ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain of Drosophila melanogaster

To date, different strategies of whole-genome sequencing (WGS) have been developed in order to understand the genome structure and functions. However, the analysis of genomic sequences obtained from natural populations is challenging and the biological interpretation of sequencing data remains the main issue. The MinION device developed by Oxford Nanopore Technologies (ONT) is able to generate long reads with minimal costs and time requirements. These valuable assets qualify it as a suitable method for performing WGS, especially in small laboratories. The long reads resulted using this sequencing approach can cover large structural variants and repetitive sequences commonly present in the genomes of eukaryotes. Using MinION, we performed two WGS assessments of a Romanian local strain of Drosophila melanogaster, referred to as Horezu_LaPeri (Horezu). In total, 1,317,857 reads with a size of 8.9 gigabytes (Gb) were generated. Canu and Flye de novo assembly tools were employed to obtain four distinct assemblies with both unfiltered and filtered reads, achieving maximum reference genome coverages of 94.8% (Canu) and 91.4% (Flye). In order to test the quality of these assemblies, we performed a two-step evaluation. Firstly, we considered the BUSCO scores and inquired for a supplemental set of genes using BLAST. Subsequently, we appraised the total content of natural transposons (NTs) relative to the reference genome (ISO1 strain) and mapped the mdg1 retroelement as a resolution assayer. Our results reveal that filtered data provide only slightly enhanced results when considering genes identification, but the use of unfiltered data had a consistent positive impact on the global evaluation of the NTs content. Our comparative studies also revealed differences between Flye and Canu assemblies regarding the annotation of unique versus repetitive genomic features. In our hands, Flye proved to be moderately better for gene identification, while Canu clearly outperformed Flye for NTs analysis. Data concerning the NTs content were compared to those obtained with ONT for the D. melanogaster ISO1 strain, revealing that our strategy conducted to better results. Additionally, the parameters of our ONT reads and assemblies are similar to those reported for ONT experiments performed on various model organisms, revealing that our assembly data are appropriate for a proficient annotation of the Horezu genome.     

Face preference at birth

Four experiments are reported that were aimed at elucidating some of the controversial issues concerning the preference for facelike patterns in newborns. The experiments were devised to contrast the original and the revised versions of the sensory hypothesis and the structural hypothesis as accounts of face preference in newborns. Experiments 1A and 1B supported the structural hypothesis by showing a visual preference for the stimulus for which components were located in the correct arrangement for a human face. Experiment 2 supported the sensory hypothesis by showing a visual preference for stimuli that were designed to have the optimal spatial frequency components for the newborn visual system. Experiment 3 showed that babies directed attention to a facelike pattern also when it was presented simultaneously with a nonfacelike stimulus with optimal spatial frequency for the newborn visual system.     

Aromatic polyureas and polythioureas by a new polycondensation reaction using ethylene chlorophosphite as reagent

Summary Aromatic polyureas and polythioureas are prepared from aromatic diamines and carbon dioxide or carbon disulfide, by a new direct polycondensation reaction with ethylene chlorophosphite as reagent in pyridine as solvent and acceptor for hydrochloric acid at 50–60° for 6–7 hours.     

Thermopower oscillations in magnesium

Relative measurements of the thermopower, the magnetoresistance, and the Hall voltage of magnesium single crystals were made at 4.2 K in a transverse magnetic field as a function of the magnetic field and the crystallographic direction. It was found that, for a magnetic field parallel to the [0001] orientation, the thermopower is an oscillatory function of magnetic field, with a period of 4.35×10^?7 G^?1, while the magnetoresistance and the Hall voltage have shown nonoscillatory behavior for the same orientation.     

Mechanochemically initiated polymerisations. 12. Spectral and thermal characterisation of some products obtained by vibratory milling of benzene and pyridine

Vibratory milling is used to open the aromatic ring of compounds such as benzene and pyridine and this is followed by concatenation of the structural units. The products obtained form both the soluble fractions in methanol, i.e. dimethylformamide and the insoluble fraction, the latter being found in the prevalent amount. Analysis of the soluble fractions by infrared spectroscopy (i.r.) and pyrolysis-gas chromatography (p.-g.c.) conforms their linear structure of the polyenic type with some short crosslinkings and a great sensitivity to the action of atmospheric oxygen.     

GBR with an e-PTFE membrane associated with DFDBA: histologic and histochemical analysis in a human implant retrieved after 4 years of loading

As a result of a fracture to the cemented post and core, a pure titanium implant was extracted from a 54-year-old patient after 4 years of clinical loading. At implantation, the implant was positioned into an extraction socket and the defect was treated with an e-PTFE membrane associated with a DFDBA graft. At retrieval the implant underwent histologic and histochemical examination to assess the characteristics of the regenerated bone after 4 years of prosthetic loading. The implant showed an angular bony defect at the smooth collar, but the bone-implant direct contact rate seemed to be elevated in the remaining implant surface. Normal transmitted and polarized light examinations demonstrated that most of the DFDBA particles were resorbed and substituted by vital newly formed bone. The regenerated bone appeared compact with secondary osteons and large haversian canals; however, some partially mineralized remnants residuated in the spaces, between the osteons. Within the limits of this study, the authors concluded that DFDBA can be substituted by the host bone, but the rate of substitution is very slow and not complete after 4 years. From a clinical point of view, however, the load-bearing capacity of the bone regenerated with the membrane technique associated with DFDBA appeared to be similar to that of normal bone.     

Dual-energy X-ray absorptiometry in osteonecrosis of the femoral head

Osteonecrosis of the hip classically produces a heterogeneous density in the femoral head, although the bone marrow ischemia extends down to the femoral neck and trochanters. Also, bone insufficiency fractures due to diffuse bone loss have been implicated in the genesis of osteonecrosis. OBJECTIVES: To use dual-energy X-ray absorptiometry to quantify the bone changes produced by osteonecrosis of the hip and to compare bone mineral density values in patients with osteonecrosis of the hip and in controls. METHODS: Bone mineral density was measured at the femoral neck (total femoral neck, Ward's triangle, and trochanter), femoral head and lumbar spine using dual-energy X-ray absorptiometry (DPX, L Lunar) in 22 patients with osteonecrosis of the hip and in 22 age- and sex-matched controls. RESULTS: In the patients with osteonecrosis, bone mineral density on the affected side was higher than on the opposite side at the femoral head (+18%), femoral neck (+7%), and Ward's triangle (+6%) and lower at the trochanter (-4%). These differences were most marked at the more advanced end of the osteonecrosis spectrum. As compared to age-specific normative values, the osteonecrosis patients had moderately decreased bone mineral density values at the lumbar spine (-0.53 +/- 1.1 SD or -6 +/- 1.5%) and at the femoral neck on the normal side (-0.9 +/- 1.4 SD or 12 +/- 1.8%). As compared to the controls, bone mineral density was significantly decreased at Ward's triangle (-25%; P: 0.04) and nonsignificantly decreased at the lumbar spine (-4.7%; P: 0.15) and at the femoral neck (-15%; P: 0.09).     

Modification of (CH)x chains during thermal cis-trans isomerization

It is shown that the isomerization of cis polyacetylene at 195°C for long periods is accompanied by structural modifications. Infra-red and pyrolysis gas-chromatography data suggest that the aromatization process occurs even at this temperature.     

Aromatic Polyamides

Summary Aromatic polyamides are prepared by a direct condensation reaction using phenyldichloropnosphite as reagent at 80–90°(2h) and 95–100°(4h) in N-methyl-2-pirrolidone and pyridine as acceptor for hydrochloric acid.