GIL: a python package for designing custom indexing primers.

SUMMARY: Generate Indexes for Libraries (GIL) is a software tool for generating primers to be used in the production of multiplexed sequencing libraries. GIL can be customized in numerous ways to meet user specifications, including length, sequencing modality, color balancing, and compatibility with existing primers, and produces ordering and demultiplexing-ready outputs. AVAILABILITY AND IMPLEMENTATION: GIL is written in Python and is freely available on GitHub under the MIT license: https://github.com/de-Boer-Lab/GIL and can be accessed as a web-application implemented in Streamlit at https://dbl-gil.streamlitapp.com.

The mutations frequency of enhancer II/HBx regions of hepatitis B virus in acutely infected Iranian patients: a cross-sectional study.

Background and Objectives: The viral transactivator HBx protein affect cellular, viral and pregenomic factors pathway. Mutations in this protein can produce new viruses with new antigenic determinants that are generally related to developing cancerous. Materials and Methods: In this cross-sectional study, 33 serum samples of patients diagnosed with acute HBV infection were investigated for HBeAg and HBV DNA viral load and HBx gene mutations. mutation in the HBx protein detected by sequencing analysis. Results: Out of the 33 samples, 19 samples were males (57.6%), and 14 samples were females. 15 (45.5%) were positive for HBx DNA and 18 patients were negative for HBx DNA (54.5%). After sequencing, three mutations were recognized in HBx at nucleotide positions 147, 148, and 391 that were stationed to G1524A, G1525A, and G1767C mutations. Conclusion: The analysis result of this study shows G1524A and G1525A mutations that an important role in altering the inhibition function of the HBx activity domain. The G1767C mutation inactivates HBx transactivation activity. These mutations have a critical role in the pathogenicity of the virus, and the intensity of hepatic tissue demolition and the development of cirrhosis or carcinoma in patients can be understood.

The RNA binding activity of the first identified trypanosome protein with Z-DNA-binding domains.

RNA-binding proteins play a particularly important role in regulating gene expression in trypanosomes. A map of the network of protein complexes in Trypanosoma brucei uncovered an essential protein (Tb927.10.7910) that is postulated to be an RNA-binding protein implicated in the regulation of the mitochondrial post-transcriptional gene regulatory network by its association with proteins that participate in a multi-protein RNA editing complex. However, the mechanism by which this protein interacts with its multiple target transcripts remained unknown. Using sensitive database searches and experimental data, we identify Z-DNA-binding domains in T. brucei in the N- and C-terminal regions of Tb927.10.7910. RNA-binding studies of the wild-type protein, now referred to as RBP7910 (RNA binding protein 7910), and site-directed mutagenesis of residues important for the Z-DNA binding domains show that it preferentially interacts with RNA molecules containing poly(U) and poly(AU)-rich sequences. The interaction of RBP7910 with these regions may be involved in regulation of RNA editing of mitochondrial transcripts.

TrypsNetDB: An integrated framework for the functional characterization of trypanosomatid proteins.

Trypanosomatid parasites cause serious infections in humans and production losses in livestock. Due to the high divergence from other eukaryotes, such as humans and model organisms, the functional roles of many trypanosomatid proteins cannot be predicted by homology-based methods, rendering a significant portion of their proteins as uncharacterized. Recent technological advances have led to the availability of multiple systematic and genome-wide datasets on trypanosomatid parasites that are informative regarding the biological role(s) of their proteins. Here, we report TrypsNetDB (http://trypsNetDB.org), a web-based resource for the functional annotation of 16 different species/strains of trypanosomatid parasites. The database not only visualizes the network context of the queried protein(s) in an intuitive way but also examines the response of the represented network in more than 50 different biological contexts and its enrichment for various biological terms and pathways, protein sequence signatures, and potential RNA regulatory elements. The interactome core of the database, as of Jan 23, 2017, contains 101,187 interactions among 13,395 trypanosomatid proteins inferred from 97 genome-wide and focused studies on the interactome of these organisms.

The interaction of a Trypanosoma brucei KH-domain protein with a ribonuclease is implicated in ribosome processing.

Ribosomal RNA maturation is best understood in yeast. While substantial efforts have been made to explore parts of these essential pathways in animals, the similarities and uniquenesses of rRNA maturation factors in non-Opisthokonts remain largely unexplored. Eukaryotic ribosome synthesis requires the coordinated activities of hundreds of Assembly Factors (AFs) that transiently associate with pre-ribosomes, many of which are essential. Pno1 and Nob1 are two of six AFs that are required for the cytoplasmic maturation of the 20S pre-rRNA to 18S rRNA in yeast where it has been almost exclusively analyzed. Specifically, Nob1 ribonucleolytic activity generates the mature 3'-end of 18S rRNA. We identified putative Pno1 and Nob1 homologues in the protist Trypanosoma brucei, named TbPNO1 and TbNOB1, and set out to explore their rRNA maturation role further as they are both essential for normal growth. TbPNO1 is a nuclear protein with limited cytosolic localization relative to its yeast homologue. Like in yeast, it interacts directly with TbNOB1, with indications of associations with a larger AF-containing complex. Interestingly, in the absence of TbPNO1, TbNOB1 exhibits non-specific degradation activity on RNA substrates, and its cleavage activity becomes specific only in the presence of TbPNO1, suggesting that TbPNO1-TbNOB1 interaction is essential for regulation and site-specificity of TbNOB1 activity. These results highlight a conserved role of the TbPNO1-TbNOB1 complex in 18S rRNA maturation across eukaryotes; yet reveal a novel role of their interaction in regulation of TbNOB1 enzymatic activity.

A Protein Complex Map of Trypanosoma brucei.

The functions of the majority of trypanosomatid-specific proteins are unknown, hindering our understanding of the biology and pathogenesis of Trypanosomatida. While protein-protein interactions are highly informative about protein function, a global map of protein interactions and complexes is still lacking for these important human parasites. Here, benefiting from in-depth biochemical fractionation, we systematically interrogated the co-complex interactions of more than 3354 protein groups in procyclic life stage of Trypanosoma brucei, the protozoan parasite responsible for human African trypanosomiasis. Using a rigorous methodology, our analysis led to identification of 128 high-confidence complexes encompassing 716 protein groups, including 635 protein groups that lacked experimental annotation. These complexes correlate well with known pathways as well as for proteins co-expressed across the T. brucei life cycle, and provide potential functions for a large number of previously uncharacterized proteins. We validated the functions of several novel proteins associated with the RNA-editing machinery, identifying a candidate potentially involved in the mitochondrial post-transcriptional regulation of T. brucei. Our data provide an unprecedented view of the protein complex map of T. brucei, and serve as a reliable resource for further characterization of trypanosomatid proteins. The presented results in this study are available at: www.TrypsNetDB.org.

In vitro evaluation of anti-herpes simplex-1 activity of three standardized medicinal plants from Lamiaceae.

BACKGROUND: Rosmarinic acid (RA) is a phenolic acid with antioxidant and anti-viral effects. We have studied anti-herpes simplex virus type 1 (HSV-1) effect of three medicinal plants from Lamiaceae family which have been standardized on the basis of RA content. MATERIALS AND METHODS: Methanolic extract of Teucrium polium, Ziziphora clinopoides, and Salvia rhytidea was prepared by maceration method and RA content of the plants was determined using a spectrophotometric method. Maximum nontoxic concentration (MNTC) of the extracts was determined using neutral red method. Serial dilutions of extracts up to MNTC were examined on Vero cells for anti-HSV-1 effect by plaque assay in comparison to acyclovir as a positive control. RESULTS: Among the tested extracts, T. polium contained the highest percentage of RA (1.8%w/w) and exhibited the least toxicity (MNTC = 1000 µg/ml). The greatest anti-HSV-1 was shown by T. polium and Z. clinopoides extracts which exhibited both time and concentration-dependent plaque inhibition. CONCLUSION: Considering the low toxicity and significant anti-viral effect of T. polium extract, this plant would prove valuable as an active anti-viral drug.