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.     

Combining genetic variation and phenotypic plasticity in tradeoff modelling

Tradeoffs lead to antagonistic relationships between phenotypic traits and are thought to be determined both genetically and environmentally. We present here an allocation model that distinguishes between the genetic and environmental components of variation in resource allocation. In this model we introduced plasticity of resource allocation which was considered to be an adaptive response to environmental variations. The results show that resource allocation plasticity is a key parameter for the existence of environmental (i.e. inter environments and intra genotype) correlations and is therefore necessary to detect environment-induced tradeoffs. We also investigated the impact of the resource allocation plasticity and other factors on genetic (i.e. inter genotypes) correlations. Our results show that resource allocation plasticity induces a masking effect of tradeoffs when studying genetic correlations and increases the masking effect of resource variation by making apparent correlations positive when negative correlations are expected. In addition, by simulating different sources of resource acquisition variation, we demonstrated that resource variation might have different effects on correlations according to the experimental design and the studied biological material. Further development of this model may be used to investigate the theoretical implications of tradeoffs in evolutionary biology and to improve design and interpretation of experimental studies.     

Apport de la TEP-FDG dans le staging initial des cancers du sein localement avancés traités par chimiothérapie néo-adjuvante

Axillary lymph node and distant metastases are unfavourable prognostic factors in breast cancer. The aim of our study was to evaluate the performance of PET-FDG in the staging of locally advanced breast cancer (LABC) treated with neoadjuvant chemotherapy (NAC) and surgery, and to compare the findings of pretherapeutic PET to those of axillary nodal status obtained by surgery after NAC (Sataloff classification). This retrospective study involved 89 patients with LABC explored at presentation by PET in addition to conventional clinical and imaging staging (CS). Breast cancer excision and axillary dissection were performed after NAC. PET and CS found an axillary involvement in 58 patients (65%) and 39 patients (44%), respectively. Compared to the histology of post-NAC axillary dissection, PET had sensitivity and specificity of 80% and 63%, respectively. PET revealed an extra-axillary lymph node involvement, not suspected by the CS, in 25 patients (28%). Bone and lung metastases, not suspected by the CS were found in two and one patients, respectively. A case of false-positive PET in the liver was observed (adenomatosis). This study confirms the value of PET in the initial staging of LABC, especially in assessing extra-axillary nodal status. In the determination of axillary status, PET has a high positive predictive value, cases of doubtful interpretation suggesting to perform ultrasound-guided fine needle aspiration in addition.     

Antibiotic resistance plasmids from Serratia marcescens and their elimination by DNA-gyrase inhibitors

We studied the effects of ciprofloxacin on 73 strains of Serratia marcescens. In the first place, we have tested their plasmidic content: 76% of Serratia marcescens strains contained plasmids by electrophoresis, and 29% of these plasmids were self-transmissible by conjugation. Secondly, we studied the plasmid stability with regard to ciprofloxacin. We obtained a spontaneous cure with 19% of plasmids, and ciprofloxacin, at very low concentrations (0.4 mg/l), increased the rate of cure and more efficiently than novobiocin, a compound used as a known curing agent.     

Influence of two cell harvesting methods on intracellular ATP and amino acid concentrations in human fibroblast cultures

The intracellular ATP and amino acid concentrations were determined in human fibroblast cultures reaching confluence. The values obtained were very different, depending on the cell harvesting method: trypsinization or scraping. Trypsinization appeared to be the better method for measuring the ATP concentrations (21.25 +/- 0.96 nmol per mg cell protein), this level being much lower with scraping. On the contrary, scraping was the most appropriate method for amino acid measurement. This work underlines the importance of harvesting methods for metabolic studies in human cell cultures.     

Chromosome imbalances in endometrial adenocarcinomas: a possible adaptation to abnormal metabolic pathways

Chromosome studies of endometrial carcinomas show several recurrent trisomies or tetrasomies: 1 (long arm), 10, 2, 7, 12, 3 and possibly X (long arm). These chromosomes or chromosome segments carry the majority of the genes coding for enzymes of glucidic metabolism, citrate cycle, and initial steps of nucleotide synthesis. Their excess, which does not appear as a primary event in tumorigenesis, is interpreted as an adaptation of the cancer cells to abnormalities of metabolic pathways. The increase of gene copies, by chromosome duplication, would facilitate the synthesis of enzymes the activity of which is increased. If this view is correct and has a general value, it would mean that, in addition to primary chromosome changes, which may induce oncogene activation, most anomalies, which are obviously secondary, may reflect a disturbance of metabolic pathways coded by housekeeping genes.     

Great degree of homology between the ancestral karyotype of squirrels (rodents) and that of primates and carnivores

The karyotype of 7 species of Sciurinae representative of 6 tribes were compared: Atlantoxerus getulus, Menetes berdmorei, Callosciurus flavimanus, Heliosciurus gambianus, Sciurus vulgaris, Eutamias sibiricus, and Marmota monax. Homoeologies between almost all chromosome segments were found. Numerous similarities with the karyotypes of certain Primates and Carnivora were observed. A presumed ancestral karyotype of the Sciurinae is proposed.     

Presence of abundant heterochromatin in the karyotype of Cebus: C. cappucinus and C. nigrivittatus]

The karyotypes of Cebus capucinus and C. nigrivittatus (Primates, Platyrrhini) are compared after applying several banding techniques. The chromosomes have abundant intercallary heterochromatin which can be stained by R-, T- and C-band techniques and which are late replicating. The X chromosome resembles that of man and of numerous primates. However, the late replicating pattern of the X in female lymphocytes resembles that of the late replicating X of human fibroblasts rather than of human lymphocytes. Banding patterns of certain chromosomes appear analogous in Cebus and Cattarhini, including Man.