Domain Adaptation-Based Deep Learning for Automated Tumor Cell (TC) Scoring and Survival Analysis on PD-L1 Stained Tissue Images.

We report the ability of two deep learning-based decision systems to stratify non-small cell lung cancer (NSCLC) patients treated with checkpoint inhibitor therapy into two distinct survival groups. Both systems analyze functional and morphological properties of epithelial regions in digital histopathology whole slide images stained with the SP263 PD-L1 antibody. The first system learns to replicate the pathologist assessment of the Tumor Cell (TC) score with a cut-point for positivity at 25% for patient stratification. The second system is free from assumptions related to TC scoring and directly learns patient stratification from the overall survival time and event information. Both systems are built on a novel unpaired domain adaptation deep learning solution for epithelial region segmentation. This approach significantly reduces the need for large pixel-precise manually annotated datasets while superseding serial sectioning or re-staining of slides to obtain ground truth by cytokeratin staining. The capacity of the first system to replicate the TC scoring by pathologists is evaluated on 703 unseen cases, with an addition of 97 cases from an independent cohort. Our results show Lin's concordance values of 0.93 and 0.96 against pathologist scoring, respectively. The ability of the first and second system to stratify anti-PD-L1 treated patients is evaluated on 151 clinical samples. Both systems show similar stratification powers (first system: HR = 0.539, p = 0.004 and second system: HR = 0.525, p = 0.003) compared to TC scoring by pathologists (HR = 0.574, p = 0.01).

tRNA sequences can assemble into a replicator.

Can replication and translation emerge in a single mechanism via self-assembly? The key molecule, transfer RNA (tRNA), is one of the most ancient molecules and contains the genetic code. Our experiments show how a pool of oligonucleotides, adapted with minor mutations from tRNA, spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The pool of cross-complementary hairpins self-selected by agglomeration and sedimentation. The metastable DNA hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. The molecular assembly could encode and replicate binary sequences with a replication fidelity corresponding to 85-90 % per nucleotide. The replication by a self-assembly of tRNA-like sequences suggests that early forms of tRNA could have been involved in molecular replication. This would link the evolution of translation to a mechanism of molecular replication.

The genetic code stored within DNA contains the instructions for manufacturing all the proteins organisms need to develop, grow and survive. This requires molecular machines that 'transcribe' regions of the genetic code into RNA molecules which are then 'translated' into the string of amino acids that form the final protein. However, these molecular machines and other proteins are also needed to replicate and synthesize the sequences stored in DNA. This presents evolutionary biologists with a 'chicken-and-egg' situation: which came first, the DNA sequences needed to manufacture proteins or the proteins needed to transcribe and translate DNA? Understanding the order in which DNA replication and protein translation evolved is challenging as these processes are tightly intertwined in modern-day species. One theory, known as the 'RNA world hypothesis', suggests that all life on Earth began with a single RNA molecule that was able to make copies of itself, as DNA does today. To investigate this hypothesis, Kühnlein, Lanzmich and Braun studied a molecule called transfer RNA (or tRNA for short) which is responsible for translating RNA into proteins. tRNA is assumed to be one of the earliest evolved molecules in biology. Yet, why it was present in early life forms before it was needed for translation still remained somewhat of a mystery. To gain a better understanding of tRNA's role early in evolution, Kühnlein, Lanzmich and Braun made small changes to its genetic code and then carried out tests on these tRNA-like sequences. The experiments showed these 'early' forms of tRNA can actually self-assemble into a molecule which is capable of replicating the information stored in its sequence. It suggests early forms of tRNA could have been involved in replication before modern tRNA developed its role in protein translation. With these experiments, Kühnlein, Lanzmich and Braun have identified a possible evolutionary link between DNA replication and protein translation, suggesting the two processes emerged through one shared pathway: tRNA. This deepens our understanding about the origins of early life, while taking biochemists one step closer to their distant goal of recreating self-replicating molecular machines in the laboratory.

Probing of molecular replication and accumulation in shallow heat gradients through numerical simulations.

How can living matter arise from dead matter? All known living systems are built around information stored in RNA and DNA. To protect this information against molecular degradation and diffusion, the second law of thermodynamics imposes the need for a non-equilibrium driving force. Following a series of successful experiments using thermal gradients, we have shown that heat gradients across sub-millimetre pores can drive accumulation, replication, and selection of ever longer molecules, implementing all the necessary parts for Darwinian evolution. For these lab experiments to proceed with ample speed, however, the temperature gradients have to be quite steep, reaching up to 30 K per 100 µm. Here we use computer simulations based on experimental data to show that 2000-fold shallower temperature gradients - down to 100 K over one metre - can still drive the accumulation of protobiomolecules. This finding opens the door for various environments to potentially host the origins of life: volcanic, water-vapour, or hydrothermal settings. Following the trajectories of single molecules in simulation, we also find that they are subjected to frequent temperature oscillations inside these pores, facilitating e.g. template-directed replication mechanisms. The tilting of the pore configuration is the central strategy to achieve replication in a shallow temperature gradient. Our results suggest that shallow thermal gradients across porous rocks could have facilitated the formation of evolutionary machines, significantly increasing the number of potential sites for the origin of life on young rocky planets.

Heat flux across an open pore enables the continuous replication and selection of oligonucleotides towards increasing length.

The replication of nucleic acids is central to the origin of life. On the early Earth, suitable non-equilibrium boundary conditions would have been required to surmount the effects of thermodynamic equilibrium such as the dilution and degradation of oligonucleotides. One particularly intractable experimental finding is that short genetic polymers replicate faster and outcompete longer ones, which leads to ever shorter sequences and the loss of genetic information. Here we show that a heat flux across an open pore in submerged rock concentrates replicating oligonucleotides from a constant feeding flow and selects for longer strands. Our experiments utilize the interplay of molecular thermophoresis and laminar convection, the latter driving strand separation and exponential replication. Strands of 75 nucleotides survive whereas strands half as long die out, which inverts the above dilemma of the survival of the shortest. The combined feeding, thermal cycling and positive length selection opens the door for a stable molecular evolution in the long-term microhabitat of heated porous rock.

Thermophoresis in nanoliter droplets to quantify aptamer binding.

Biomolecule interactions are central to pharmacology and diagnostics. These interactions can be quantified by thermophoresis, the directed molecule movement along a temperature gradient. It is sensitive to binding induced changes in size, charge, or conformation. Established capillary measurements require at least 0.5 µL per sample. We cut down sample consumption by a factor of 50, using 10 nL droplets produced with acoustic droplet robotics (Labcyte). Droplets were stabilized in an oil-surfactant mix and locally heated with an IR laser. Temperature increase, Marangoni flow, and concentration distribution were analyzed by fluorescence microscopy and numerical simulation. In 10 nL droplets, we quantified AMP-aptamer affinity, cooperativity, and buffer dependence. Miniaturization and the 1536-well plate format make the method high-throughput and automation friendly. This promotes innovative applications for diagnostic assays in human serum or label-free drug discovery screening.

Statistically induced phase transitions and anyons in 1D optical lattices.

Anyons--particles carrying fractional statistics that interpolate between bosons and fermions--have been conjectured to exist in low-dimensional systems. In the context of the fractional quantum Hall effect, quasi-particles made of electrons take the role of anyons whose statistical exchange phase is fixed by the filling factor. Here we propose an experimental setup to create anyons in one-dimensional lattices with fully tuneable exchange statistics. In our setup, anyons are created by bosons with occupation-dependent hopping amplitudes, which can be realized by assisted Raman tunnelling. The statistical angle can thus be controlled in situ by modifying the relative phase of external driving fields. This opens the fascinating possibility of smoothly transmuting bosons via anyons into fermions and of inducing a phase transition by the mere control of the particle statistics as a free parameter. In particular, we demonstrate how to induce a quantum phase transition from a superfluid into an exotic Mott-like state where the particle distribution exhibits plateaus at fractional densities.