomopoxviruses. Transcriptional analysis of the amv248 gene by RT-PCR and qPCR showed that transcription starts at 6h post infection (hpi).

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Use of chemical pesticides in agriculture harms humans, non-target organisms and environments, and causes increase resistance against chemicals. In order to develop an effective bio-pesticide against coleopterans, particularly against Agelastica alni (Coleoptera: Chrysomelidae) which is one of the serious pests of alder leaf and hazelnut, we tested the insecticidal effect of 21 Bacillus isolates against the larvae and adults of the pest. Bacillus thuringiensis var.

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Chilo iridescent virus (CIV) is the type member of the genus Iridovirus within the family Iridoviridae. The virions of CIV contain a single linear dsDNA molecule that is circularly permuted and terminally redundant. The genome of CIV contains an open reading frame (ORF 012L) encoding a protein homologous to exonuclease II of Schizosaccharomyces pombe.

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Previously we have generated a recombinant Chilo iridescent virus (CIV) by inserting the green fluorescent protein gene (gfp) into the CIV 157L open reading frame (ORF) locus and showed that this recombinant (rCIV-Δ157L-gfp) was fully infectious both in cell culture as well as in insect larvae. This study opened up a new avenue for increasing the speed of kill of CIV and other iridoviruses by inserting virulence or toxin genes into the viral genome. In the current study we constructed a recombinant CIV (rCIV-Δ157L/gfp-AaIT) where the 157L ORF was replaced with both the AaIT neurotoxin gene from the scorpion Androctonus australis and the gfp gene, each under control of the viral major capsid protein (mcp) gene promoter.

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Insect-born entomopoxviruses (Fam: Poxviridae) are potentially important bio-pesticide against insect pests and expression vectors as well as vectors for transient human gene therapies including recombinant viral vaccines. For these reasons, it is necessary to understand the regulatory genes functions to improve its biotechnological potential. Here, we focused on the characterization of serine/threonine (Ser/Thr; ORF AMV197) protein kinase gene from the Amsacta moorei entomopoxvirus (AMEV), the type species of the genus Betaentomopoxvirus.

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Thaumetopoea pityocampa (pine processionary moth) is one of the most important pine pests in the forests of Mediterranean countries, Central Europe, the Middle East and North Africa. Apart from causing significant damage to pinewoods, T. pityocampa occurrence is also an issue for public and animal health, as it is responsible for dermatological reactions in humans and animals by contact with its irritating hairs.

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Objectives: Lipolytic genes have been investigated in several viral genomes, and some of them show enzyme activity which can be used for various functions including the production of DNA replication metabolites, rescue from endosomes, and membrane fusion. Amsacta moorei entomopoxvirus (AMEV) replicates in nearly the entire insect body, especially in the adipose tissue. One of the open reading frames (ORFs) in the AMEV genome, amv133, encodes a putative lipase enzyme.

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