Polar features in the flagellar propulsion of E. coli bacteria

E. coli bacteria swim following a run and tumble pattern. In the run state all flagella join in a single helical bundle that propels the cell body along approximately straight paths. When one or more flagellar motors reverse direction the bundle unwinds and the cell randomizes its orientation. This basic picture represents an idealization of a much more complex dynamical problem. Although it has been shown that bundle formation can occur at either pole of the cell, it is still unclear whether this two run states correspond to asymmetric propulsion features. Using holographic microscopy we record the 3D motions of individual bacteria swimming in optical traps. We find that most cells possess two run states characterised by different propulsion forces, total torque and bundle conformations. We analyse the statistical properties of bundle reversal and compare the hydrodynamic features of forward and backward running states. Our method is naturally multi-particle and opens up the way towards controlled hydrodynamic studies of interacting swimming cells

Artemether resistance in vitro is linked to mutations in PfATP6 that also interact with mutations in PfMDR1 in travellers returning with Plasmodium falciparum infections.

BACKGROUND: Monitoring resistance phenotypes for Plasmodium falciparum, using in vitro growth assays, and relating findings to parasite genotype has proved particularly challenging for the study of resistance to artemisinins. METHODS: Plasmodium falciparum isolates cultured from 28 returning travellers diagnosed with malaria were assessed for sensitivity to artemisinin, artemether, dihydroartemisinin and artesunate and findings related to mutations in pfatp6 and pfmdr1. RESULTS: Resistance to artemether in vitro was significantly associated with a pfatp6 haplotype encoding two amino acid substitutions (pfatp6 A623E and S769N; (mean IC50 (95% CI) values of 8.2 (5.7 - 10.7) for A623/S769 versus 623E/769 N 13.5 (9.8 - 17.3) nM with a mean increase of 65%; p = 0.012). Increased copy number of pfmdr1 was not itself associated with increased IC50 values for artemether, but when interactions between the pfatp6 haplotype and increased copy number of pfmdr1 were examined together, a highly significant association was noted with IC50 values for artemether (mean IC50 (95% CI) values of 8.7 (5.9 - 11.6) versus 16.3 (10.7 - 21.8) nM with a mean increase of 87%; p = 0.0068). Previously described SNPs in pfmdr1 are also associated with differences in sensitivity to some artemisinins. CONCLUSIONS: These findings were further explored in molecular modelling experiments that suggest mutations in pfatp6 are unlikely to affect differential binding of artemisinins at their proposed site, whereas there may be differences in such binding associated with mutations in pfmdr1. Implications for a hypothesis that artemisinin resistance may be exacerbated by interactions between PfATP6 and PfMDR1 and for epidemiological studies to monitor emerging resistance are discussed

A Formal Model of Algorand Smart Contracts

We develop a formal model of Algorand stateless smart contracts (stateless ASC1). We exploit our model to prove fundamental properties of the Algorand blockchain, and to establish the security of some archetypal smart contracts. While doing this, we highlight various design patterns supported by Algorand. We perform experiments to validate the coherence of our formal model w.r.t. the actual implementation

Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs

The recent emergence of the novel SARS-CoV-2 in China and its rapid spread in the human population has led to a public health crisis worldwide. Like in SARS-CoV, horseshoe bats currently represent the most likely candidate animal source for SARS-CoV-2. Yet, the specific mechanisms of cross-species transmission and adaptation to the human host remain unknown. Here we show that the unsupervised analysis of conservation patterns across the beta-CoV spike protein family, using sequence information alone, can provide valuable insights on the molecular basis of the specificity of beta-CoVs to different host cell receptors. More precisely, our results indicate that host cell receptor usage is encoded in the amino acid sequences of different CoV spike proteins in the form of a set of specificity determining positions (SDPs). Furthermore, by integrating structural data, in silico mutagenesis and coevolution analysis we could elucidate the role of SDPs in mediating ACE2 binding across the Sarbecovirus lineage, either by engaging the receptor through direct intermolecular interactions or by affecting the local environment of the receptor binding motif. Finally, by the analysis of coevolving mutations across a paired MSA we were able to identify key intermolecular contacts occurring at the spike-ACE2 interface. These results show that effective mining of the evolutionary records held in the sequence of the spike protein family can help tracing the molecular mechanisms behind the evolution and host-receptor adaptation of circulating and future novel b-CoVs. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology

Radon concentration in self-bottled mineral spring waters as a possible public health issue

Since 2013, the Council Directive 2013/51/Euratom has been regulating the content of radioactive substances in water intended for human consumption. However, mineral waters are exempted from this regulation, including self-bottled springs waters, where higher radon concentration are expected. Therefore, a systematic survey has been conducted on all the 33 mineral spring waters of Lazio (a region of Central Italy) in order to assess if such waters, when self-bottled, may be of concern for public health. Waters have been sampled in two different ways to evaluate the impact of bottling on radon concentration. Water sampling was possible for 20 different spring waters, with 6 samples for each one. The results show that 2 (10%) of measured mineral spring waters returned radon concentrations higher than 100 Bq L−1, i.e., the parametric value established by the Council Directive. These results, if confirmed by other surveys involving a higher number of mineral spring waters, would suggest regulating also these waters, especially in countries like Italy for which: (i) mineral water consumption is significant; (ii) mineral concession owners generally allow the consumers to fill bottles and containers, intended for transport and subsequent consumption, directly from public fountains or from fountains within the plant; (iii) the consumers’ habit of drinking self-bottled mineral water is widespread

DGLinker: flexible knowledge-graph prediction of disease-gene associations

As a result of the advent of high-throughput technologies, there has been rapid progress in our understanding of the genetics underlying biological processes. However, despite such advances, the genetic landscape of human diseases has only marginally been disclosed. Exploiting the present availability of large amounts of biological and phenotypic data, we can use our current understanding of disease genetics to train machine learning models to predict novel genetic factors associated with the disease. To this end, we developed DGLinker, a webserver for the prediction of novel candidate genes for human diseases given a set of known disease genes. DGLinker has a user-friendly interface that allows non-expert users to exploit biomedical information from a wide range of biological and phenotypic databases, and/or to upload their own data, to generate a knowledge-graph and use machine learning to predict new disease-associated genes. The webserver includes tools to explore and interpret the results and generates publication-ready figures. DGLinker is available at https://dglinker.rosalind.kcl.ac.uk. The webserver is free and open to all users without the need for registration

Assessing the accuracy of contact and distance predictions in CASP14

We present the results of the assessment of the intramolecular residue-residue contact and distance predictions from groups participating in the 14th round of the CASP experiment. The performance of contact prediction methods was evaluated with the measures used in previous CASPs, while distance predictions were assessed based on a new protocol, which considers individual distance pairs as well as the whole predicted distance matrix, using a graph-based framework. The results of the evaluation indicate that predictions by the tFold framework, TripletRes and DeepPotential were the most accurate in both categories. With regards to progress in method performance, the results of the assessment in contact prediction did not reveal any discernible difference when compared to CASP13. Arguably, this could be due to CASP14 FM targets being more challenging than ever before.We present the results of the assessment of the intramolecular residue-residue contact and distance predictions from groups participating in the 14th round of the CASP experiment. The performance of contact prediction methods was evaluated with the measures used in previous CASPs, while distance predictions were assessed based on a new protocol, which considers individual distance pairs as well as the whole predicted distance matrix, using a graph-based framework. The results of the evaluation indicate that predictions by the tFold framework, TripletRes and DeepPotential were the most accurate in both categories. With regards to progress in method performance, the results of the assessment in contact prediction did not reveal any discernible difference when compared to CASP13. Arguably, this could be due to CASP14 FM targets being more challenging than ever before

Mass assembly and AGN activity at z≳1.5z\gtrsim1.5 in the dense environment of XDCPJ0044.0-2033

XDCP0044.0-2033 is the most massive galaxy cluster known at z>1.5 and its core shows a high density of galaxies which are experiencing mergers and hosting nuclear activity. We present a multi-wavelength study of a region located 157 kpc from the center of this galaxy cluster, for which we have photometric and spectroscopic multi-wavelength observations (high resolution HST images in F105W, F140W and F160W bands, NIR KMOS data in H and YJ bands and Chandra ACIS-S X-ray data). Our main goal is to investigate the environmental effects acting on the galaxies inhabiting this high density region. We find that the analyzed region hosts at least nine different sources, six of them confirmed to be cluster members within a narrow redshift range 1.5728<z<1.5762. These sources form two different complexes at a projected distance of $\sim$13 kpc, which are undergoing merging on an estimated timescale off 10-30 Myr. One of the sources shows the presence of a broad H alpha emission line and is classified as Type 1 AGN. This AGN is associated to an X-ray point-like source, whose emission appears moderately obscured (with intrinsic absorption $N_{H} \sim 10^{22} cm^{-2}$) and hosts a relatively massive black hole with mass $M_{BH} \sim 10^{7} M_{\odot}$, which is accreting with an Eddington ratio of $\sim$0.2. We conclude that the analyzed region is consistent with being the formation site of a secondary BCG. These findings, together with an in-depth analysis the X-ray morphology of the cluster, suggest a merging scenario of the entire cluster, with two massive halos both harbouring two rapidly evolving BCGs on the verge of being assembled. Our results are also consistent with the scenario in which the AGN phase in member galaxies is triggered by gas-rich mergers, playing a relevant role in the formation of the red sequence of elliptical galaxies observed in the center of local galaxy clusters

Sperm ultrastructure and spermiogenesis in two Exogone species (Polychaeta, Syllidae, Exogoninae)

The spermatozoa of Exogone naidina and E. dispar are characterized by a prominent bell-shaped acrosome, a spheroidal nucleus, and a conventional flagellum. During spermiogenesis, the acrosomal vesicle undergoes conspicuous modifications leading to its final bell shape with a posterior opening. The subacrosomal material initially shows radiating filaments but in mature sperms it appears as a meshwork of electron-opaque material. The acrosomal axis is oblique with respect to the main longitudinal sperm axis. The chromatin is arranged in electronopaque strands in the early spermatids, then becomes amorphous, and is finally organized in filaments in mature sperms. Centrioles are orthogonally arranged beneath the nucleus and fibers radiate from the distal centriole to contact the plasma membrane and the single mitochondrion. The latter is located eccentrically on the side of the nucleus opposite the acrosome. A disk-shaped structure is evident beneath the distal centriole. The flagellar axoneme has a 9+2 microtubule pattern. A conspicuous glycocalyx surrounds the flagellar plasma membrane, and an electron-lucent space is present between these two structures at the distal tip of the flagellum. We compare the sperm morphology of these two species of Exogone with that described in other members of the subfamily Exogoninae. The fine structure of these two species supports the occurrence of an ent-aquasperm type within Exogoninae, in accordance with the brood strategy present within this subfamily. The mode of reproduction is of taxonomic importance for defining subfamilies within Syllidae, and is likely also of phylogenetic significance. Because epitoky is probably plesiomorphic, the ent-aquasperm type found in Exogoninae can be considered a derived feature within Syllidae

DGLinker: flexible knowledge-graph prediction of disease-gene associations

As a result of the advent of high-throughput technologies, there has been rapid progress in our understanding of the genetics underlying biological processes. However, despite such advances, the genetic landscape of human diseases has only marginally been disclosed. Exploiting the present availability of large amounts of biological and phenotypic data, we can use our current understanding of disease genetics to train machine learning models to predict novel genetic factors associated with the disease. To this end, we developed DGLinker, a webserver for the prediction of novel candidate genes for human diseases given a set of known disease genes. DGLinker has a user-friendly interface that allows non-expert users to exploit biomedical information from a wide range of biological and phenotypic databases, and/or to upload their own data, to generate a knowledge-graph and use machine learning to predict new disease-associated genes. The webserver includes tools to explore and interpret the results and generates publication-ready figures. DGLinker is available at https://dglinker.rosalind.kcl.ac.uk. The webserver is free and open to all users without the need for registration