Taming Cell-to-Cell Heterogeneity in Acute Myeloid Leukaemia With Machine Learning.

Acute Myeloid Leukaemia (AML) is a phenotypically and genetically heterogenous blood cancer characterised by very poor prognosis, with disease relapse being the primary cause of treatment failure. AML heterogeneity arise from different genetic and non-genetic sources, including its proposed hierarchical structure, with leukemic stem cells (LSCs) and progenitors giving origin to a variety of more mature leukemic subsets. Recent advances in single-cell molecular and phenotypic profiling have highlighted the intra and inter-patient heterogeneous nature of AML, which has so far limited the success of cell-based immunotherapy approaches against single targets. Machine Learning (ML) can be uniquely used to find non-trivial patterns from high-dimensional datasets and identify rare sub-populations. Here we review some recent ML tools that applied to single-cell data could help disentangle cell heterogeneity in AML by identifying distinct core molecular signatures of leukemic cell subsets. We discuss the advantages and limitations of unsupervised and supervised ML approaches to cluster and classify cell populations in AML, for the identification of biomarkers and the design of personalised therapies

Electrostatic extraction of cold molecules from a cryogenic reservoir

We present a method which delivers a continuous, high-density beam of slow and internally cold polar molecules. In our source, warm molecules are first cooled by collisions with a cryogenic helium buffer gas. Cold molecules are then extracted by means of an electrostatic quadrupole guide. For ND$_3$ the source produces fluxes up to $(7 \pm ^{7}_{4}) \times 10^{10}$ molecules/s with peak densities up to $(1.0 \pm ^{1.0}_{0.6}) \times 10^9$ molecules/cm$^3$. For H$_2$CO the population of rovibrational states is monitored by depletion spectroscopy, resulting in single-state populations up to $(82 \pm 10)$.Comment: 4 pages, 4 figures, changes to the text, updated figures and reference

Rational design of a (S)-selective-transaminase for asymmetric synthesis of (1S)-1-(1,1′-biphenyl-2-yl)ethanamine

Amine transaminases offer an environmentally sustainable synthesis route for the production of pure chiral amines. However, their catalytic efficiency toward bulky ketone substrates is greatly limited by steric hindrance and therefore presents a great challenge for industrial synthetic applications. We hereby report an example of rational transaminase enzyme design to help alleviate these challenges. Starting from the Vibrio fluvialis amine transaminase that has no detectable catalytic activity toward the bulky aromatic ketone 2-acetylbiphenyl, we employed a rational design strategy combining in silico and in vitro studies to engineer the transaminase enzyme with a minimal number of mutations, achieving an high catalytic activity and high enantioselectivity. We found that, by introducing two mutations W57G/R415A, detectable enzyme activity was achieved. The rationally designed variant, W57F/R88H/V153S/K163F/I259M/R415A/V422A, showed an improvement in reaction rate by more than 1716-fold toward the bulky ketone under study, producing the corresponding enantiomeric pure (S)-amine (enantiomeric excess (ee) value of >99%)

Development of a backward-mode photoacoustic microscope using a Fabry-Perot sensor

Optical-resolution photoacoustic microscopy (PAM) has been shown to enable the acquisition of high resolution (μm) functional and anatomical images. For backward-mode operation, conventional piezoelectric ultrasound transducers need to be placed far away from the signal source due to their opacity and size. This can result in reduced acoustic sensitivity. Planar Fabry-Perot polymer film interferometer (FPI) sensors have the potential to overcome this limitation since they are transparent to the excitation wavelength, can be placed immediately adjacent to the signal source for high acoustic sensitivity, and offer a broadband frequency response (0 –50 MHz). In this study, we present a high frame rate, backward-mode OR-PAM system based on a planar FPI ultrasound sensor. A ns-pulsed laser provides excitation pulses (<200 nJ, maximum pulse repetition frequency = 200 kHz, 532 nm) to generate photoacoustic waves that are detected using a planar FPI sensor interrogated at 765-781 nm. For backwardmode operation and highest acoustic sensitivity, the excitation and interrogation beams are coaxially aligned and rasterscanned. The optical transfer function of the sensor, the spatial resolution and the detection sensitivity were determined to characterise the set-up. Images of a leaf phantom and first in vivo images of zebrafish larvae were acquired. This approach will enable fast 3D OR-PAM with high resolution and high sensitivity for functional and molecular imaging applications. FPI-based ultrasound detection also has the potential to enable dual-mode optical- and acousticresolution PAM and the integration of photoacoustic imaging with purely optical modalities such as multi-photon microscopy

ITERATIVE CLOSEST POINT ALGORITHM FOR ACCURATE REGISTRATION OF COARSELY REGISTERED POINT CLOUDS WITH CITYGML MODELS

The Iterative Closest Point algorithm (ICP) is a standard tool for registration of a source to a target point cloud. In this paper, ICP in point-to-plane mode is adopted to city models that are defined in CityGML. With this new point-to-model version of the algorithm, a coarsely registered photogrammetric point cloud can be matched with buildings’ polygons to provide, e.g., a basis for automated 3D facade modeling. In each iteration step, source points are projected to these polygons to find correspondences. Then an optimization problem is solved to find an affine transformation that maps source points to their correspondences as close as possible. Whereas standard ICP variants do not perform scaling, our algorithm is capable of isotropic scaling. This is necessary because photogrammetric point clouds obtained by the structure from motion algorithm typically are scaled randomly. Two test scenarios indicate that the presented algorithm is faster than ICP in point-to-plane mode on sampled city models

Development and application of novel engineered transaminase panels assisted by in- silico rational design for the production of chiral amines

There is a high demand for the synthesis of chiral amines as building blocks for a large number of industrially valuable compounds. Transaminases (TAm) offer an enzymatic route for the synthesis of chiral amines that avoids complex chemical synthesis [1]. However, their catalytic efficiency towards bulky ketone substrates is greatly limited by steric hinderance [2]. This poster highlights a rational design strategy of combining in silico and in vitro methods to engineer the transaminase enzyme with a minimal number of mutations, achieving high catalytic activity and high enantioselectivity. The wildtype TAm showed no detectable activity towards the ketone 2-acetylbiphenyl but upon introduction of two mutations detectable enzyme activity was observed. The reaction rate was improved a further 1716-fold with the rationally designed variant, that contained a further 5 mutations, producing the corresponding enantiomeric pure (S)-amine (enantiomeric excess (ee) value of \u3e99%)[3]. In addition, screening of in silico designed (R)-TAm mutant panels in resolution mode offered an attractive and efficient route for the preparation of problematic (S)-amines. A mutant was identified from the panels that gave complete resolution of the racemic amine (high substrate loading) to leave the desired enantiomer at a low enzyme loading fit for process development towards an economically viable scale up process. [1] R. C. Simon, et al, ACS Catal. 2014, 4(1) [2] F. Steffen-Munsberg, et al, ChemCatChem 2013, 5, (1) [3]D.F.A.R.Dourado et al, ACS Catal. 2016, 6 (11

Chemoenzymatic Probes for Detecting and Imaging Fucose-α(1-2)-galactose Glycan Biomarkers

The disaccharide motif fucose-α(1-2)-galactose (Fucα(1-2)Gal) is involved in many important physiological processes, such as learning and memory, inflammation, asthma, and tumorigenesis. However, the size and structural complexity of Fucα(1-2)Gal-containing glycans have posed a significant challenge to their detection. We report a new chemoenzymatic strategy for the rapid, sensitive detection of Fucα(1-2)Gal glycans. We demonstrate that the approach is highly selective for the Fucα(1-2)Gal motif, detects a variety of complex glycans and glycoproteins, and can be used to profile the relative abundance of the motif on live cells, discriminating malignant from normal cells. This approach represents a new potential strategy for biomarker detection and expands the technologies available for understanding the roles of this important class of carbohydrates in physiology and disease

Socially-mediated arousal and contagion within domestic chick broods

Emotional contagion – an underpinning valenced feature of empathy – is made up of simpler, potentially dissociable social processes which can include socially-mediated arousal and behavioural/physiological contagion. Previous studies of emotional contagion have often conflated these processes rather than examining their independent contribution to empathic response. We measured socially-mediated arousal and contagion in 9-week old domestic chicks (n = 19 broods), who were unrelated but raised together from hatching. Pairs of observer chicks were exposed to two conditions in a counterbalanced order: air puff to conspecifics (AP) (during which an air puff was applied to three conspecifics at 30 s intervals) and control with noise of air puff (C) (during which the air puff was directed away from the apparatus at 30 s intervals). Behaviour and surface eye temperature of subjects and observers were measured throughout a 10-min pre-treatment and 10-min treatment period. Subjects and observers responded to AP with increased freezing, and reduced preening and ground pecking. Subjects and observers also showed reduced surface eye temperature - indicative of stress-induced hyperthermia. Subject-Observer behaviour was highly correlated within broods during both C and AP conditions, but with higher overall synchrony during AP. We demonstrate the co-occurrence of socially-mediated behavioural and physiological arousal and contagion; component features of emotional contagion