Entropology: an information-theoretic approach to understanding archaeological data

The main objective of this paper is to develop quantitative measures for describing the diversity, homogeneity, and similarity of archaeological data. It presents new approaches to characterize the relationship between archaeological assemblages by utilizing entropy and its related attributes, primarily diversity, and by drawing inspiration from ecology. Our starting premise is that diachronic changes in our data provide a distorted reflection of social processes and that spatial differences in data indicate cultural distancing. To investigate this premise, we adopt a parsimonious approach for comparing assemblage profiles employing and comparing a range of (Hill) diversities, which enable us to exploit different aspects of the data. The modelling is tested on two seemingly large datasets: a Late Bronze Age Cretan dataset with circa 13,700 entries (compiled by PG); and a 4th millennium Western Tripolye dataset with circa 25,000 entries (compiled by AD). The contrast between the strongly geographically and culturally heterogeneous Bronze Age Crete and the strongly homogeneous Western Tripolye culture in the Southern Bug and Dnieper interfluve show the successes and limitations of our approach. Despite the seemingly large size of our datasets, these data highlight limitations that confine their utility to non-semantic analysis. This requires us to consider different ways of treating and aggregating assemblages, either as censuses or samples, contingent upon the degree of representativeness of the data. While our premise, that changes in data reflect societal changes, is supported, it is not definitively confirmed. Consequently, this paper also exemplifies the limitations of large archaeological datasets for such analyses

A novel experimental setup for evaluating the stiffness of ankle foot orthoses

Abstract Objective The purpose of this study was the construction of a new semi-automated experimental setup for the evaluation of the stiffness of ankle foot orthoses (AFOs) around an axis aligned to the anatomical ankle joint during the second rocker of the gait. The setup, developed in close collaboration with the orthopedic device company V!GO NV (Wetteren, Belgium), allows measurement of plantarflexion and dorsiflexion in the sagittal plane for a maximal range of motion of 50° (− 25° plantarflexion up to 25° dorsiflexion) in a non-destructive way. Results The mechanical properties of four 3D printed AFOs are investigated, based on the ranges of motion derived from the gait assessment of the patients when they walked with their AFO. The reliability of the stiffness measures was studied by the evaluation of the test–retest repeatability and the intra-tester and inter-tester variability. These studies revealed that the ankle stiffness can be measured with high reliability (ICC = 0.94–1.00). The obtained outcomes indicate that the experimental setup could be applied to measure the ankle stiffness of any topology of AFOs and, in the future, help finding the correlation with the information coming from the gait assessment of the patients

Conformational Flexibility in the Immunoglobulin-Like Domain of the Hepatitis C Virus Glycoprotein E2

International audienceABSTRACT The hepatitis C virus (HCV) glycoprotein E2 is the major target of neutralizing antibodies and is therefore highly relevant for vaccine design. Its structure features a central immunoglobulin (Ig)-like β-sandwich that contributes to the binding site for the cellular receptor CD81. We show that a synthetic peptide corresponding to a β-strand of this Ig-like domain forms an α-helix in complex with the anti-E2 antibody DAO5, demonstrating an inside-out flip of hydrophobic residues and a secondary structure change in the composite CD81 binding site. A detailed interaction analysis of DAO5 and cross-competing neutralizing antibodies with soluble E2 revealed that the Ig-like domain is trapped by different antibodies in at least two distinct conformations. DAO5 specifically captures retrovirus particles bearing HCV glycoproteins (HCVpp) and infectious cell culture-derived HCV particles (HCVcc). Infection of cells by DAO5-captured HCVpp can be blocked by a cross-competing neutralizing antibody, indicating that a single virus particle simultaneously displays E2 molecules in more than one conformation on its surface. Such conformational plasticity of the HCV E2 receptor binding site has important implications for immunogen design. IMPORTANCE Recent advances in the treatment of hepatitis C virus (HCV) infection with direct-acting antiviral drugs have enabled the control of this major human pathogen. However, due to their high costs and limited accessibility in combination with the lack of awareness of the mostly asymptomatic infection, there is an unchanged urgent need for an effective vaccine. The viral glycoprotein E2 contains regions that are crucial for virus entry into the host cell, and antibodies that bind to these regions can neutralize infection. One of the major targets of neutralizing antibodies is the central immunoglobulin (Ig)-like domain within E2. We show here that this Ig-like domain is conformationally flexible at the surface of infectious HCV particles and pseudoparticles. Our study provides novel insights into the interactions of HCV E2 with the humoral immune system that should aid future vaccine development

Robust and low cost uniform (15)N-labeling of proteins expressed in Drosophila S2 cells and Spodoptera frugiperda Sf9 cells for NMR applications.

International audienceNuclear magnetic resonance spectroscopy is a powerful tool to study structural and functional properties of proteins, provided that they can be enriched in stable isotopes such as (15)N, (13)C and (2)H. This is usually easy and inexpensive when the proteins are expressed in Escherichiacoli, but many eukaryotic (human in particular) proteins cannot be produced this way. An alternative is to express them in insect cells. Labeled insect cell growth media are commercially available but at prohibitive prices, limiting the NMR studies to only a subset of biologically important proteins. Non-commercial solutions from academic institutions have been proposed, but none of them is really satisfying. We have developed a (15)N-labeling procedure based on the use of a commercial medium depleted of all amino acids and supplemented with a (15)N-labeled yeast autolysate for a total cost about five times lower than that of the currently available solutions. We have applied our procedure to the production of a non-polymerizable mutant of actin in Sf9 cells and of fragments of eukaryotic and viral membrane fusion proteins in S2 cells, which typically cannot be produced in E. coli, with production yields comparable to those obtained with standard commercial media. Our results support, in particular, the putative limits of a self-folding domain within a viral glycoprotein of unknown structure

Determinants Involved in Hepatitis C Virus and GB Virus B Primate Host Restriction

International audienceHepatitis C virus (HCV) only infects humans and chimpanzees, while GB virus B (GBV-B), another hepatotropic hepacivirus, infects small New World primates (tamarins and marmosets). In an effort to develop an immunocompetent small primate model for HCV infection to study HCV pathogenesis and vaccine approaches, we investigated the HCV life cycle step(s) that may be restricted in small primate hepatocytes. First, we found that replication-competent, genome-length chimeric HCV RNAs encoding GBV-B structural proteins in place of equivalent HCV sequences designed to allow entry into simian hepatocytes failed to induce viremia in tamarins following intrahepatic inoculation, nor did they lead to progeny virus in permissive, transfected human Huh7.5 hepatoma cells upon serial passage. This likely reflected the disruption of interactions between distantly related structural and nonstructural proteins that are essential for virion production, whereas such cross talk could be restored in similarly designed HCV intergenotypic recombinants via adaptive mutations in NS3 protease or helicase domains. Next, HCV entry into small primate hepatocytes was examined directly using HCV-pseudotyped retroviral particles (HCV-pp). HCV-pp efficiently infected tamarin hepatic cell lines and primary marmoset hepatocyte cultures through the use of the simian CD81 ortholog as a coreceptor, indicating that HCV entry is not restricted in small New World primate hepatocytes. Furthermore, we observed genomic replication and modest virus secretion following infection of primary marmoset hepatocyte cultures with a highly cell culture-adapted HCV strain. Thus, HCV can successfully complete its life cycle in primary simian hepatocytes, suggesting the possibility of adapting some HCV strains to small primate hosts. IMPORTANCE: Hepatitis C virus (HCV) is an important human pathogen that infects over 150 million individuals worldwide and leads to chronic liver disease. The lack of a small animal model for this infection impedes the development of a preventive vaccine and pathogenesis studies. In seeking to establish a small primate model for HCV, we first attempted to generate recombinants between HCV and GB virus B (GBV-B), a hepacivirus that infects small New World primates (tamarins and marmosets). This approach revealed that the genetic distance between these hepaciviruses likely prevented virus morphogenesis. We next showed that HCV pseudoparticles were able to infect tamarin or marmoset hepatocytes efficiently, demonstrating that there was no restriction in HCV entry into these simian cells. Furthermore, we found that a highly cell culture-adapted HCV strain was able to achieve a complete viral cycle in primary marmoset hepatocyte cultures, providing a promising basis for further HCV adaptation to small primate hosts

Tables S4-S5 from Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity

Primer + shRNA + Taqman probe sequences</p

Figure S1 from Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity

Proliferation + Apoptosis assays</p

Figure S5 from Inhibition of METTL3 Results in a Cell-Intrinsic Interferon Response That Enhances Antitumor Immunity

Co-culture assays + human PBMC data</p