Computational Prediction of MicroRNAs from Toxoplasma gondii Potentially Regulating the Hosts’ Gene Expression

AbstractMicroRNAs (miRNAs) were discovered two decades ago, yet there is still a great need for further studies elucidating their genesis and targeting in different phyla. Since experimental discovery and validation of miRNAs is difficult, computational predictions are indispensable and today most computational approaches employ machine learning. Toxoplasma gondii, a parasite residing within the cells of its hosts like human, uses miRNAs for its post-transcriptional gene regulation. It may also regulate its hosts’ gene expression, which has been shown in brain cancer. Since previous studies have shown that overexpressed miRNAs within the host are causal for disease onset, we hypothesized that T. gondii could export miRNAs into its host cell. We computationally predicted all hairpins from the genome of T. gondii and used mouse and human models to filter possible candidates. These were then further compared to known miRNAs in human and rodents and their expression was examined for T. gondii grown in mouse and human hosts, respectively. We found that among the millions of potential hairpins in T. gondii, only a few thousand pass filtering using a human or mouse model and that even fewer of those are expressed. Since they are expressed and differentially expressed in rodents and human, we suggest that there is a chance that T. gondii may export miRNAs into its hosts for direct regulation

H pylori iceA alleles are disease-specific virulence factors

Aim: To characterize and compare genotype profiles of H pylori strains isolated from patients with chronic gastritis and duodenal ulcer in western part of Turkey. Methods: A total of 46 patients [30 chronic gastritis (CG) and 16 duodenal ulcer (DU)] who had undergone endoscopy because of dyspeptic complaints were studied. The antral biopsy specimens were evaluated for the presence of H pylori by rapid urease test and culture, and the genotype profiles were determined by real-time PCR. Results: The cagA gene was observed in 43 (93.5%) isolates. The vacA s1m2 genotype was the predominant subtype, found in 63.3% and 68.7% of isolates in patients with CG and DU, respectively. Twenty (66.6%) isolates from patients with CG were iceA2 positive while the iceA1 was predominant in those with DU (68.8%). In terms of the association of the iceA alleles to other genes, both alleles were significantly associated with the cagA vacA s1m2 genotype. Conclusion: The prevalent circulating genotypes in CG and DU were cagA vacA s1m2 iceA2 and cagA vacA s1m2 iceA1 genotype, respectively. It was found that cagA vacA s1m2 genotype seems to be common virulence factors in both CG and DU while iceA alleles show specificity for gastroduodenal pathologies in this study. © 2007 The WJG Press. All rights reserved

Possible role of GADD45γ methylation in diffuse large B-cell Lymphoma: Does it affect the progression and tissue involvement?

Objective: Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphoma among adults and is characterized by heterogeneous clinical, immunophenotypic, and genetic features. Different mechanisms deregulating cell cycle and apoptosis play a role in the pathogenesis of DLBCL. Growth arrest DNA damage-inducible 45 (GADD45γ) is an important gene family involved in these mechanisms. The aims of this study are to determine the frequency of GADD45γ methylation, to evaluate the correlation between GADD45γ methylation and protein expression, and to investigate the relation between methylation status and clinicopathologic parameters in DLBCL tissues and reactive lymphoid node tissues from patients with reactive lymphoid hyperplasia. Materials and Methods: Thirty-six tissue samples of DLBCL and 40 nonmalignant reactive lymphoid node tissues were analyzed in this study. Methylation-sensitive high-resolution melting analysis was used for the determination of GADD45γ methylation status. The GADD45γ protein expression was determined by immunohistochemistry. Results: GADD45γ methylation was frequent (50.0%) in DLBCL. It was also significantly higher in advanced-stage tumors compared with early-stage (p=0.041). In contrast, unmethylated GADD45γ was associated with nodal involvement as the primary anatomical site (p=0.040). Conclusion: The results of this study show that, in contrast to solid tumors, the frequency of GADD45γ methylation is higher and this epigenetic alteration of GADD45γ may be associated with progression in DLBCL. In addition, nodal involvement is more likely to be present in patients with unmethylated GADD45γ. © 2015 Turkish Society of Hematology. All rights reserved

Removing contamination from genomic sequences based on vector reference libraries

7th International Symposium on Health Informatics and Bioinformatics, HIBIT 2012; Cappadocia; Turkey; 19 April 2012 through 22 April 2012DNA is often sequenced after being cloned into a vector since this provides the possibility for using standard primers and removes the need to develop custom primers. In this way a certain amount of vector is sequenced along with the sequence of interest. Unfortunately, occasionally these contaminating vector sequences find their way into public databases as part of submitted sequences. It has been pointed out that SeqClean, a program used to remove vector contamination from sequences, does not take into account that vectors are circular structures. A workaround has been presented before, but we were able to simplify the process and, additionally, we provide an implementation. We further applied our method to a test set of EST sequences and also analyzed the amount of contamination found in the EST sequences available on NCBI. © 2012 IEEE

The Role of MicroRNAs in Parasitology

Epigenetik düzenleyiciler olarak mikroRNA’lar (miRNA’lar), biyolojik fonksiyonları kontrol etmek için transkripsiyon sonrası seviyede ökaryotlarda gen ekspresyonunu düzenleyen küçük kodlayıcı olmayan RNA’lardır. MikroRNA’lar, parazitlerin gelişimi, fizyolojisi, enfeksiyonu, bağışıklığı ve karmaşık yaşam döngülerinde rol oynamaktadır. Ayrıca parazitler, konak miRNA ekspresyonunu değiştirerek parazitlerin kontrolüne/temizlenmesine veya enfeksiyonun oluşmasına neden olmaktadır. Son 20 yılda, Caenorhabditis elegans ve diğer parazitlerde binlerce miRNA tanımlanmıştır. Bu nedenle, miRNA yolakları paraziter hastalıkların teşhisi ve terapötik kontrolü için potansiyel hedefler arasında yer almaktadır. Bu derlemede, protozoonlar, helmintler ve artropodlar ile ilgili miRNA’ların mevcut durumunu ve potansiyel fonksiyonlarını gözden geçirmeyi planladık.MicroRNAs (miRNAs), as epigenetic regulators, are small non-coding RNAs regulating gene expression in eukaryotes at the posttranscriptional level to control biological functions. MicroRNAs play a role in development, physiology, infection, immunity and the complex life cycles of parasites. Also, parasite infection can alter host miRNA expression that might result in either parasite clearance or infection. Over the past 20 years, thousands of miRNAs have been identified in the nematode Caenorhabditis elegans and other parasites. Thus, miRNA pathways are potential targets for the diagnostic and therapeutic control of parasitic diseases. Here, we review the current status and potential functions of miRNAs related to protozoans, helminths, and arthropods

One Step Forward, Two Steps Back; Xeno-MicroRNAs Reported in Breast Milk Are Artifacts

<div><p>Background</p><p>MicroRNAs (miRNAs) are short RNA sequences that guide post-transcriptional regulation of gene expression via complementarity to their target mRNAs. Discovered only recently, miRNAs have drawn a lot of attention. Multiple protein complexes interact to first cleave a hairpin from nascent RNA, export it into the cytosol, trim its loop, and incorporate it into the RISC complex which is important for binding its target mRNA. This process works within one cell, but circulating miRNAs have been described suggesting a role in cell-cell communication.</p><p>Motivation</p><p>Viruses and intracellular parasites like <i>Toxoplasma gondii</i> use miRNAs to manipulate host gene expression from within the cellular environment. However, recent research has claimed that a rice miRNA may regulate human gene expression. Despite ongoing debates about these findings and general reluctance to accept them, a recent report claimed that foodborne plant miRNAs pass through the digestive tract, travel through blood to be incorporated by alveolar cells excreting milk. The miRNAs are then said to have some immune-related function in the newborn.</p><p>Principal Findings</p><p>We acquired the data that supports their claim and performed further analyses. In addition to the reported miRNAs, we were able to detect almost complete mRNAs and found that the foreign RNA expression profiles among samples are exceedingly similar. Inspecting the source of the data helped understand how RNAs could contaminate the samples.</p><p>Conclusion</p><p>Viewing these findings in context with the difficulties foreign RNAs face on their route into breast milk and the fact that many identified foodborne miRNAs are not from actual food sources, we can conclude beyond reasonable doubt that the original claims and evidence presented may be due to artifacts. We report that the study claiming their existence is more likely to have detected RNA contamination than miRNAs.</p></div

Read Coverage Across Transcripts.

<p>Distribution of transcript coverage for <i>Nicotiana tabacum</i> in human (first 4) and porcine (last 8) samples. Data can be found in Table N in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145065#pone.0145065.s005" target="_blank">S4 File</a>.</p

Comparison of the number of unique miRNAs found in different samples, the number of known miRNAs for that species and the number of publications in respect to that species during the time period 2010–2013 at the institute where measurements were performed.

<p>Data is also available as Table G in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145065#pone.0145065.s003" target="_blank">S2 File</a>.</p

Leishmania major ve Leishmania infantum Promastigot Formlarının Karşılaştırmalı Gen Ekspresyon Profilleri

Amaç: Bu çalışmada, Leishmania major ve Leishmania infantum promastigotlarındaki gen ekspresyonlarının karşılaştırmalı analizi yapılarak, iki tür arasında gen ekspresyon profillerindeki farklılıkların tespit edilmesi amaçlanmıştır. Yöntemler: L. major (MHOM/IL/80) ve L. infantum (MHOM/MA/67/ITMAP/263) hücre hatları kullanılarak hücre kültürü oluşturulmuştur. Daha sonra, total RNA izolasyonu ve cDNA sentezi gerçekleştirilerek; revers transkriptaz polimeraz zincir reaksiyonu ile metabolik yolaklarda ve nükleik asit sentezinde rol oynayan ve her iki türde ortak olan 30 genin ekspresyon seviyelerindeki kat değişimi hesaplanmıştır. LeishDB ve KEGG veri tabanları kullanılarak genlerin fonksiyonel işlevleri belirlenmiştir. Bulgular: Bu çalışmada, L. major ile L. infantum promastigotlarında ortak olarak eksprese edilen ve protein kodlayan 30 farklı gen profili değerlendirilmiş ve iki tür arasında anlamlı farklılık saptanmıştır (p1). Bu genler; phosphoglycan beta 1,3 galactosyltransferase-like, lathosterol oxidase-like, fatty acid elongase, 3-oxo-5 alpha-steroid 4-dehydrogenase, calpain-like cysteine peptidase, acetyl-coA synthetase, 3’-nucleotidase/nuclease, 3’-nucleotidase/nuclease precursor ve 3-ketoacyl-coA thiolase-like olarak belirlenmiştir. İki türde ortak olan genlerin karşılık geldiği proteinlerin fonksiyonları veri tabanlarında ayrıntılı olarak incelendiğinde ise, bu genlerin parazitin lipit, protein ve karbonhidrat mekanizmalarında, nükleik asit ve metabolizma fonksiyonlarında rol oynadığı saptanmıştır. Sonuç: L. major ile L. infantum türlerinde ortak olarak bulunan genlerin ekspresyon profillerindeki değişiklikler, parazit türleri arasında virülans, patogenez, klinik ve tedavi farklılıklarına neden olabilir. Ayrıca parazite karşı aşı ve ilaç çalışmaları için türlere özgü spesifik veya ortak hedeflerin seçilmesinde gen profillerinin değerlendirilmesi önem arz etmektedir

Correlation of Transcripts Between Samples.

<p>Correlation among transcripts of <i>Oryza sativa</i> found in human and porcine samples. The first 4 samples across the top and the first 4 rows from top correspond to human samples; the remainder is of pig origin. High correlation is visualized via darker color and larger circles. Corresponding figures for <i>A</i>. <i>thaliana</i> (<b>Fig D in</b> <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145065#pone.0145065.s002" target="_blank">S1 File</a>) and <i>N</i>. <i>tabacum</i> (<b>Fig E in</b> <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0145065#pone.0145065.s002" target="_blank">S1 File</a>).</p