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On page 1 showing 1 ~ 11 papers out of 11 papers

Small RNA Sequencing Based Identification of MiRNAs in Daphnia magna.

  • Ercan Selçuk Ünlü‎ et al.
  • PloS one‎
  • 2015‎

Small RNA molecules are short, non-coding RNAs identified for their crucial role in post-transcriptional regulation. A well-studied example includes miRNAs (microRNAs) which have been identified in several model organisms including the freshwater flea and planktonic crustacean Daphnia. A model for epigenetic-based studies with an available genome database, the identification of miRNAs and their potential role in regulating Daphnia gene expression has only recently garnered interest. Computational-based work using Daphnia pulex, has indicated the existence of 45 miRNAs, 14 of which have been experimentally verified. To extend this study, we took a sequencing approach towards identifying miRNAs present in a small RNA library isolated from Daphnia magna. Using Perl codes designed for comparative genomic analysis, 815,699 reads were obtained from 4 million raw reads and run against a database file of known miRNA sequences. Using this approach, we have identified 205 putative mature miRNA sequences belonging to 188 distinct miRNA families. Data from this study provides critical information necessary to begin an investigation into a role for these transcripts in the epigenetic regulation of Daphnia magna.


Recovery of T-cell function in healthy dogs following cessation of oral cyclosporine administration.

  • Lakshmi Narayanan‎ et al.
  • Veterinary medicine and science‎
  • 2020‎

Cyclosporine is a potent immunosuppressive agent used to treat immune-mediated disorders in dogs. Secondary infections sometimes necessitate withdrawal of cyclosporine, but it is not known how long it takes for the immune system to recover after cessation of cyclosporine. Our goal was to utilize a validated RT-qPCR assay in dogs to assess recovery time of the T-cell cytokines IL-2 and IFN-γ after discontinuation of cyclosporine. Six healthy dogs were given oral cyclosporine (10 mg/kg every 12 hr) for 1 week, with samples collected for measurement of cytokine gene expression prior to treatment, and on the last day of therapy. Cyclosporine was then discontinued, and samples were collected daily for an additional 7 days. Results revealed that there was a significant difference in cytokine expression when comparing pre-treatment and immediate post-treatment values, corresponding to marked suppression of T-cell function. There was no significant difference between pre-treatment values for either cytokine when compared with any day during the recovery period. Cytokine expression, evaluated as a percentage of pre-treatment baseline samples, demonstrated progressing return of T-cell function after drug cessation, with full recovery seen in all dogs by Day 4 of the recovery period.


Role of FruR transcriptional regulator in virulence of Listeria monocytogenes and identification of its regulon.

  • Hossam Abdelhamed‎ et al.
  • PloS one‎
  • 2022‎

Listeria monocytogenes is a ubiquitous opportunistic foodborne pathogen capable of survival in various adverse environmental conditions. Pathogenesis of L. monocytogenes is tightly controlled by a complex regulatory network of transcriptional regulators that are necessary for survival and adaptations to harsh environmental conditions both inside and outside host cells. Among these regulatory pathways are members of the DeoR-family transcriptional regulators that are known to play a regulatory role in sugar metabolism. In this study, we deciphered the role of FruR, a DeoR family protein, which is a fructose operon transcriptional repressor protein, in L. monocytogenes pathogenesis and growth. Following intravenous (IV) inoculation in mice, a mutant strain with deletion of fruR exhibited a significant reduction in bacterial burden in liver and spleen tissues compared to the parent strain. Further, the ΔfruR strain had a defect in cell-to-cell spread in L2 fibroblast monolayers. Constitutive activation of PrfA, a pleiotropic activator of L. monocytogenes virulence factors, did not restore virulence to the ΔfruR strain, suggesting that the attenuation was not a result of impaired PrfA activation. Transcriptome analysis revealed that FruR functions as a positive regulator for genes encoding enzymes involved in the pentose phosphate pathway (PPP) and as a repressor for genes encoding enzymes in the glycolysis pathway. These results suggested that FruR may function to facilitate NADPH regeneration, which is necessary for full protection from oxidative stress. Interestingly, deletion of fruR increased sensitivity of L. monocytogenes to H2O2, confirming a role for FruR in survival of L. monocytogenes during oxidative stress. Using anti-mouse neutrophil/monocyte monoclonal antibody RB6-8C5 (RB6) in an in vivo infection model, we found that FruR has a specific function in protecting L. monocytogenes from neutrophil/monocyte-mediated killing. Overall, this work clarifies the role of FruR in controlling L. monocytogenes carbon flow between glycolysis and PPP for NADPH homeostasis, which provides a new mechanism allowing metabolic adaptation of L. monocytogenes to oxidative stress.


Gemcitabine-(5'-phosphoramidate)-[anti-IGF-1R]: molecular design, synthetic organic chemistry reactions, and antineoplastic cytotoxic potency in populations of pulmonary adenocarcinoma (A549).

  • Cody P Coyne‎ et al.
  • Chemical biology & drug design‎
  • 2017‎

One molecular-based approach that increases potency and reduces dose-limited sequela is the implementation of selective 'targeted' delivery strategies for conventional small molecular weight chemotherapeutic agents. Descriptions of the molecular design and organic chemistry reactions that are applicable for synthesis of covalent gemcitabine-monophosphate immunochemotherapeutics have to date not been reported. The covalent immunopharmaceutical, gemcitabine-(5'-phosphoramidate)-[anti-IGF-1R] was synthesized by reacting gemcitabine with a carbodiimide reagent to form a gemcitabine carbodiimide phosphate ester intermediate which was subsequently reacted with imidazole to create amine-reactive gemcitabine-(5'-phosphorylimidazolide) intermediate. Monoclonal anti-IGF-1R immunoglobulin was combined with gemcitabine-(5'-phosphorylimidazolide) resulting in the synthetic formation of gemcitabine-(5'-phosphoramidate)-[anti-IGF-1R]. The gemcitabine molar incorporation index for gemcitabine-(5'-phosphoramidate)-[anti-IGF-R1] was 2.67:1. Cytotoxicity Analysis - dramatic increases in antineoplastic cytotoxicity were observed at and between the gemcitabine-equivalent concentrations of 10-9  M and 10-7  M where lethal cancer cell death increased from 0.0% to a 93.1% maximum (100.% to 6.93% residual survival), respectively. Advantages of the organic chemistry reactions in the multistage synthesis scheme for gemcitabine-(5'-phosphoramidate)-[anti-IGF-1R] include their capacity to achieve high chemotherapeutic molar incorporation ratios; option of producing an amine-reactive chemotherapeutic intermediate that can be preserved for future synthesis applications; and non-dedicated organic chemistry reaction scheme that allows substitutions of either or both therapeutic moieties, and molecular delivery platforms.


Identification of alternative oxidase encoding genes in Caulerpa cylindracea by de novo RNA-Seq assembly analysis.

  • Ercan Selçuk Ünlü‎ et al.
  • Marine genomics‎
  • 2019‎

Alternative oxidases (AOX) are defined in plants, fungi and algae. The main function of AOX proteins has been described for electron flow through electron transport chain and regulation of mitochondrial retrograde signaling pathway. The roles of AOX proteins have been characterized in reproduction and resistance against oxidative stress, cold stress, starvation, and biotic attacks. Caulerpa cylindracea is an invasive marine green alga. Although the natural habitats of the species are Australia coasts, the impact of the invasion has been monitored through the Mediterranean Sea and the Aegean Sea. C. cylindracea species have advantages against others by showing higher resistance to stress conditions such as cold, starvation, pathogen attacks and by their capability of sexual and vegetative reproduction. Comparing the advantages of C. cylindracea over the niche and defined functional roles of mitochondrial AOX proteins, it is evident that AOX proteins are likely involved in developing those advantageous skills in C. cylindracea. However, there is limited data about biochemical and molecular mechanisms that take part in stress resistance and invasion characteristics. We aimed to identify mitochondrial alternative oxidase encoding genes in C. cylindracea while annotating whole transcriptome data for the species. Samples were collected from Seferihisar/İzmir. Transcriptome analysis from pooled RNA samples revealed 47,400 assembled contigs represented by 33,340 unigenes. Using standalone Blast analysis, we were able to identify two alternative oxidase encoding genes.


Identification of conserved miRNA molecules in einkorn wheat (Triticum monococcum subsp. monococcum) by using small RNA sequencing analysis.

  • Ercan Selçuk Ünlü‎ et al.
  • Turkish journal of biology = Turk biyoloji dergisi‎
  • 2018‎

Triticum monococcum subsp. monococcum as a first cultivated diploid wheat species possesses desirable agronomic and quality characteristics. Drought and salinity are the most dramatic environmental stress factors that have serious impact on yield and quality of crops; however, plants can use alternative defense mechanisms against these stresses. The posttranscriptional alteration of gene expression by microRNAs (miRNAs) is one of the most conserved mechanisms. In plant species including wheat genomes, miRNAs have been implicated in the management of salt and drought stress; however, studies on einkorn wheat (Triticum monococcum subsp. monococcum) are not yet available. In this study, we aimed to identify conserved miRNAs in einkorn wheat using next generation sequencing technology and bioinformatics analysis. In order to include a larger set of miRNAs, small RNA molecules from pooled plant samples grown under normal, drought, and salinity conditions were used for the library preparation and sequence analysis. After bioinformatics analysis, we identified 167 putative mature miRNA sequences belonging to 140 distinct miRNA families. We also presented a comparative analysis to propose that miRNAs and their target genes were involved in salt and drought stress control in addition to a comprehensive analysis of the scanned target genes in the T. aestivum genome.


Secreted Extracellular Products of Flavobacterium covae as Potential Immunogenic Factors for Protection against Columnaris Disease in Channel Catfish (Ictalurus punctatus).

  • Mohamed Sayed‎ et al.
  • Pathogens (Basel, Switzerland)‎
  • 2023‎

Columnaris disease caused by Flavobacterium covae leads to substantial economic losses in commercially important fish species worldwide. The US channel catfish (Ictalurus punctatus) industry is particularly vulnerable to this disease. Therefore, there is an urgent need to develop a vaccine to reduce the economic losses caused by this disease. Secreted extracellular products (SEPs) are considered to be essential bacterial virulence factors that often provide immunogenicity and protection. The current study sought to identify the main SEPs of F. covae and to evaluate their potential to provide protection in channel catfish against columnaris disease. SDS-PAGE analysis of SEPs revealed five protein bands with molecular weights ranging from 13 to 99 kDa. Mass spectrometry analysis showed that these SEPs were hypothetical protein (AWN65_11950), zinc-dependent metalloprotease (AWN65_10205), DNA/RNA endonuclease G (AWN65_02330), outer membrane protein beta-barrel domain (AWN65_12620), and chondroitin-sulfate-ABC endolyase/exolyase (AWN65_08505). Catfish fingerlings were vaccinated with SEPs, SEPs emulsified with mineral oil adjuvant, or heat-inactivated SEPs, or they were sham-immunized through intraperitoneal (IP) injection. After 21 days, an F. covae challenge showed 58.77% and 46.17% survival in the catfish vaccinated with the SEPs and the SEPs emulsified with adjuvant compared to the sham-vaccinated control (100% mortality within 120 h post-infection). However, the heat-inactivated SEPs failed to provide significant protection (23.15% survival). In conclusion, although SEPs contain potentially important immunogenic proteins, further work is needed to optimize their use for long-lasting protection against columnaris disease in fish. These results are significant given the economic impact of columnaris disease on fish farming worldwide.


A Study of the Gut Bacterial Community of Reticulitermes virginicus Exposed to Chitosan Treatment.

  • Telmah Telmadarrehei‎ et al.
  • Insects‎
  • 2020‎

A thorough understanding of microbial communities in the gut of lower termites is needed to develop target-specific and environmentally benign wood protection systems. In this study, the bacterial community from Reticulitermes virginicus was examined by Illumina sequencing of 16S ribosomal RNA (rRNA) spanning the V3 and V4 regions. Prior to library preparation, the termites were subjected to five treatments over an 18-day period: three groups were fed on wood treated with 0.5% chitosan, 25% acetic acid, or water, the fourth group was taken directly from the original collection log, and the fifth group was starved. Metagenomic sequences were analyzed using QIIME 2 to understand the treatments' effects on the dynamics of the gut bacteria. Four dominant phyla were detected: Bacteroidetes (34.4% of reads), Firmicutes (20.6%), Elusimicrobia (15.7%), and Proteobacteria (12.9%). A significant effect of chitosan treatment was observed in two phyla; Firmicutes abundance was significantly lower with chitosan treatment when compared to other groups, while Actinobacteria was lower in unexposed and starved termites. The results suggest that chitosan treatment not only affects the structure of the microbial community in the gut, but other treatments such as starving also cause shifts in termite gut communities.


Dexamethasone-(C21-phosphoramide)-[anti-EGFR]: molecular design, synthetic organic chemistry reactions, and antineoplastic cytotoxic potency against pulmonary adenocarcinoma (A549).

  • Cody P Coyne‎ et al.
  • Drug design, development and therapy‎
  • 2016‎

Corticosteroids are effective in the management of a variety of disease states, such as several forms of neoplasia (leukemia and lymphoma), autoimmune conditions, and severe inflammatory responses. Molecular strategies that selectively "target" delivery of corticosteroids minimize or prevents large amounts of the pharmaceutical moiety from passively diffusing into normal healthy cell populations residing within tissues and organ systems.


Characterization of fungal RTG2 genes in retrograde signaling of Saccharomyces cerevisiae.

  • Ercan Selçuk Ünlü‎ et al.
  • FEMS yeast research‎
  • 2013‎

Changes in the functional status of mitochondria result in the transcriptional activation of a subset of nuclear-encoded genes in a process referred to as retrograde signaling. In Saccharomyces cerevisiae, this molecular link between mitochondria and the nuclear genome is controlled by three key signaling proteins: Rtg1p, Rtg2p, and Rtg3p. Although the retrograde signaling response has been well characterized in S. cerevisiae, very little is known about this pathway in other fungi. In this study, we selected four species having uncharacterized open reading frames (ORFs) with more than 66% amino acid identity to Rtg2p for further analysis. To determine whether these putative RTG2 ORFs encoded bona fide regulators of retrograde signaling, we tested their ability to complement the defects associated with the S. cerevisiae rtg2Δ mutant. Specifically, we tested for complementation of citrate synthase (CIT2) and aconitase (ACO1) at the transcript and protein levels, glutamate auxotrophy, and changes in the interaction between Rtg2p and the negative regulator Mks1p. Our findings show that all four Rtg2p homologs are functional upon activation of retrograde signaling, although their degree of complementation varied. In addition, all Rtg2p homologs showed a marked reduction in Mks1p binding, which may contribute to their altered responses to retrograde signaling.


Effects of oral administration of 5 immunosuppressive agents on activated T-cell cytokine expression in healthy dogs.

  • Todd M Archer‎ et al.
  • Journal of veterinary internal medicine‎
  • 2020‎

Dogs are often adminstered >1 immunosuppressive medication when treating immune-mediated diseases, and determining whether these different medications affect IL-2 expression would be useful when performing pharmacodynamic monitoring during cyclosporine therapy.


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