The TR Prize are monthly awards for the best new research.

Below is this month's biology research from Biorxiv and Arxiv. TR Prizes based on your donations and peer reviews of these works are given at the end of each month.

1. Characterization of the impact of daclizumab beta on circulating natural killer cells by mass cytometry

5 December 2019 | Biorxiv link | Write review

Daclizumab beta is a humanized monoclonal antibody that binds to CD25 and selectively inhibits high-affinity IL-2 receptor signaling. As a former treatment for relapsing forms of multiple sclerosis (RMS), daclizumab beta induces robust expansion of the CD56bright subpopulation of NK cells that is correlated with the drugs therapeutic effects. As NK cells represent a heterogeneous population of lymphocytes with a range of phenotypes and functions, the goal of this study was to better understand how daclizumab beta altered the NK cell repertoire to provide further insight into the possible mechanism(s) of action in RMS. We used mass cytometry to evaluate expression patterns of NK cell markers and provide a comprehensive assessment of the NK cell repertoire in individuals with RMS treated with daclizumab beta or placebo over the course of one year. Treatment with daclizumab beta significantly altered the NK cell repertoire compared to placebo treatment. As previously reported, daclizumab beta significantly increased expression of CD56 on total NK cells. Within the CD56bright NK cells, treatment was associated with multiple phenotypic changes, including increased expression of NKG2A and NKp44, and diminished expression of CD244, CD57, and NKp46. While the changes were less dramatic, CD56dim NK cells responded distinctly to daclizumab beta treatment, with higher expression of CD2 and NKG2A, and lower expression of FAS-L, HLA-DR, NTB-A, NKp30, and Perforin. Together, these data indicate that the expanded NK cells share features of both immature and mature NK cells. These findings show that daclizumab beta treatment is associated with unique changes in NK cells that may enhance their ability to kill autoreactive T cells or to exert immunomodulatory functions.

2. Cancer recurrence times from a branching process model

5 December 2019 | Arxiv link | Write review

As cancer advances, cells often spread from the primary tumor to other parts of the body and form metastases. This is the main cause of cancer related mortality. Here we investigate a conceptually simple model of metastasis formation where metastatic lesions are initiated at a rate which depends on the size of the primary tumor. The evolution of each metastasis is described as an independent branching process. We assume that the primary tumor is resected at a given size and study the earliest time at which any metastasis reaches a minimal detectable size. The parameters of our model are estimated independently for breast, colorectal, headneck, lung and prostate cancers. We use these estimates to compare predictions from our model with values reported in clinical literature. For some cancer types, we find a remarkably wide range of resection sizes such that metastases are very likely to be present, but none of them are detectable. Our model predicts that only very early resections can prevent recurrence, and that small delays in the time of surgery can significantly increase the recurrence probability.

3. Surfactin production is not essential for pellicle and root-associated biofilm development of Bacillus subtilis

5 December 2019 | Biorxiv link | Write review

Secondary metabolites have an important impact on the biocontrol potential of soil-derived microbes. In addition, various microbe-produced chemicals have been suggested to impact the development and phenotypic differentiation of bacteria, including biofilms. The non-ribosomal synthesized lipopeptide of Bacillus subtilis, surfactin, has been described to impact the plant promoting capacity of the bacterium. Here, we investigated the impact of surfactin production on biofilm formation of B. subtilis using the laboratory model systems; pellicle formation at the air-medium interface and architecturally complex colony development, in addition to plant root-associated biofilms. We found that the production of surfactin by B. subtilis is not essential for pellicle biofilm formation neither in the well-studied strain, NCIB 3610, nor in the newly isolated environmental strains, but lack of surfactin reduces colony expansion. Further, plant root colonization was comparable both in the presence or absence of surfactin synthesis. Our results suggest that surfactin-related biocontrol and plant promotion in B. subtilis strains are independent of biofilm formation.

4. Surround suppression explained by long-range recruitment of local competition, in a columnar V1 model

5 December 2019 | Arxiv link | Write review

Although neurons in columns of visual cortex of adult carnivores and primates share similar orientation tuning preferences, responses of nearby neurons are surprisingly sparse and temporally uncorrelated, especially in response to complex visual scenes. The mechanisms underlying this counter-intuitive combination of response properties are still unknown. Here we present a computational model of columnar visual cortex which explains experimentally observed integration of complex features across the visual field, and which is consistent with anatomical and physiological profiles of cortical excitation and inhibition. In this model, sparse local excitatory connections within columns, coupled with strong unspecific local inhibition and functionally-specific long-range excitatory connections across columns, give rise to competitive dynamics that reproduce experimental observations. Our results explain surround modulation of responses to simple and complex visual stimuli, including reduced correlation of nearby excitatory neurons, increased excitatory response selectivity, increased inhibitory selectivity, and complex orientation-tuning of surround modulation.

5. Evaluating the data quality of iNaturalist termite records

4 December 2019 | Biorxiv link | Write review

Citizen science (CS) contributes to the combined knowledge about species distributions, which is a critical foundation in the studies of invasive species, biological conservation, and response to climatic change. In this study, we assessed the value of CS for termites worldwide. First, we compared the abundance and species diversity of geo-tagged termite records in iNaturalist to that of the University of Florida termite collection (UFTC) and the Global Biodiversity Information Facility (GBIF). Second, we quantified how the combination of these data sources affected the number of genera that satisfy data requirements for ecological niche modeling. Third, we assessed the taxonomic correctness of iNaturalist termite records in the Americas at the genus and family level through expert review based on photo identification. Results showed that iNaturalist records were less abundant than those in UFTC and in GBIF, although they complemented the latter two in selected world regions. A combination of GBIF and UFTC led to a significant increase in the number of termite genera satisfying the abundance criterion for niche modeling compared to either of those two sources alone, whereas adding iNaturalist observations as a third source only had a moderate effect on the number of termite genera satisfying that criterion. Although research grade observations in iNaturalist require a community-supported and agreed upon ID below the family taxonomic rank, our results indicated that iNaturalist data do not exhibit a higher taxonomic classification accuracy when they are designated research grade. This means that non-research grade observations can be used to more completely map the presence of termite locations in certain geographic locations without significantly jeopardizing data quality. We concluded that CS termite observation records can, to some extent, complement expert termite collections in terms of geographic coverage and species diversity. Based on recent data contribution patterns in CS data, the role of CS termite contributions is expected to grow significantly in the near future.

6. Renewal Approach to the Analysis of the Asynchronous State for Coupled Noisy Oscillators

4 December 2019 | Arxiv link | Write review

We develop a framework in which the activity of nonlinear pulse-coupled oscillators is posed within the renewal theory. In this approach, the evolution of inter-event density allows for a self-consistent calculation that determines the asynchronous state and its stability. This framework, can readily be extended to the analysis of systems with more state variables. To exhibit this, we study a nonlinear pulse-coupled system, where couplings are dynamic and activity dependent. We investigate stability of this system and we show it undergoes a super-critical Hopf bifurcation to collective synchronization.

7. Uncharacteristic task-evoked pupillary responses implicate atypical locus coeruleus activity in autism

4 December 2019 | Biorxiv link | Write review

Autism spectrum disorder (ASD) is characterized partly by atypical attentional engagement, such as hypersensitivity to environmental stimuli. Attentional engagement is known to be regulated by the locus coeruleus (LC). Moderate baseline LC activity globally dampens neural responsivity and is associated with adaptive deployment and narrowing of attention to task-relevant stimuli. In contrast, increased baseline LC activity enhances neural responsivity across cortex and widening of attention to environmental stimuli regardless of their task relevance. Given attentional atypicalities in ASD, this study is the first to evaluate whether individuals with ASD exhibit a different profile of LC activity compared to typically developing controls under different attentional task demands. Males and females with ASD and age- and gender-matched controls participated in a one-back letter detection test while task-evoked pupillary responses--an established inverse correlate for baseline LC activity--were recorded. Participants completed this task in two conditions, either in the absence or presence of distractor auditory tones. Compared to controls, individuals with ASD evinced atypical pupillary responses in the presence versus absence of distractors. Notably, this atypical pupillary profile was evident despite the fact that both groups exhibited equivalent task performance. Moreover, between-group differences in pupillary responses were observed only in response to task-relevant and not to task-irrelevant stimuli, providing confirmation that the group differences are specifically associated with distinctions in LC activity. These findings suggest that individuals with ASD show atypical modulation of LC activity with changes in attentional demands, offering a possible mechanistic and neurobiological account for attentional atypicalities in ASD.

8. Discrimination emerging through spontaneous symmetry breaking in a spatial prisoner's dilemma model with multiple labels

4 December 2019 | Arxiv link | Write review

Social discrimination seems to be a persistent phenomenon in many cultures. It is important to understand the mechanisms that lead people to judge others by the group to which they belong, rather than individual qualities. It was recently shown that evolutionary (imitation) dynamics can lead to a hierarchical discrimination between agents marked with observable, but otherwise meaningless, labels. These findings suggest that it can give useful insight, to describe the phenomenon of social discrimination in terms of spontaneous symmetry breaking. The investigations so far have, however, only considered binary labels. In this contribution we extend the investigations to models with up to seven different labels. We find the features known from the binary label model remain remarkably robust when the number of labels is increased. We also discover a new feature, namely that it is more likely for neighbours to have strategies which are similar, in the sense that they agree on how to act towards a subset of the labels.

9. Apical Constriction Reversal upon Mitotic Entry Underlies Different Morphogenetic Outcomes of Cell Division

3 December 2019 | Biorxiv link | Write review

During development, coordinated cell shape changes and cell divisions sculpt tissues. While these individual cell behaviors have been extensively studied, how cell shape changes and cell divisions that occur concurrently in epithelia influence tissue shape is less understood. We addressed this question in two contexts of the early Drosophila embryo: premature cell division during mesoderm invagination, and native ectodermal cell divisions with ectopic activation of apical contractility. Using quantitative live-cell imaging, we demonstrated that mitotic entry reverses apical contractility by interfering with medioapical RhoA signaling. While premature mitotic entry inhibits mesoderm invagination, which relies on apical constriction, mitotic entry in an artificially contractile ectoderm induced ectopic tissue invaginations. Ectopic invaginations resulted from medioapical myosin loss in neighboring mitotic cells. This myosin loss enabled non-mitotic cells to apically constrict through mitotic cell stretching. Thus, the spatial pattern of mitotic entry can differentially regulate tissue shape through signal interference between apical contractility and mitosis.

10. Theory of chemical evolution of molecule compositions in the universe, in the Miller-Urey experiment and the mass distribution of interstellar and intergalactic molecules

3 December 2019 | Arxiv link | Write review

Chemical evolution is essential in understanding the origins of life. We present a theory for the evolution of molecule masses and show that small molecules grow by random diffusion and large molecules by a preferential attachment process leading eventually to life's molecules. It reproduces correctly the distribution of molecules found via mass spectroscopy for the Murchison meteorite and estimates the start of chemical evolution back to 12.8 billion years following the birth of stars and supernovae. From the Frontier mass between the random and preferential attachment dynamics the birth time of molecule families can be estimated. Amino acids emerge about 165 million years after chemical elements emerge in stars. Using the scaling of reaction rates with the distance of the molecules in space we recover correctly the few days emergence time of amino acids in the Miller-Urey experiment. The distribution of interstellar and extragalactic molecules are both consistent with the evolutionary mass distribution, and their age is estimated to 108 and 65 million years after the start of evolution. From the model, we can determine the number of different molecule compositions at the time of the emergence of Earth to be 1.6 million and the number of molecule compositions in interstellar space to a mere 719 species.

11. Prediction of fruit texture with training population optimization for efficient genomic selection in apple

3 December 2019 | Biorxiv link | Write review

Texture plays a major role in the determination of fruit quality in apple. Due to its physiological and economic relevance, this trait has been largely investigated, leading to the fixation of the major gene PG1 controlling firmness in elite cultivars. To further improve fruit texture, the targeting of an undisclosed reservoir of loci with minor effects is compelling. In this work, we aimed to unlock this potential with a genomic selection approach by predicting fruit acoustic and mechanical features as obtained with a TA.XTplus texture analyzer in 537 individuals genotyped with 8,294 SNP markers. The best prediction accuracies following cross-validations within the training set (TRS) of 259 individuals were obtained for the acoustic linear distance (0.64). Prediction accuracy was further improved through the optimization of TRS size and composition according to the test set. With this strategy, a maximal accuracy of 0.81 was obtained when predicting the synthetic trait PC1 in the family 'Gala x Pink Lady'. We discuss the impact of genetic relatedness and clustering on trait variability and predictability. Moreover, we demonstrated the need for a comprehensive dissection of the complex texture phenotype and the potentiality of using genomic selection to improve fruit quality in apple.

12. Evolutionary dynamics with game transitions

3 December 2019 | Arxiv link | Write review

The environment has a strong influence on a population's evolutionary dynamics. Driven by both intrinsic and external factors, the environment is subject to continual change in nature. To capture an ever-changing environment, we consider a model of evolutionary dynamics with game transitions, where individuals' behaviors together with the games they play in one time step influence the games to be played next time step. Within this model, we study the evolution of cooperation in structured populations and find a simple rule: weak selection favors cooperation over defection if the ratio of the benefit provided by an altruistic behavior, $b$, to the corresponding cost, $c$, exceeds $k-k'$, where $k$ is the average number of neighbors of an individual and $k'$ captures the effects of the game transitions. Even if cooperation cannot be favored in each individual game, allowing for a transition to a relatively valuable game after mutual cooperation and to a less valuable game after defection can result in a favorable outcome for cooperation. In particular, small variations in different games being played can promote cooperation markedly. Our results suggest that simple game transitions can serve as a mechanism for supporting prosocial behaviors in highly-connected populations.

13. Fluorescent polysome profiling reveals stress-mediated regulation of HSPA14-ribosome interactions

2 December 2019 | Biorxiv link | Write review

Ribosome-associated factors play important roles in regulation of translation in response to various physiological and environmental signals. Here we present fluorescent polysome profiling, a new method that provides simultaneous detection of UV and fluorescence directly from polysome gradients. We demonstrate the capabilities of the method by following the polysome incorporation of different fluorescently tagged ribosomal proteins in human cells. Additionally, we used fluorescent polysome profiling to examine chaperone-ribosome interactions, and characterized their changes in response to proteotoxic stresses. We revealed dynamic regulation of HSPA14-polysome association in response to heat shock, showing a marked heat shock-mediated increased in the polysome-association of HSPA14. Our data further support a model whereby HSPA14 dimerization is increased upon heat shock. We therefore established fluorescent polysome profiling as a powerful, streamlined method that can significantly enhance the study of ribosome-associated factors and their regulation.

14. Cholinergic switch between two types of slow waves in cerebral cortex

2 December 2019 | Arxiv link | Write review

Sleep slow waves are known to participate in memory consolidation, yet slow waves occurring under anesthesia present no positive effects on memory. Here, we shed light onto this paradox, based on a combination of extracellular recordings in vivo, in vitro, and computational models. We find two types of slow waves, based on analyzing the temporal patterns of successive slow-wave events. The first type is consistently observed in natural slow-wave sleep, while the second is shown to be ubiquitous under anesthesia. Network models of spiking neurons predict that the two slow wave types emerge due to a different gain on inhibitory vs excitatory cells and that different levels of spike-frequency adaptation in excitatory cells can account for dynamical distinctions between the two types. This prediction was tested in vitro by varying adaptation strength using an agonist of acetylcholine receptors, which demonstrated a neuromodulatory switch between the two types of slow waves. Finally, we show that the first type of slow-wave dynamics is more sensitive to external stimuli, which can explain how slow waves in sleep and anesthesia differentially affect memory consolidation, as well as provide a link between slow-wave dynamics and memory diseases.

15. Liposomes Under Real Cell Conditions Behave Like Real Cells with a Single Pulsed Electric Field

2 December 2019 | Biorxiv link | Write review

Liposomes are widely assumed to present a straightforward physical model of cells. However, almost all previous liposome experiments with pulsed electric fields (PEFs) have been conducted in low-conductivity liquids, a condition that differs significantly from that of cells in medium. Here, we prepared liposomes consisting of soy bean lecithin and cholesterol, at a molar ratio of 1:1, in higher-conductivity liquid that approximated the conditions of red blood cells in phosphate-buffered saline, with inner and outer liquid conductivities of 0.6 and 1.6 S/m, respectively. We found that a single 1.1 kV/cm, 400 us PEF promoted cell-like spontaneous division of liposomes.

16. TNFPred: Identifying tumor necrosis factors using hybrid features based on word embeddings

1 December 2019 | Biorxiv link | Write review

Background: Cytokines are a class of small proteins that act as chemical messengers and play a significant role in essential cellular processes including immunity regulation, hematopoiesis, and inflammation. As one important family of cytokines, tumor necrosis factors have association with the regulation of a various biological processes such as proliferation and differentiation of cells, apoptosis, lipid metabolism, and coagulation. The implication of these cytokines can also be seen in various diseases such as insulin resistance, autoimmune diseases, and cancer. Considering the interdependence between this kind of cytokine and others, classifying tumor necrosis factors from other cytokines is a challenge for biological scientists. In this research, we employed a word embedding technique to create hybrid features which was proved to efficiently identify tumor necrosis factors given cytokine sequences. We segmented each protein sequence into protein words and created corresponding word embedding for each word. Then, word embedding-based vector for each sequence was created and input into machine learning classification models. When extracting feature sets, we not only diversified segmentation sizes of protein sequence but also conducted different combinations among split grams to find the best features which generated the optimal prediction. Furthermore, our methodology follows Chou 5-step rules to build a reliable classification tool. Results: With our proposed hybrid features, prediction models obtain more promising performance compared to seven prominent sequenced-based feature kinds. Results from 10 independent runs on the surveyed dataset show that on an average, our optimal models obtain an area under the curve of 0.984 and 0.998 on 5-fold cross-validation and independent test, respectively. Conclusions: These results show that biologists can use our model to identify tumor necrosis factors from other cytokines efficiently. Moreover, this study proves that natural language processing techniques can be applied reasonably to help biologists solve bioinformatics problems efficiently.

17. Mass-spectrometry based proteomics reveals mitochondrial supercomplexome plasticity

1 December 2019 | Biorxiv link | Write review

Mitochondrial respiratory complex subunits assemble in supercomplexes. Studies of supercomplexes have typically relied upon antibody-based protein quantification, often limited to the analysis of a single subunit per respiratory complex. To provide a deeper insight into mitochondrial and supercomplex plasticity, we combined Blue Native Polyacrylamide Gel Electrophoresis (BN-PAGE) and mass spectrometry to determine the supercomplexome of skeletal muscle from sedentary and exercise-trained mice. We quantified 422 mitochondrial proteins within ten supercomplex bands, in which we showed the debated presence of complex II and V. Upon exercise-induced mitochondrial biogenesis, non-stoichiometric changes in subunits and incorporation into supercomplexes was apparent. We uncovered the dynamics of supercomplex-related assembly proteins and mtDNA-encoded subunits within supercomplexes, as well as the complexes of ubiquinone biosynthesis enzymes and Lactb, a mitochondrial-localized protein implicated in obesity. Our approach can be applied to broad biological systems. In this instance, comprehensively analyzing respiratory supercomplexes illuminates previously undetectable complexity in mitochondrial plasticity.