Sungeun Lee

Christina Hazard

Graeme W Nicol

Active host-virus interactions

Low %GC pH 7.5

Low %GC pH 4.5

Bin.9_Nitrosopumilaceae_Nitrosotalea

Bin.12_Nitrososphaeraceae

Bin.52_Nitrososphaeraceae_Nitrososphaera

Bin.61_Nitrosopumilaceae_Nitrosotalea

Bin.63_Nitrososphaeraceae

Bin.77_Nitrosopumilaceae_Nitrosotalea

Bin.96_Nitrososphaeraceae

Bin.107_Nitrosopumilaceae_Nitrosotalea

Bin.112_Nitrososphaeraceae Low %GC pH 7.5

Low %GC pH 4.5

Bin.9_Nitrosopumilaceae_Nitrosotalea

Bin.12_Nitrososphaeraceae

Bin.52_Nitrososphaeraceae_Nitrososphaera

Bin.61_Nitrosopumilaceae_Nitrosotalea

Bin.63_Nitrososphaeraceae

Bin.77_Nitrosopumilaceae_Nitrosotalea

Bin.96_Nitrososphaeraceae

Bin.107_Nitrosopumilaceae_Nitrosotalea

Bin.112_Nitrososphaeraceae

Bin.11_Nitrososphaeraceae

Unbinned %GC content

While there is substantial knowledge of the diversity and function of prokaryotes contributing to nitrification in soil, nothing is known of the scale or frequency of interactions with viruses in situ. Recent advances in bioinformatic tools has enabled identification of linkages between viruses and hosts, typically at broad taxonomic levels. However, this does not determine if these represent current or historical interactions nor whether a virus or host are active.

The aim of this study was to identify interactions between viruses and nitrifying prokaryotic hosts. Specifically, we aimed to identify active interactions in situ between AOA cells and lytic viruses by following the transfer of recently assimilated inorganic carbon (Fig 1).

Fig 2 .

 2 Fig 1. Viruses derived from lysed cells incorporating C from 13 CO2 will be isotopically enriched in 13 C

Fig 3 .

 3 Fig 3. AOA MAGs recovered from 13 Cenriched HBD DNA and 12 C-enriched LBD DNA.

Fig 4 .

 4 Fig 4. Mapping of reads derived from metagenomic sequencing of HBD DNA of 12 C and 13 C incubations to viral contigs. Each row represents one of twelve individual microcosms.

Fig 5 .

 5 Fig 5. Network of shared homologues between predicted viruses and proviruses using vConTACT (Jang et al., 2019)

Fig 6 .

 6 Fig 6. Network of shared homologues between predicted viruses and proviruses using vConTACT (Jang et al., 2019) Conclusion


domain: shs sdv

text:
Edwin De Jager

Laurent Risser

Muriel Mescam

Caroline Fonta

Amélie Beaudet

From skull to brain: 3D density maps of cortical sulci as a powerful tool for paleoneurology

Key questions in palaeoscience concern the timing and mode of emergence of derived cerebral features of extant human brains. Human brains We modern human crania from Pretoria Bone Collection (South Africa; L' Abbé et al., 2005), and scanned them using Microfocus X-ray Computed Tomography (micro-CT). These specimens were selected based on strict systematic exclusion of known pathology or defects that affects the inner table of the cranium.

Automatic imprint detection:

Endocasts were automatically segmented from micro-CT images using Endex software [START_REF] Subsol | Annual Meeting of the American Association of Physical Anthropologists[END_REF]. The automatic detection of sulcal imprints on the endocasts was performed using a C++ program [START_REF] Yoshizawa | 15th Pacific Conference on Computer Graphics and Applications[END_REF].

Atlas of sulcal imprints:

Using a MATLAB program (Beaudet et al., 2016), and brain atlases [START_REF] Connolly | External Morphology of the Primate Brain[END_REF] sulci where manually labelled to create an atlas of sulcal imprint variation [START_REF] Connolly | External Morphology of the Primate Brain[END_REF].

Density maps:

Specialised statistical methods commonly used in population-based brain atlases were used to iteratively deform the imprints from our entire sample onto an average endocast template.

Notable results: Red = mean distribution, Blue = +2 standard deviations.

Key questions in palaeoscience concern the timing and mode of emergence of derived cerebral features of modern human brains. Endocasts, a replica of the internal table of the bony brain case, constitute a proxy for reconstructing a timeline and process of cerebral changes within the human lineage [START_REF] Holloway | The Human Fossil Record; L'Abbé[END_REF]. Accurate identification of sulcal imprints in endocasts is critical for evaluating the topographic extension and structural organisation of cortical regions in fossil hominins (Alatorre Warren et al., 2019). High sulcal imprint variation on endocasts and the distortion of these imprints (caused by intra-cranial components) renders accurately identifying sulcal imprints a challenging task (Neubauer, 2014), giving rise to historical debates (e.g., Holloway, 1981). High-resolution imaging techniques combined with established methods used in population-specific brain atlases offer new opportunities for tracking evolutionary changes in endocranial characteristics (Beaudet et al., 2016). We aim to provide a population-level reference from which to guide future analysis of fossil endocasts, with the vision of reducing bias in future sulcal imprint identification endeavours.

Overlapping of imprints were observed when viewing imprints of the frontal lobe (A), as well as laterally (B) between the precentral, central and postcentral sulci with severe overlapping superiorly. Major overlapping was observed in sulci bordering the Broca's cap (C) and the sulci of the occipital lobe (D) involving the lunate sulcus.

This approach an innovative, non-invasive, statistically modelled method from which to infer human endocranial sulcal imprint variation, correlating with observations from previous studies and literature [START_REF] Connolly | External Morphology of the Primate Brain[END_REF]Fillard et al., 2007). For the first time, we could observe topographic overlap in sulci that are critically discussed in palaeoscience such as sulci on the occipital lobe, involving the lunate sulcus (e.g., Holloway, 1981), and sulci bordering the Broca's area. This analytical protocol afforded an objective perspective to contribute towards more refined endocranial research in paleoneurology. Expansion of our specimen database (i.e., primates and hominins) is expected to further improve the statistical power of observed features. This expansion will improve the detection of observable remodelling of these cortical features, and consequently contribute towards a completely observer independent approach; thereby guiding discussions surrounding fossil classifications and the contentious hypotheses on the evolution of cognitive abilities among hominins.

This research has been funded by South Africa/France (PROTEA) Joint Research Programme (grant number 129923) as well as the University of Cambridge Harding Distinguished Postgraduate Scholars Programme. We thank the DST-NRF for sponsoring the Micro-XCT facility at Necsa. We thank G. Krüger for collection access; AN van Schoor for anatomical expertise; F. de Beer and L. Bam (Necsa) for data acquisition; J. Dumoncel (AMIS -UMR5288) for technical support. Ethical clearance was obtained from the Main Research Ethics committee of the Faculty of Health Science, University of Pretoria August 2017 (No:339/2017). Additional ethical clearance was obtained from the ethical committee at Cambridge.

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Caroline Fonta

Germain Arribarat

Muriel Mescam

Franck Desmoulin

Effect of ageing on the cerebral hemodynamics in the marmoset monkey

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Effect of ageing on the cerebral hemodynamics in the marmoset monkey

Age

results in a deterioration of cardiovascular functionality, leading to an increased risk of cerebrovascular diseases, whose links with alteration/loss of cerebral activity and cognitive abilities deserve intensive exploration. Nonhuman primates, being closer to humans than the commonly used rodent species, are precious models for developing studies on human health and diseases. Thus we analyzed blood flow dynamics in intracranial arteries and venous sinuses of young (4 years old) and old (9 years old) adult, male and female, marmoset monkeys Callithrix jacchus. This species is particularly invaluable with a lifespan around 10 years.

MRI scans were performed using a 7-T MRI scanner (Brukerbiospec), (emitting coil =Φ 72 mm, receiving surface coil = Φ 30 mm). Each study took ~90 min/marmoset to acquire successively T2w, Time Of Flight (TOF) and Phase Contrast Angiography (PCA) images. The TOF images were used to position the two PCA scanning planes perpendicular to flow direction in the arterial vessels and the venous sinuses.

The marmoset was placed in a thermostated cradle in a prone position under oxygen ventilation with Isoflurane (1.5 to 2.5%). Cardiac and respiratory frequencies were monitored. Blood flow velocity acquisition (PCA) was synchronized with ECG signal. Data acquisition : Bruker ParaVision 6.0.1 software. Data analyses : Data were analyzed using an in-house processing method with an optimised region growing algorithm for blood speed segmentation, which automatically extracts the region of interest at each level over the segments of the cardiac cycle. Velocity was averaged for each ROI and blood flow was calculated (vessel area x mean velocity ). Data were extrapolated to cover the whole cardiac cycle (CC), and interpolated to obtain similar segmentation of the CC for all marmosets (32 steps of 3.13 % CC).

INTRODUCTION Methods

This cross sectional study originally shows that intracranial blood flow parameters differ in several ways between young and old adult marmosets : -the arterial blood flow peaks earlier in old monkeys, suggesting age-related changes in the vessel structural properties (vessel wall rigidity).

-the kinetics of blood flow input-output in the brain tissue is different in old monkeys. Both brain vessels and tissue mechanical characteristics may be altered by age (compliance). The time interval (in terms of CC) between arterial (red) and venous (blue) maximal blood flow peaks appears smaller in old (n=7) than in young marmosets (n=7). The green rectangle symbolises the time interval between the mean maximal arterial and the mean maximal venous flow peaks (young: 29-42 %CC, old: 25-31%CC). This would suggest a faster blood transit inside the brain tissue in old than in young marmosets.

Arterial-venous time lapse

A longitudinal study, on a larger population, is necessary to formalize the temporal evolution of these changes and to test whether some parameters could be used to detect signs of early/pathological ageing. The marmoset model can easily be used to couple non invasive imaging and behavioral studies all along the marmoset life, at a high and adjustable frequency. Such a screening would help to define the timing of normal/pathological changes in the cerebrovascular system of the ageing primate.

  Caroline FONTA 1 , Germain ARRIBARAT 1 , Muriel MESCAM 1 , Franck DESMOULIN 2 (1) CerCo/Brain and Cognition Research Center, CNRS-Toulouse University (2) TONIC, INSERM -Toulouse University, Toulouse, France The marmosets originated from the CerCo marmoset colony (Toulouse). All experiments were carried out according to the National Committee for Ethical Reflection on Animal Testing (authorization n°: 05215.03 delivered by MESRI).

  T2 and TOF images of a marmoset brain. Horizontal plane. T2:TR/TE:6859/36 ms, FOV:48x48mm, Matrix: 240x240, voxel size: 0.2x0.2x0.3 mm 3 . TOF: TR/TE: 11/3 ms, flip angle=80°, FOV: 48x48mm, Matrix: 320x320, voxel size =0.15x0.15x0.3 mm 3 . TOF: Coronal (A) and sagittal (B) planes. One intracranial section across the inferior part of the Willis polygon was chosen to measure blood velocity simultaneously in both the left and right internal carotids and the basilary trunk (C). Position for signal acquisition of blood velocity in sinuses was chosen on a sagittal section PCA: TR/TE: 15/4.2 ms, flip angle=20°, FOV: 30x24mm, Matrix: 200x160, voxel size: 0.15x0.15x1 mm 3 , VENC:50cm/s (arteries), 20cm/s (sinuses). Images were acquired according to prospective cardiac gating (15-22 frames as a function of heart rate) and covered in average 75% of the cardiac cycle. The cardiac frequency averaged 170 bpm.

When normalizing flow values to the first one (P wave of the cardiac cycle), arterial blood flow rapidly increases and peaks when 20-30% of the cardiac cycle (CC) is reached, which occurs significantly earlier in old (21.8% CC, n=7) than in young marmousets (28.1% CC, n=7) (p<0,05). Arterial blood flow cumulated from both carotids and basilary trunk reaches higher relative increase in young (320%) than in old marmosets (291%). Venous flow timecourse is rather steady in young marmosets but tends to show a peak shortly after the arterial peak in old marmosets (28% CC, versus 38% in young adult marmosets).

Basilary and carotid arteries contribution

We evaluated that the carotid system provides 57.2 ± 8,5% of the blood (µl/mn) dispatched to the brain, with an equal contribution of the two internal carotids (49% and 51%, (right and left respectively (n=14)). In humans, the carotid system appears more prominent (75 to 78% of the blood supply).

The blood flow peak recorded in the basilary trunk preceeds those of the carotids in the old marmosets (n=7). This difference is not significant in the young marmosets (n=7)