A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing

<p>Abstract</p> <p>Background</p> <p>The structurally complex network of minicircles and maxicircles comprising the mitochondrial DNA of kinetoplastids mirrors the complexity of the RNA editing process that is required for faithful expression of encrypted maxicircle genes. Although a few of the guide RNAs that direct this editing process have been discovered on maxicircles, guide RNAs are mostly found on the minicircles. The nuclear and maxicircle genomes have been sequenced and assembled for <it>Trypanosoma cruzi</it>, the causative agent of Chagas disease, however the complement of 1.4-kb minicircles, carrying four guide RNA genes per molecule in this parasite, has been less thoroughly characterised.</p> <p>Results</p> <p>Fifty-four CL Brener and 53 Esmeraldo strain minicircle sequence reads were extracted from <it>T. cruzi </it>whole genome shotgun sequencing data. With these sequences and all published <it>T. cruzi </it>minicircle sequences, 108 unique guide RNAs from all known <it>T. cruzi </it>minicircle sequences and two guide RNAs from the CL Brener maxicircle were predicted using a local alignment algorithm and mapped onto predicted or experimentally determined sequences of edited maxicircle open reading frames. For half of the sequences no statistically significant guide RNA could be assigned. Likely positions of these unidentified gRNAs in <it>T. cruzi </it>minicircle sequences are estimated using a simple Hidden Markov Model. With the local alignment predictions as a standard, the HMM had an ~85% chance of correctly identifying at least 20 nucleotides of guide RNA from a given minicircle sequence. Inter-minicircle recombination was documented. Variable regions contain species-specific areas of distinct nucleotide preference. Two maxicircle guide RNA genes were found.</p> <p>Conclusion</p> <p>The identification of new minicircle sequences and the further characterization of all published minicircles are presented, including the first observation of recombination between minicircles. Extrapolation suggests a level of 4% recombinants in the population, supporting a relatively high recombination rate that may serve to minimize the persistence of gRNA pseudogenes. Characteristic nucleotide preferences observed within variable regions provide potential clues regarding the transcription and maturation of <it>T. cruzi </it>guide RNAs. Based on these preferences, a method of predicting <it>T. cruzi </it>guide RNAs using only primary minicircle sequence data was created.</p

The biodiversity of freshwater Crustaceans revealed by taxonomy and mitochondrial DNA barcodes

Cytochrome oxidase subunit I (COI) barcode sequences in this file were obtained from specimens collected by plankton net in western Lake Erie in 2012 & 2013, along with later specimens collected at various locations and times, including some collected in Belize in 2015. Methods and other details about these sequences are described in a paper by the same authors in a submitted publication (2021: URL to be given here when published). The right columns below contain additional notes on lengths of sequences, GenBank accession ID (when obtained), and annotation as to whether the sequence represents a new barcode for its genus or species taxon. According to our experience, a DNA identity of \u3e96.5% with previous GenBank barcodes is a reliable range for determining a species level barcode for that morpho species; a DNA identity of 90.5% to 96.5% with previous barcodes is sufficient to identify genus. DNA identities within these ranges are considered to be barcode confirmations. Conversely, DNA identities outside of these ranges are considered to be new barcodes for that species or genus, respectively. Contradictions with previous GenBank sequences are discussed in the manuscript. The submitted manuscript includes the highest percentage identity to a previous sequence in GenBank as determined by BLASTN in June2021. The FASTA file name given here begins with a Ram Lab ID number-location and date of collection with format varying somewhat between various collections/collectors but generally including several (usually three) location letters (e.g., BHL stands for Blue Heron Lagoon) and the date usually in a 6-character format of MMDDYY, and optionally a sample number for that date either preceding the location letters or following the date. Collection location abbreviations include the following: All sequences starting with PM, Toledo Harbor in western Lake Erie; LMUSK, Lake Muskoday, Belle Isle, Detroit; SCL, Saint Clair River; BHL, Blue Heron Lagoon, Belle Isle; LE, LakeErie; LSC, Lake St.Clair; MMLE; Metzgers Marsh, LakeErie; MM, Metzgers Marsh; LP, Leonard Preserve, Manchester, Michigan; HR, Huron River Drive, Ypsilanti, Michigan; LCL, Little Cedar Lake, Orion, MI; HLE, Harbor Lake Erie; LHLE, Lorain Harbor Lake Erie; BZEB1P, Cenote in Shipstern Reserve, Corozal, Belize, Central America

Peroxidase-Like Activity of Ferrihydrite and Hematite Nanoparticles for the Degradation of Methylene Blue

The peroxidase-like catalytic properties of 2-line ferrihydrite (2LFh) and hematite nanoparticles (NPs) for the degradation of methylene blue (MB) were studied. It is highlighted that the hematite NPs were prepared from the transformation of the metastable 2LFh NPs. It was found that the 2LFh NPs exhibited poor crystallinity with an average size of 5 nm, while the hematite NPs exhibited high crystallinity with an average size of ca. 100 nm. It was found that the total degradation of MB occurred for hematite NPs, while only a maximum degradation of 69% was possible for the 2LFh NPs. The Michaelis–Menten parameters indicated that the hematite NPs present higher catalytic activity than the 2LFh NPs at basic pH. It was found that the ordered surface of the hematite NPs has a stronger effect for the degradation of MB than its low surface area. It was concluded that the crystal planes of the hematite NPs affect the catalytic process more significantly than the high surface area of 2LFh NPs

Complete Genome Sequence of Houston Virus, a Newly Discovered Mosquito-Specific Virus Isolated from Culex quinquefasciatus in Mexico

ABSTRACT We fully sequenced the genome of Houston virus, a recently discovered mosquito-associated virus belonging to the newly established family Mesoniviridae. The isolate was recovered from Culex quinquefasciatus in southern Mexico, which shows that the geographic range of Houston virus is not restricted to the United States in North America

Differential Regulation of the Variations Induced by Environmental Richness in Adult Neurogenesis as a Function of Time: A Dual Birthdating Analysis

Adult hippocampal neurogenesis (AHN) augments after environmental enrichment (EE) and it has been related to some of the anxiolytic, antidepressant and neuroprotective effects of EE. Indeed, it has been suggested that EE specifically modulates hippocampal neurogenic cell populations over the course of time. Here we have used dual-birthdating to study two subpopulations of newborn neuron in mice (Mus musculus): those born at the beginning and at the end of enrichment. In this way, we demonstrate that while short-term cell survival is upregulated after an initial 1 week period of enrichment in 2 month old female mice, after long-term enrichment (2 months) neither cell proliferation nor the survival of the younger newly born cell populations are distinguishable from that observed in non-enriched control mice. In addition, we show that the survival of older newborn neurons alone (i.e. those born at the beginning of the enrichment) is higher than in controls, due to the significantly lower levels of cell death. Indeed, these parameters are rapidly adjusted to the sudden cessation of the EE conditions. These findings suggest both an early selective, long-lasting effect of EE on the neurons born in the initial stages of enrichment, and a quick response when the environment again becomes impoverished. Therefore, EE induces differential effects on distinct subpopulations of newborn neurons depending on the age of the immature cells and on the duration of the EE itself. The interaction of these two parameters constitutes a new, specific regulation of these neurogenic populations that might account for the long-term enrichment's behavioral effects

Mifepristone Prevents Stress-Induced Apoptosis in Newborn Neurons and Increases AMPA Receptor Expression in the Dentate Gyrus of C57/BL6 Mice

Chronic stress produces sustained elevation of corticosteroid levels, which is why it is considered one of the most potent negative regulators of adult hippocampal neurogenesis (AHN). Several mood disorders are accompanied by elevated glucocorticoid levels and have been linked to alterations in AHN, such as major depression (MD). Nevertheless, the mechanism by which acute stress affects the maturation of neural precursors in the dentate gyrus is poorly understood. We analyzed the survival and differentiation of 1 to 8 week-old cells in the dentate gyrus of female C57/BL6 mice following exposure to an acute stressor (the Porsolt or forced swimming test). Furthermore, we evaluated the effects of the glucocorticoid receptor (GR) antagonist mifepristone on the cell death induced by the Porsolt test. Forced swimming induced selective apoptotic cell death in 1 week-old cells, an effect that was abolished by pretreatment with mifepristone. Independent of its antagonism of GR, mifepristone also induced an increase in the percentage of 1 week-old cells that were AMPA+. We propose that the induction of AMPA receptor expression in immature cells may mediate the neuroprotective effects of mifepristone, in line with the proposed antidepressant effects of AMPA receptor potentiators

Search for resonances in the mass spectrum of muon pairs produced in association with b quark jets in proton-proton collisions at root 8 and 13 TeV

A search for resonances in the mass range 12-70 GeV produced in association with a b quark jet and a second jet, and decaying to a muon pair, is reported. The analysis is based on data from proton-proton collisions at center-of-mass energies of 8 and 13 TeV, collected with the CMS detector at the LHC and corresponding to integrated luminosities of 19.7 and 35.9 fb(-1), respectively. The search is carried out in two mutually exclusive event categories. Events in the first category are required to have a b quark jet in the central region (|| 2.4) and at least one jet in the forward region (|| > 2.4). Events in the second category are required to have two jets in the central region, at least one of which is identified as a b quark jet, no jets in the forward region, and low missing transverse momentum. An excess of events above the background near a dimuon mass of 28 GeV is observed in the 8 TeV data, corresponding to local significances of 4.2 and 2.9 standard deviations for the first and second event categories, respectively. A similar analysis conducted with the 13 TeV data results in a mild excess over the background in the first event category corresponding to a local significance of 2.0 standard deviations, while the second category results in a 1.4 standard deviation deficit. The fiducial cross section measurements and 95% confidence level upper limits on those for a resonance consistent with the 8 TeV excess are provided at both collision energies