Construction of integrated genetic linkage maps by means of a new computer package: Join Map

A computerized procedure to contruct integrate genetic maps is presented. The computer program (J oin M ap ) can handle raw data from F₂s, backcrosses and recombinant inbred lines, as well as listed pair-wise recombination frequencies. The procedure is useful for combining linkage data that have been collected in different experiments; the result is a mathematical alignment of the distinct genetic maps. Data from single experiments can be dealt with as well. In view of the fast growing amount of linkage information for molecular markers, which is often being generated by different research groups, integrated maps provide useful information on the map position of genes and DNA markers.
The procedure performs a sequential build-up of the map and, at each step, a numerical search for the best fitting order of markers. Weighted least squares is used for the estimation of map distances.     

The SARS-CoV-2 and other human coronavirus spike proteins are fine-tuned towards temperature and proteases of the human airways

The high transmissibility of SARS-CoV-2 is related to abundant replication in the upper airways, which is not observed for the other highly pathogenic coronaviruses SARS-CoV and MERS-CoV. We here reveal features of the coronavirus spike (S) protein, which optimize the virus towards the human respiratory tract. First, the S proteins exhibit an intrinsic temperature preference, corresponding with the temperature of the upper or lower airways. Pseudoviruses bearing the SARS-CoV-2 spike (SARS-2-S) were more infectious when produced at 33°C instead of 37°C, a property shared with the S protein of HCoV-229E, a common cold coronavirus. In contrast, the S proteins of SARS-CoV and MERS-CoV favored 37°C, in accordance with virus preference for the lower airways. Next, SARS-2-S-driven entry was efficiently activated by not only TMPRSS2, but also the TMPRSS13 protease, thus broadening the cell tropism of SARS-CoV-2. Both proteases proved relevant in the context of authentic virus replication. TMPRSS13 appeared an effective spike activator for the virulent coronaviruses but not the low pathogenic HCoV-229E virus. Activation of SARS-2-S by these surface proteases requires processing of the S1/S2 cleavage loop, in which both the furin recognition motif and extended loop length proved critical. Conversely, entry of loop deletion mutants is significantly increased in cathepsin-rich cells. Finally, we demonstrate that the D614G mutation increases SARS-CoV-2 stability, particularly at 37°C, and, enhances its use of the cathepsin L pathway. This indicates a link between S protein stability and usage of this alternative route for virus entry. Since these spike properties may promote virus spread, they potentially explain why the spike-G614 variant has replaced the early D614 variant to become globally predominant. Collectively, our findings reveal adaptive mechanisms whereby the coronavirus spike protein is adjusted to match the temperature and protease conditions of the airways, to enhance virus transmission and pathology.     

GAFF-IC: realistic viscosities for isocyanate molecules with a GAFF-based force field

Aliphatic diisocyanates and their derivatives are key liquid components in the industrial processing of polyurethane materials. In particular, for the synthesis of crosslinked polyurethane materials, the higher functionality molecules obtained by reacting three -or more- diisocyanates are of interest. However, despite their widespread application, the relation between molecular structure and macroscopic physical properties, in particular viscosity, is poorly understood in these systems. In this work, we introduce a new force field parameter set, GAFF-IC, based on the widely-used and versatile GAFF force field, meant for accurate predictions of physical properties of isocyanate-based molecular liquids. The new parameters allow to predict the vaporization enthalpies and densities of several isocyanate-based molecules, which are found in excellent agreement with the available experimental data. The effectiveness and transferability of the improved parameters is verified by calculating the viscosities of several isocyanates, isocyanate dimers (uretdiones) and isocyanate trimers (isocyanurates), resulting in accurate viscosity predictions in excellent agreement with experimental values.     

Isomerization of butyrate to isobutyrate by Desulforhabdus amnigenus

Abstract The isomerization of butyrate and isobutyrate was investigated for the sulfate reducer Desulforhabdus amnigenus . Nuclear magnetic resonance (NMR) studies with ¹³C-labelled butyrate showed that isobutyrate was formed by migration of the carboxyl group, in conformity with the butyrate isomerization reaction reported for methanogenic consortia. In addition to D. amnigenus , several other butyrate-degrading sulfate reducers ( Desulfobacterium vacuolatum, Desulfoarculus baarsii and Desulfotomaculum sp.) were capable of butyrate isomerization.     

Tail spine length in the Daphnia galeata complex: costs and benefits of induction by fish

We studied the combined effect of fish kairomones and food conditions on the relative tail spine length (RTL) of five Daphnia taxa, and the interaction of these factors with the vertical distribution of the daphnids. The experiment was done in two large-scale indoor containers, the so-called plankton towers in Plön, Germany. We conducted a competition experiment in which food level and the presence of fish chemicals and later fish were varied. A strong response of RTL to fish kairomones (e.g., longer tail spines), significant differences in RTL between species, but no differences in RTL with water depth were found. Further, we observed that these Daphnia taxa produced a higher RTL only under high food conditions. This suggests that there is a cost related to the production of longer tail spines.In a preliminary study in lake Plußsee, we found that Daphnia had longer average RTL than in the towers. Further, we noted significant differences in RTL between the two sampling dates, which may be related to a lower food level. We also detected a strong inverse correlation between RTL and depth. We discuss the implications of these findings for the co-existence of co-occurring Daphnia species and their hybrids.     

A cobblestone cell isolated from the human omentum: the mesothelial cell; isolation,identification, and growth characteristics

Summary Normal human mesothelial cells (NHMC) were isolated from pieces of human omentum. The cell yield was approximately one million cells per square centimeter omentum. The mesothelial cells were identified by their positive staining with monoclonal antibodies against cytokeratins 6 and 18. Transmission electronmicroscopy of cultured NHMC revealed many microvilli on the apical surface and many mitochondria and pinocytotic vesicles in the cytoplasm, indicating active transmembrane transport. Growth of NHMC was directly related to the concentration of human serum or of fetal bovine serum in the growth medium. Addition of epidermal growth factor with or without hydrocortisone resulted in a significant increase of NHMC growth; when endothelial cell growth factor, insulin, or hydrocortisone were added no such increase was observed. Seeding NHMC at densities less than 3000/cm² did not result in monolayer formation. The mesothelial cells were serially passed in growth medium M199 with added 10% fetal bovine serum up to 7 passages. However, after Passage 4 the cells changed into giant cells with an irregular pattern, and a lack of intracellular cytokeratin expression was observed for most of the cells.