Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis

Background We previously reported that a Human Ro52 gene sequence (TRIM21) produced a significant stretch of protein sequence homologous to T. cruzi Antigen 36 (Ag 36) protein sequence, when Ag 36 was translated in the second reading frame. Comparison of their respective DNA sequences demonstrated a 114 nucleotide region of both genes having ~ 70 percent partial homology. After Ro52 was shown to be an E3 Ubiquitin dependent Type I ligase for transcription factors for Interferon genes, we proposed that the Ag 36 gene, which contains a repetitive motif within it, may function to repress Ro52 in the human heart through RNA interference, or other unknown mechanism, giving rise to autoimmunity found in Chronic Chagas Cardiomyopathy (CCC). Results To test that hypothesis, we compared various mammalian TRIM genes to the T. cruzi Ag 36 DNA sequence using the Needleman-Wunsch algorithm in the http:\\usegalaxy.eu bioinformatics tool base. In addition to human and chimpanzee, TRIM21 comparable gene regions from canine, shrew, ferret, bat, feline, and armadillo, and aardvark showed homology to the gene for Ag 36 ranging from 68 to 30 percent. However, mouse and eight other mammalian species showed no significant homology. Since mice have been shown to have severe cardiac cardiomyopathy after infection, but their TRIM21 was not homologous to Ag 36 in this study, we conclude that the gene homology has no causative link to CCC. Conclusions In addition to human TRIM21, eight mammalian species showed partial gene homology to T. cruzi Ag 36, and some of these have been demonstrated to have CCC. However, rats and mice TRIM21 showed no partial homology to Ag 36. Since these species have been demonstrated to have CCC, the partial gene homology between Ag36 and TRIM 21 may not be causative or associated with CCC, as was originally hypothesized.

Gene Homologies Identified between Trypanosoma cruzi Antigen 36 and Mammalian TRIM21 Genes Using Bioinformatics Analysis

Background: We previously reported that a Human Ro52 gene sequence (TRIM21) produced a significant stretch of protein sequence homologous to T. cruzi Antigen 36 (Ag 36) protein sequence, when Ag 36 was translated in the second reading frame. Comparison of their respective DNA sequences demonstrated a 114 nucleotide region of both genes having ~70 percent partial homology. After Ro52 was shown to be an E3 Ubiquitin dependent Type I ligase for transcription factors for Interferon genes, we proposed that the Ag 36 gene, which contains a repetitive motif within it, may function to repress Ro52 in the human heart through RNA interference, or other unknown mechanism, giving rise to autoimmunity found in Chronic Chagas Cardiomyopathy (CCC).Results: To test that hypothesis, we compared various mammalian TRIM genes to the T. cruzi Ag 36 DNA sequence using the Needleman-Wunsch algorithm in the http:\\usegalaxy.eu bioinformatics tool base. In addition to human and chimpanzee, TRIM21 comparable gene regions from canine, shrew, ferret, bat, feline, and armadillo, and aardvark showed homology to the gene for Ag 36 ranging from 68 to 30 percent. However, mouse and eight other mammalian species showed no significant homology. Since mice have been shown to have severe cardiac cardiomyopathy after infection, but their TRIM21 was not homologous to Ag 36 in this study, we conclude that the gene homology has no causative link to CCC.Conclusions: In addition to human TRIM21, eight mammalian species showed partial gene homology to T. cruzi Ag 36, and some of these have been demonstrated to have CCC. However, rats and mice TRIM21 showed no partial homology to Ag 36. Since these species have been demonstrated to have CCC, the partial gene homology between Ag36 and TRIM 21 may not be causative or associated with CCC, as was originally hypothesized.

Ultrafast, alignment-free detection of repeat expansions in NGS and RNAseq data

Short tandem repeat expansions are an established cause of diseases such as Huntington’s disease. Bioinformatic methods for detecting repeat expansions in short-read sequencing have revealed new repeat expansions in humans. Current bioinformatic methods to detect repeat expansions require alignment information to identify repetitive motif enrichment at genomic locations. We present superSTR, an ultrafast method that does not require alignment, capable of efficiently processing DNA and RNA sequencing data. superSTR is applied to UK Biobank data to efficiently analyse 49,953 whole exomes in a screening experiment, identifying known mutations as well as diseases not previously associated with REs. superSTR also identifies repeat expansion motifs in RNAseq data, demonstrated in several disorders and cell lines. superSTR is a new tool for the most efficient repeat expansion detection currently possible and complements existing locus-specific, reference dependent repeat expansion analysis tools. superSTR is available from https://github.com/bahlolab/superSTR.

Development of 14 Microsatellite Markers for Zoonotic Tapeworm Dibothriocephalus dendriticus (Cestoda: Diphyllobothriidea)

Dibothriocephalus dendriticus is one of the causative agents of the fish-borne zoonosis diphyllobothriosis. Polymorphic microsatellite markers were originally developed for future genetic studies using microsatellite library screening and next-generation sequencing (NGS). Out of 128 microsatellite candidates selected after NGS analysis, 126 yielded PCR products of the expected size. A declared repetitive motif was confirmed in 92 loci by Sanger sequencing. The level of polymorphism was tested by fragment analysis. Statistical tests for observed and expected heterozygosities and deviations from Hardy–Weinberg equilibrium revealed 14 polymorphic microsatellite loci suitable for studies on the finer genetic structure of global populations of D. dendriticus.

Motiv smrti u romanima Dževada Karahasana

The motif of death in the novels of Dževad KarahasanDževad Karahasan’s novels The Eastern Diwan and Shahriar’s Ring, being the classic examples of postmodernism, feature various forms of play with genres and narrative patterns, the presence of historical persons and events, and significant intertextual dialogue, namely, quotations, with cultural and other elements of Islam. The motif of death is analyzed within the context of the plot, which is founded on this theme, as it consists of several political assassinations; whereas the idea of death as a repetitive motif is one of the compositional anchors of the novelistic structure. On the other hand, through the analysis of Karahasan’s novels it is possible to follow the attitude towards death in different periods of development of Islamic philosophy. In particular, the Hellenized strain of Islamic philosophy, rooted in esoteric thinking and spiritual religion, has led to the development of Islamic mysticism. The idea of the path of returning to the original source, which is transmitted through inner cognition and craving, is found to be the basic determinant of certain characters in the novel, as well as of the novel as a whole. Motyw śmierci w powieściach Dževada KarahasanaUtwory autorstwa Dževada Karahasana Istočni diwan i Šahrijarov prsten, jako klasyczne powieści postmodernistyczne, cechuje gra prowadzona z różnorodnymi formami gatunkowymi i wzorcami narracyjnymi, sięgnięcie po postaci i wydarzenia historyczne oraz — za sprawą licznych cytatów — dialog prowadzony z kulturą i pozostałymi elementami islamu. Analizie poddana zostanie śmierć, uwidoczniająca się w warstwie fabularnej powieści i będąca podstawą spisku w serii zabójstw politycznych, jako motyw powtarzający się — jeśli jest specyficzna — oraz jako jeden z węzłów kompozycyjnych struktur powieściowych. Jednocześnie podczas analizy powieści autorstwa Karahasana można śledzić stosunek wobec śmierci w różnych okresach rozwoju filozofii islamu. Mianowicie, zhellenizowany strumień filozofi muzułmańskiej, zanużony w myśli ezoterycznej i spirytualizmie religijnym doprowadził do rozwoju mistycyzmu muzułmańskiego. Idea powrotu do źródła, który prowadzi przez wewnętrzne poznanie i pragnienie, okazuje się podstawowym wyznacznikiem zarówno niektórych postaci, jak i powieści jako całości.

A Preview of a Construction of a Crystal Lattice Based on Intermolecular Interactions

A general procedure of crystal packing reconstruction using a certain number of intermolecular interactions is introduced and demonstrated on the crystal structure of l-histidine·HCl·H2O. Geometric restrictions based on intermolecular interactions are used for formation of a molecular pair as a basic repetitive motif of the crystal packing. The geometric restrictions were applied gradually within a supervised procedure, narrowing the scope of possible arrangement of two adjacent molecules. Subsequently, a pair of histidine molecules was used for construction of a molecular chain. The chain formed contained translation information on histidine molecules in one dimension, which coincided with one of the cell parameters. Furthermore, the periodicity in the second and third dimensions can be accomplished by chain assembly into sheets (2D), and sheets can be arranged into the final 3D structure. For this purpose, the rest of the available intermolecular interactions could be used to control the mutual assembly of molecular chains and sheets. Complete molecular packing would enable derivation of standard crystallographic parameters that can be used for verification of the structural model obtained. However, the procedure described for construction of the whole 3D structure from molecular chains was not attempted, and is only briefly outlined here. The procedure described can be employed especially when standard crystallographic parameters are not available and traditional methods based on X-ray diffraction fail.

A Comparative Study of the Antimicrobial and Structural Properties of Short Peptides and Lipopeptides Containing a Repetitive Motif KLFK

Background:In the last years, Antimicrobial Peptides (AMPs) and lipopeptides have received attention as promising candidates to treat infections caused by resistant microorganisms. </P><P> Objective: The main objective of this study was to investigate the effect of repetitive KLFK motifs and the attachment of aliphatic acids to the N-terminus of (KLFK)n peptides on therapeutic properties.Methods:Minimal inhibitory concentration against Gram (+) and (-) bacteria and yeast of synthetic compounds were determined by broth microtiter dilution method, and the toxicity was evaluated by hemolysis assay. Membrane-peptide interaction studies were performed with model phospholipid membranes mimicking those of bacterial and mammalian cells by Fluorescence Spectroscopy. The secondary structure in solution and membranes was determined by Circular Dichroism.Results:Our results showed that the resulting compounds have inhibitory activity against bacteria and fungi. The (KLFK)3 peptide showed the highest therapeutic index against bacterial and yeast strains, and the (KLFK)2 peptide conjugated with octanoic acid was the most active against yeasts. All the lipopeptides containing long-chain fatty acids (C14 or longer) were highly hemolytic at low concentrations. The antimicrobial activity of (KLFK)2 and (KLFK)3 lipopeptides was mainly associated with improved stability of the amphipathic secondary structure, which showed high contributions of α-helix in dipalmitoylphosphatidylglycerol (DPPG) vesicles.Conclusion:The repetition of the KLFK sequence and the conjugation with lipid tails allowed obtained compounds with high antimicrobial activity and low toxicity, becoming good candidates for treating infectious diseases.

Laccaria bicolor MiSSP8 is a small-secreted protein decisive for the establishment of the ectomycorrhizal symbiosis

The ectomycorrhizal symbiosis is a predominant tree-microbe interaction in forest ecosystems sustaining tree growth and health. Its establishment and functioning implies a long-term and intimate relationship between the soil-borne fungi and the roots of trees. Mycorrhiza-induced Small Secreted Proteins (MiSSPs) are hypothesized as keystone symbiotic proteins, required to set up the symbiosis by modifying the host metabolism and/or building the symbiotic interfaces.L. bicolor MiSSP8 is the third most highly induced MiSSPs in symbiotic tissues and it is also expressed in fruiting bodies. The MiSSP8-RNAi knockdown mutants are strongly impaired in their mycorrhization ability with Populus, with the lack of fungal mantle and Hartig net development due to a lack of hyphal aggregation. MiSSP8 C-terminus displays a repetitive motif containing a kexin cleavage site, recognized by KEX2 in vitro. This suggests MiSSP8 protein might be cleaved into small peptides. Moreover, the MiSSP8 repetitive motif is found in other proteins predicted secreted by both saprotrophic and ectomycorrhizal fungi. Thus, our data indicate that MiSSP8 is a small-secreted protein involved at early stages of ectomycorrhizal symbiosis, likely by regulating hyphal aggregation and pseudoparenchyma formation.

Sequence stratigraphic model for repeated “butter shale” Lagerstätten in the Ordovician (Katian) of the Cincinnati, Ohio region, USA

The “butter shale” Lagerstätten of the Cincinnati Arch have produced an abundance of articulated trilobites, along with assorted bivalves and cephalopods. These bluish gray shales are rich in clay, poorly calcified, and show vague internal bedding in outcrop. Butter shales form a repetitive motif with similar lithological and paleontological characteristics, suggesting conditions existed that can be explained by the interference between different orders of sequence stratigraphic cyclicity. The characteristics that define butter shales include rarity of coarser interbeds, homogenous, fine grain size, and abundance of burial horizons. The overriding control is siliciclastic sediment supply. During third-order transgressions, sediment supply to the basin is too low to produce thick shale-prone intervals. Conversely, during third-order falling stages, sediment supply is generally too high to favor butter shale deposition. Butter shales formed preferentially during a third-order highstand systems tract, and two subtly different variants resulted from the superimposed effects of higher order cycles. Highstands moderated by small-scale transgressions are characterized by lower background sedimentation and fewer, thinner mud deposition events. Superposition of small-scale sea-level fall on highstands produced increased background sedimentation, higher silt, and patchy fossil occurrences. Juxtaposition of various scaled highstand systems tracts provided the optimal butter shale conditions, characterized by elevated mud influx and frequent episodic burial events, leading to abundant, articulated trilobites and associated fauna. In these scenarios, episodic events provide sufficient mud to smother local faunas and create a soft, fine-grained substrate that prohibited recolonization by taxa adapted to firm substrates. Each scenario differs from the others with respect to sedimentology and faunal composition.

Ribosomal ITS2 structure in Caryophyllaeus laticeps and Caryophyllaeus brachycollis (Cestoda: Caryophyllidea), parasites of cyprinid fish

Ribosomal internal transcribed spacer 2 (ITS2) structure was studied in monozoic tapeworms Caryophyllaeus laticeps (Pallas, 1781) from freshwater bream Abramis brama (L.) and white-eyed bream Ballerus sapa (Pallas) and Caryophyllaeus brachycollis Janiszewska, 1951 from A. brama and Mediterranean barbel Barbus meridionalis (Risso). Homologous intragenomic ITS2 structure (474 bp) was determined for C. brachycollis from both fish hosts and for C. laticeps from A. brama (486 bp). Contrary to this, divergent intragenomic ITS2 copies (ITS2 paralogues) were detected in C. laticeps from B. sapa. They were mostly induced by different numbers of short repetitive motif (TA)n within the sequences, allowing their assortment into two ITS2 variants (457 and 467 bp). Current data represent first information on ITS2 structure/ITS paralogues in the caryophyllidean family Caryophyllaeidae with focus on their applicability in the molecular taxonomy of the genus Caryophyllaeus.