Phylogenetic Analysis of SARS-CoV-2 Data Is Difficult

Numerous studies covering some aspects of SARS-CoV-2 data analyses are being published on a daily basis, including a regularly updated phylogeny on nextstrain.org. Here, we review the difficulties of inferring reliable phylogenies by example of a data snapshot comprising a quality-filtered subset of 8,736 out of all 16,453 virus sequences available on May 5, 2020 from gisaid.org. We find that it is difficult to infer a reliable phylogeny on these data due to the large number of sequences in conjunction with the low number of mutations. We further find that rooting the inferred phylogeny with some degree of confidence either via the bat and pangolin outgroups or by applying novel computational methods on the ingroup phylogeny does not appear to be credible. Finally, an automatic classification of the current sequences into subclasses using the mPTP tool for molecular species delimitation is also, as might be expected, not possible, as the sequences are too closely related. We conclude that, although the application of phylogenetic methods to disentangle the evolution and spread of COVID-19 provides some insight, results of phylogenetic analyses, in particular those conducted under the default settings of current phylogenetic inference tools, as well as downstream analyses on the inferred phylogenies, should be considered and interpreted with extreme caution.     

SPART: A versatile and standardized data exchange format for species partition information

A wide range of data types can be used to delimit species and various computer-based tools dedicated to this task are now available. Although these formalized approaches have significantly contributed to increase the objectivity of species delimitation (SD) under different assumptions, they are not routinely used by alpha-taxonomists. One obvious shortcoming is the lack of interoperability among the various independently developed SD programs. Given the frequent incongruences between species partitions inferred by different SD approaches, researchers applying these methods often seek to compare these alternative species partitions to evaluate the robustness of the species boundaries. This procedure is excessively time consuming at present, and the lack of a standard format for species partitions is a major obstacle. Here, we propose a standardized format, SPART, to enable compatibility between different SD tools exporting or importing partitions. This format reports the partitions and describes, for each of them, the assignment of individuals to the “inferred species”. The syntax also allows support values to be optionally reported, as well as original trees and the full command lines used in the respective SD analyses. Two variants of this format are proposed, overall using the same terminology but presenting the data either optimized for human readability (matricial SPART) or in a format in which each partition forms a separate block (SPART.XML). ABGD, DELINEATE, GMYC, PTP and TR2 have already been adapted to output SPART files and a new version of LIMES has been developed to import, export, merge and split them.     

A cell‐based model system links chromothripsis with hyperploidy

A remarkable observation emerging from recent cancer genome analyses is the identification of chromothripsis as a one‐off genomic catastrophe, resulting in massive somatic DNA structural rearrangements (SRs). Largely due to lack of suitable model systems, the mechanistic basis of chromothripsis has remained elusive. We developed an integrative method termed “complex alterations after selection and transformation (CAST),” enabling efficient in vitro generation of complex DNA rearrangements including chromothripsis, using cell perturbations coupled with a strong selection barrier followed by massively parallel sequencing. We employed this methodology to characterize catastrophic SR formation processes, their temporal sequence, and their impact on gene expression and cell division. Our in vitro system uncovered a propensity of chromothripsis to occur in cells with damaged telomeres, and in particular in hyperploid cells. Analysis of primary medulloblastoma cancer genomes verified the link between hyperploidy and chromothripsis in vivo. CAST provides the foundation for mechanistic dissection of complex DNA rearrangement processes.     

Further in vitro exploration fails to support the allosteric three-site model

Ongoing debate in the ribosome field has focused on the role of bound E-site tRNA and the Shine-Dalgarno-anti-Shine-Dalgarno (SD-aSD) interaction on A-site tRNA interactions and the fidelity of tRNA selection. Here we use an in vitro reconstituted Escherichia coli translation system to explore the reported effects of E-site-bound tRNA and SD-aSD interactions on tRNA selection events and find no evidence for allosteric coupling. A large set of experiments exploring the role of the E-site tRNA in miscoding failed to recapitulate the observations of earlier studies (Di Giacco, V., Márquez, V., Qin, Y., Pech, M., Triana-Alonso, F. J., Wilson, D. N., and Nierhaus, K. H. (2008) Proc. Natl. Acad. Sci. U.S.A. 105, 10715-10720 and Geigenmüller, U., and Nierhaus, K. H. (1990) EMBO J. 9, 4527-4533); the frequency of miscoding was unaffected by the presence of E-site-bound cognate tRNA. Moreover, our data provide clear evidence that the reported effects of the SD-aSD interaction on fidelity can be attributed to the binding of ribosomes to an unanticipated site on the mRNA (in the absence of the SD sequence) that provides a cognate pairing codon leading naturally to incorporation of the purported "noncognate" amino acid.     

Cyclin D1 determines mitochondrial function in vivo

The cyclin D1 gene encodes a regulatory subunit of the holoenzyme that phosphorylates and inactivates the pRb tumor suppressor to promote nuclear DNA synthesis. cyclin D1 is overexpressed in human breast cancers and is sufficient for the development of murine mammary tumors. Herein, cyclin D1 is shown to perform a novel function, inhibiting mitochondrial function and size. Mitochondrial activity was enhanced by genetic deletion or antisense or small interfering RNA to cyclin D1. Global gene expression profiling and functional analysis of mammary epithelial cell-targeted cyclin D1 antisense transgenics demonstrated that cyclin D1 inhibits mitochondrial activity and aerobic glycolysis in vivo. Reciprocal regulation of these genes was observed in cyclin D1-induced mammary tumors. Cyclin D1 thus integrates nuclear DNA synthesis and mitochondrial function.     

Influence of sampling time and sap extraction methodology on xylem pH values in two grapevine varieties grown under drought conditions

The effect of differences in applied pressure and time of sampling on pH values of xylem sap collected using the leaf pressurization technique was examined in two grapevine varieties originating from contrasting habitats (Vitis vinifera L., cvs. Sabatiano and Mavrodafni) after subjecting them to drought. Three fractions of xylem sap exudates were collected from each leaf according to differences in applied pressure; fractions (I), (II) and (III) corresponding to 1 MPa, 2 MPa and 2.5 MPa pressure, respectively. The pH values in fraction (I) were significantly lower than those in fractions (II) and (III). The sap pH values in fraction (III) seemed to better correspond to changes in leaf apoplastic pH. The time of sampling was found to strongly influence xylem pH values. In particular, a positive relationship between predawn xylem pH values and soil drying was observed. Conversely, xylem pH values measured later during the day (i.e. at 8:00, 9:00 and 10:00 am) were not significantly affected by the reduction in soil water availability in both varieties. It is suggested that the most suitable period for sap sampling in order to better discriminate drought effects on xylem sap pH is at predawn. Furthermore, there were significant differences in pH values as well as in the sensitivity of stomatal conductance to pH between the two varieties. These differences might be related to strategy differences between grapevine varieties for adaptation to drought.     

Synthesis and biological evaluation of benzopyran analogues bearing class III antiarrhythmic pharmacophores

We have synthesized a series of compounds combining the hydroxy-benzopyran ring of vitamin E with the methylsulfonylaminophenyl group of class III antiarrhythmic drugs, connected through tertiary amine moieties. Evaluation of the antiarrhythmic and antioxidant activity of the new compounds was carried out on isolated rat heart preparations using the non-recirculating Langendorff mode. The new analogues were present, at 10 microM concentration, during ischemia and reperfusion. Selected compounds were further studied by a conventional microelectrode method in order to get insight into their cellular mode of action. The most active compound, N-[4-[2-[[2-(3,4-dihydro-6-hydroxy-2,2,7,8-tetramethyl-2H-1-benzopyran-5-yl)ethyl] methylamine]ethyl]phenyl]methanesulfonamide (19a), reduces premature beats, prolongs QT and QRS intervals during ischemia and reperfusion, and reduces MDA content, leading to a fast recovery of the heart. In addition, it exhibits moderate class III antiarrhythmic action.     

High aeration rate enhances flow stratification in full-scale oxidation ditch

Aerated channel reactors with a uniform field of aeration may display flow stratification and short-circuit phenomena in wastewater treatment systems. In this study, we present data suggesting that flow stratification is closely related to the aeration rate and the arrangement of aerators. A full-scale oxidation ditch, with a total volume of 6,500 m³ and a membrane-diffused aerated zone of 60 × 7 × 5 m (length–width–depth), was selected for water velocity measurements. Two profiles of the oxidation ditch were studied in detail: the first one was at the end of the aerated zone and the second one at the end of the anoxic zone. The results of this work demonstrate that the horizontal water velocity at the end of the aerated zone displayed significant stratification, with maximum velocity near the water surface (0.5–0.7 m/s) and almost zero velocity at a depth of 2.5 m. At the end of the anoxic zone, water velocity was uniform and equal to 0.27–0.31 m/s. Increasing the aeration rate from 1,800 to 4,300 m³/h, almost 90% of the water flow was found to discharge through the upper-half of the channel reactor profile. Different options to mitigate flow stratification of the oxidation ditch are discussed in this paper.