Deeplasmid: deep learning accurately separates plasmids from bacterial chromosomes

Plasmids are mobile genetic elements that play a key role in microbial ecology and evolution by mediating horizontal transfer of important genes, such as antimicrobial resistance genes. Many microbial genomes have been sequenced by short read sequencers and have resulted in a mix of contigs that derive from plasmids or chromosomes. New tools that accurately identify plasmids are needed to elucidate new plasmid-borne genes of high biological importance. We have developed Deeplasmid, a deep learning tool for distinguishing plasmids from bacterial chromosomes based on the DNA sequence and its encoded biological data. It requires as input only assembled sequences generated by any sequencing platform and assembly algorithm and its runtime scales linearly with the number of assembled sequences. Deeplasmid achieves an AUC–ROC of over 89%, and it was more accurate than five other plasmid classification methods. Finally, as a proof of concept, we used Deeplasmid to predict new plasmids in the fish pathogen Yersinia ruckeri ATCC 29473 that has no annotated plasmids. Deeplasmid predicted with high reliability that a long assembled contig is part of a plasmid. Using long read sequencing we indeed validated the existence of a 102 kb long plasmid, demonstrating Deeplasmid''s ability to detect novel plasmids.     

Transformation of group A streptococci by electroporation

Abstract The introduction, via electroporation, of free plasmid DNA into three strains of Streptococcus pyogenes is described. The method is very simple and rapid and efficiencies vary from 1 × 10³ to 4 × 10⁴ per μg of DNA. The method was also used to introduce an integrative plasmid and transformants were obtained, albeit at a somewhat lower frequency (2 × 10²). Some of the plasmids used in this study are derivatives of the Lactococcus lactis subsp. cremoris Wg2 plasmid pWV01. These broad host range vectors replicate in Gram-positives as well as Gram-negatives (viz. Escherichia coli ). Here we show that they also replicate in S. pyogenes and S. sanguis .     

Purification of the intact monomeric 110 kDa form of the androgen receptor from calf uterus to near homogeneity

In the present study, culf uterine tissue has been used for isolation of androgen receptors. This tissue appeared to be a favourable source for large-scale purification of androgen receptors, because of the relatively high level of androgen receptors and the low concentration of proteolytic enzymes. The purification involved differential phosphocellulose and DNA affinity chromatography as first steps. The non-transformed receptor was passed through these matrices in order to remove contaminating DNA-binding proteins. After a transformation step to the DNA-binding state, the receptor was bound to DNA cellulose and subsequently eluted with MgCl₂. A 0.5% pure androgen receptor preparation was obtained. Photoaffinity labelling with [³H]R1881 (methyltrienolone) was used to determine the size of the receptor at this stage of purification and during the following steps. Subsequently, isoelectric focussing of the partially purified androgen receptor preparation in an aqueous glycerol gradient was performed. In this step, the progesterone receptor, which is copurified with the androgen receptor protein during the first part of the purification procedure, focussed at pH 5.5, while the androgen receptor could be isolated at pH 5.8. The isoelectric focussing procedure could be applied in a preparative way for further purification of androgen receptors. After this step an approx. 8% pure preparation was obtained. Polyacrylamide gel electrophoresis of S-carboxymethylated androgen receptor was used as the final purification step. The [³H]methyltrienolone labelled androgen receptor from calf uterus was purified to homogeneity and consisted of one polypeptide with a molecular mass of 110 kDa.     

In vitro anticryptosporidial activity of dinitroaniline herbicides

Abstract Despite the evaluation of over 100 antimicrobial drugs, the diarrheal disease cryptosporidiosis has remained refractory to treatment. We report the evaluation of five dinitroaniline herbicides including trifluralin, profluralin, nitralin, pendimethalin, and fluchloralin for anticryptosporidial activity in an in vitro cultivation model of Cryptosporidium parvum . All five compounds exhibited significant anticryptosporidial activities with no corresponding evidence of toxicity. The most active compound was pendimethalin with an IC₅₀ of 0.19 μM while nitralin was the least active with an IC₅₀ of 4.5 μM. These compounds should be evaluated further in an animal model of cryptosporidiosis.     

Transplacental Zika virus transmission in ex vivo perfused human placentas

A Zika virus (ZIKV) infection during pregnancy can result in severe birth defects such as microcephaly. To date, it is incompletely understood how ZIKV can cross the human placenta. Furthermore, results from studies in pregnant mice and non-human primates are conflicting regarding the role of cross-reactive dengue virus (DENV) antibodies on transplacental ZIKV transmission. Elucidating how ZIKV can cross the placenta and which risk factors contribute to this is important for risk assessment and for potential intervention strategies for transplacental ZIKV transmission. In this study we use an ex vivo human placental perfusion model to study transplacental ZIKV transmission and the effect that cross-reactive DENV antibodies have on this transmission. By using this model, we demonstrate that DENV antibodies significantly increase ZIKV uptake in perfused human placentas and that this increased uptake is neonatal Fc-receptor-dependent. Furthermore, we show that cross-reactive DENV antibodies enhance ZIKV infection in term human placental explants and in primary fetal macrophages but not in primary trophoblasts. Our data supports the hypothesis that presence of cross-reactive DENV antibodies could be an important risk factor for transplacental ZIKV transmission. Furthermore, we demonstrate that the ex vivo placental perfusion model is a relevant and animal friendly model to study transplacental pathogen transmission.     

Optimization of α-ketoamide based p38 inhibitors through modifications to the region that binds to the allosteric site

We have optimized a novel series of potent p38 MAP kinase inhibitors based on an α-ketoamide scaffold through structure based design that due to their extended molecular architecture bind, in addition to the ATP site, to an allosteric pocket. In vitro ADME, in vivo PK and efficacy studies show these compounds to have drug-like characteristics and have resulted in the nomination of a development candidate which is currently in phase II clinical trials for the oral treatment of inflammatory conditions.     

Can a stench be beautiful? – Osmophores in stem-succulent stapeliads (Apocynaceae-Asclepiadoideae-Ceropegieae-Stapeliinae)

Carrion flower stapeliads are examples of olfactory mimicry, forming sapromyiophilous flowers, which mimic food sources or oviposition sites to attract fly pollinators. The aim of this work was to investigate the ultrastructure of osmophores involved in the release of the carrion odor of Orbea variegata and Boucerosia indica flowers. In spite of their similar architecture (epidermal epithelium+subepidermal secretory layers), the osmophores of stapeliads feature some differences in morphology and ultrastructure. The epidermal epithelial cells of O. variegata and B. indica differ in shape, but both are extremely rich in endoplasmic reticulum and flocculent material in the vacuole. Unlike the Orbea, Boucerosia has starchless leucoplasts in the epidermal epithelium. Orbea features a cuticle with microchannels, while Boucerosia has a different mechanism for the pathway of scent substances to the cell exterior. They are released by rupturing of the outer layer of cuticle at the apex of the papillae. The epidermal cells of the adaxial corolla differ even between parts of the corolla, the corolla lobes and the annulus in the flower. This diversity may be connected with an odor gradient. The morphological and anatomical features of stapeliad (subtribe Stapeliinae) osmophores are generally similar to osmophores of members of subtribe Ceropegiinae (Ceropegia), thus, we suggest that this model of osmophores evolved before early diversification of Ceropegieae. The ultrastructural features of stapeliad osmophores are generally similar to those of Araceae, Orchidaceae and Passifloraceae.     

Artificial sowing of endangered dry grassland species into disused basalt quarries

Steppe-like dry (semi) natural grasslands are valuable and endangered habitats in central Europe. In the study area (the ?eské st?edoho?í Hills, Czech Republic), they occur in fragments on southern slopes of volcanic hills, often in the vicinity of quarries, which are numerous there. We performed sowing experiments and observed seedling recruitment of six species, typical for the dry grasslands, in 9 basalt quarries located in 3 different climatic regions over 3 yr. The sowing experiments were established in young successional stages, 5–12 yr after quarrying was stopped. The objectives of the experiments were to evaluate: (i) if seedling recruitment and survival of the target species are possible regarding different climatic regions and (ii) what is the influence of weather fluctuations among years on seedling survival. Seedlings of all studied species were able to recruit and survive in the early successional stages at least in some quarries. The species, except one, showed significant differences in recruitment among the climatic regions, with the best recruitment and survival in the driest and warmest region. Seedlings of two species did not recruit in the wettest and coldest region. All species survived in the driest and warmest region, while only one did so in the coldest and wettest region. Different weather conditions in the studied years significantly influenced recruitment of two species. The number of localities (floristic records) of particular species in the regions was the best predictor of species germination and survival. Thus a traditional floristic survey may help to predict success of species in restoration projects. It emerged that artificial sowing can be considered in restoration programs as a way of contributing to restoration of dry grasslands in disused quarries.     

Differential effects of chronic agonist administration on mu-opioid receptor- and muscarinic receptor-regulated adenylate cyclase in rat striatal neurons.

In cultured rat striatal neurons exposed to 10 microM morphine or oxotremorine for 24 hours, we observed an increased (about 30%) dopamine D1 receptor-stimulated cyclic AMP production, whereas no desensitization of mu-opioid receptor or muscarinic cholinergic receptor was found. However, whereas upregulation of dopamine D1 receptor-stimulated adenylate cyclase activity upon 7 days morphine exposure was at least as pronounced as observed after 24 hours of exposure to the opioid, this adaptive phenomenon was virtually absent following one week of oxotremorine treatment. This reduced adenylate cyclase sensitization upon 7 days oxotremorine exposure appeared to coincide with desensitization of muscarinic cholinergic receptors. A possible role of the resistance of mu receptors to desensitization and the (resulting) upregulation of the neuronal adenylate cyclase system upon chronic receptor activation in the development of opiate tolerance and dependence is suggested.