Production and characterization of two medium-chain-length polydroxyalkanoates by engineered strains of Yarrowia lipolytica

Background: The oleaginous yeast Yarrowia lipolytica is an organism of choice for the tailored production of various compounds such as biofuels or biopolymers. When properly engineered, it is capable of producing medium-chain-length polyhydroxyalkanoate (mcl-PHA), a biobased and biodegradable polymer that can be used as bioplastics or biopolymers for environmental and biomedical applications.Results: This study describes the bioproduction and the main properties of two different mcl-PHA polymers. We generated by metabolic engineering, strains of Y. lipolytica capable of accumulating more than 25% (g/g) of mcl-PHA polymers. Depending of the strain genetic background and the culture conditions, we produced (i) a mcl-PHA homopolymer of 3-hydroxydodecanoic acids, with a mass-average molar mass (M-w) of 316,000 g/mol, showing soft thermoplastic properties with potential applications in packaging and (ii) a mcl-PHA copolymer made of 3-hydroxyoctanoic (3HO), decanoic (3HD), dodecanoic (3HDD) and tetradecanoic (3TD) acids with a M-w of 128,000 g/mol, behaving like a thermoplastic elastomer with potential applications in biomedical material.Conclusion: The ability to engineer Y. lipolytica to produce tailored PHAs together with the range of possible applications regarding their biophysical and mechanical properties opens new perspectives in the field of PHA bioproduction

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

: Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants

Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers

Publisher Copyright: © 2023, The Author(s).Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.Peer reviewe

Molecular Adaptation of Photoprotection: Triplet States in Light-Harvesting Proteins

The photosynthetic light-harvesting systems of purple bacteria and plants both utilize specific carotenoids as quenchers of the harmful (bacterio)chlorophyll triplet states via triplet-triplet energy transfer. Here, we explore how the binding of carotenoids to the different types of light-harvesting proteins found in plants and purple bacteria provides adaptation in this vital photoprotective function. We show that the creation of the carotenoid triplet states in the light-harvesting complexes may occur without detectable conformational changes, in contrast to that found for carotenoids in solution. However, in plant light-harvesting complexes, the triplet wavefunction is shared between the carotenoids and their adjacent chlorophylls. This is not observed for the antenna proteins of purple bacteria, where the triplet is virtually fully located on the carotenoid molecule. These results explain the faster triplet-triplet transfer times in plant light-harvesting complexes. We show that this molecular mechanism, which spreads the location of the triplet wavefunction through the pigments of plant light-harvesting complexes, results in the absence of any detectable chlorophyll triplet in these complexes upon excitation, and we propose that it emerged as a photoprotective adaptation during the evolution of oxygenic photosynthesis

Peri-operative red blood cell transfusion in neonates and infants: NEonate and Children audiT of Anaesthesia pRactice IN Europe: A prospective European multicentre observational study

BACKGROUND: Little is known about current clinical practice concerning peri-operative red blood cell transfusion in neonates and small infants. Guidelines suggest transfusions based on haemoglobin thresholds ranging from 8.5 to 12 g dl-1, distinguishing between children from birth to day 7 (week 1), from day 8 to day 14 (week 2) or from day 15 (≥week 3) onwards. OBJECTIVE: To observe peri-operative red blood cell transfusion practice according to guidelines in relation to patient outcome. DESIGN: A multicentre observational study. SETTING: The NEonate-Children sTudy of Anaesthesia pRactice IN Europe (NECTARINE) trial recruited patients up to 60 weeks' postmenstrual age undergoing anaesthesia for surgical or diagnostic procedures from 165 centres in 31 European countries between March 2016 and January 2017. PATIENTS: The data included 5609 patients undergoing 6542 procedures. Inclusion criteria was a peri-operative red blood cell transfusion. MAIN OUTCOME MEASURES: The primary endpoint was the haemoglobin level triggering a transfusion for neonates in week 1, week 2 and week 3. Secondary endpoints were transfusion volumes, 'delta haemoglobin' (preprocedure - transfusion-triggering) and 30-day and 90-day morbidity and mortality. RESULTS: Peri-operative red blood cell transfusions were recorded during 447 procedures (6.9%). The median haemoglobin levels triggering a transfusion were 9.6 [IQR 8.7 to 10.9] g dl-1 for neonates in week 1, 9.6 [7.7 to 10.4] g dl-1 in week 2 and 8.0 [7.3 to 9.0] g dl-1 in week 3. The median transfusion volume was 17.1 [11.1 to 26.4] ml kg-1 with a median delta haemoglobin of 1.8 [0.0 to 3.6] g dl-1. Thirty-day morbidity was 47.8% with an overall mortality of 11.3%. CONCLUSIONS: Results indicate lower transfusion-triggering haemoglobin thresholds in clinical practice than suggested by current guidelines. The high morbidity and mortality of this NECTARINE sub-cohort calls for investigative action and evidence-based guidelines addressing peri-operative red blood cell transfusions strategies. TRIAL REGISTRATION: ClinicalTrials.gov, identifier: NCT02350348

Analysing micro-residues on prehistoric stone tools by Raman microscopy and determining their origins

This thesis aims to contribute to the determination of prehistoric stone tool function from traces of use for reconstructing and understanding hominin prehistoric behaviour. While macro-morphological approach provides important information about the context of tool use, it does not provide secure evidence of how the tool was actually used or what materials were processed. Retouched tools that do not match formal types, and unretouched flake tools are potentially even more problematic for morphological based interpretations of function. Microscopic use-wear analysis is an essential technique to determine use of stone tools, but it needs to be complemented by residue analysis for more robust functional interpretations. Conventional use-wear analysis identifies residues in the first stages of optical microscopy, followed by targeted analysis of residues, which often need to be removed. However, optical recognition of in situ, amorphous micro-residues is difficult. Additionally, stone artefacts not preselected for macro-residues may have low levels of preservation, and in that case cannot always benefit from pre use-wear analysis. Raman microscopy offers an alternative initial approach to residue analysis because it is a fast, non-destructive analytical technique, with high spatial resolution and it can rapidly identify a wide range of organic and mineral residues (bone, lipids, proteins, cellulose, lignin, starch and iron oxides). This thesis develops a new methodology, to enhance the use of spectroscopic technique in discriminating use-related residues from contaminants, and to provide interpretations both independent of, and complementary to, conventional use-wear analysis. Indeed, microresidues on prehistoric stone tools can arise from diverse origins that may be incidental to tool-use, naturally occurring in sediment, and arising from post-depositional processes and from other sources including ancient and modern contamination. To learn about hominin behaviour from stone tools, it is critical to filter the possibilities and retain only use-related materials. Consequently, Raman microscopy is positioned as a potential first step, but needs to develop its own micro-residue discrimination strategy. A whole set of criteria and complementary observations are needed, including correlation between use-wear and microresidues distributions, which require systematic spatial localisation and secure identification. Initial Raman microscopy is bringing a new approach and has the advantages of being complementary to and independent of conventional use-wear residue analysis. Additionally, to interpret stone artefacts micro-residues Raman analysis, this work developed a reference material database that is critical to compare with analysed residues on prehistoric stone tools. Raman references for different chemical compounds, modern and natural materials have been developed here, as well as targeted stone tools experiment to investigate type of microresidues deposited. This thesis has been also planned from the beginning to be part of the “Out of Asia” ARC Laureate Project, which was designed to improve understanding of the timing and dispersal of prehistoric hominin populations into South Asia and Australia. In this project, archaeochemistry, including different types of spectroscopic methods (Infrared, Raman, GCMS), was planned to contribute to understanding hominin behaviour by analysing stone artefacts recovered from selected archaeological sites and to determine their function. Consequently, two available prehistoric stone artefacts collections were selected, from Liang Bua and Denisova cave, to apply the developed methodology in Raman spectroscopy for reconstructing and understanding hominin prehistoric behaviour. Analysis results of different sets of artefacts collected from these two prehistoric sites allow to observe continuity or variation of stone tools use and behaviour through time, which requires comparisons of worked materials and particular ways of using stone tools recovered from different archaeological layers. This thesis shows that Raman spectroscopy applied to prehistoric stone tools is a successful analysing method and can be considered as a technique with a potential pivotal role in relating use-wear and other complementary techniques like GS-MS. Indeed, as Raman spectroscopy is a non destructive technique and leaves intact micro-residues on stone surfaces, any tagged concentrated spot of micro-residues (e.g., lipids) could be targeted in a second step of analysis with application of any complementary techniques on material having being securely linked to prehistoric use on stone artefacts. In that perspective, this thesis can open a way forward to optimise information from lithic functional analysis by combining, and ensuring that, the different analysing methods (use-wear analysis, spectroscopic analysis, GC-MS separative methods) will better complement each other in the future

Raman Microscopy as a Primary Technique for Identifying Micro-residues Related to Tool-use on Prehistoric Stone Artefacts

Analyses of ancient micro-residues preserved on stone artefacts can potentially provide detailed information about how prehistoric humans used the artefacts to process materials such as food, pigments and/or adhesives. However, prehistoric micro-residues are likely to degrade and there are multiple potential sources of contamination, such as contact with sediments, groundwater, recent handling, storage materials or laboratory conditions, any of which can inhibit reliable identification of micro-residues and other traces of prehistoric use. In this chapter we illustrate the use of Raman spectroscopy as a primary method to identity ancient micro-residues preserved on stone artefact surfaces that are due specifically to prehistoric use as opposed to some form of ancient or modern source of contamination. Stone tools from Liang Bua (Flores, Indonesia) and Denisova Cave (Altai Mountains, Siberia) are used to demonstrate the methodology

X-Ray Tomography and Infrared Spectrometry for the Analysis Of Throwing Sticks and Boomerangs

Throwing sticks, including boomerangs as a subclass, are prehistoric objects as old as humanity. They have endured on many continents in different forms, uses, and traditions of manufacture. Numerous different approaches have been used to study them. Many studies of throwing sticks are dominated by morphological determination and focused on Australian objects which have been classified by the origin of their cultural area on this continent (Davidson, 1936; Jones, 1996). However, few authors give importance to a fairly complete record of Australian Aboriginal throwing stick and boomerang features (Turck, 1952; Callahan, 1999)