bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of amphipathic helix – membrane interactions with Rosetta
Authors: Gulsevin Alican , Meiler Jens
Published: June 2020

Amphipathic helices have hydrophobic and hydrophilic/charged residues situated on opposite faces of the helix. They can anchor peripheral membrane proteins to the membrane, be attached to integral membrane proteins, or exist as independent peptides. Despite the widespread presence of membrane-interacting amphipathic helices, there is no computational tool within Rosetta to model their interactions with membranes. In order to address this need, we developed the AmphiScan protocol with PyRosetta, which runs a grid search to find the most favorable position of an amphipathic helix with respect to the membrane. The performance of the algorithm was tested in benchmarks with theRosettaMembrane, ref2015_memb, andfranklin2019score functions on six engineered and 44 naturally-occurring amphipathic helices using membrane coordinates from the OPM and PDBTM databases, OREMPRO server, and MD simulations for comparison. The AmphiScan protocol predicted the coordinates of amphipathic helices within less than 3Å of the reference structures and identified membrane-embedded residues with a Matthews Correlation Constant (MCC) of up to 0.57. Overall, AmphiScan stands as fast, accurate, and highly-customizable protocol that can be pipelined with other Rosetta and Python applications.
A model-based analysis of the mechanical cost of walking on uneven terrain
Authors: Voloshina Alexandra S. , Kuo Arthur D. , Ferris Daniel P. , Remy C. David
Published: June 2020

Human walking on uneven terrain is energetically more expensive than on flat, even ground. This is in part due to increases in, and redistribution of positive work among lower limb joints. To improve understanding of the mechanical adaptations, we performed analytical and computational analyses of simple mechanical models walking over uneven terrain comprised of alternating up and down steps of equal height. We simulated dynamic walking models using trailing leg push-off and/or hip torque to power gait, and quantified the compensatory work costs vs. terrain height. We also examined the effect of swing leg dynamics by including and excluding them from the model. We found that greater work, increasing approximately quadratically with uneven terrain height variations, was necessary to maintain a prescribed average forward speed. Greatest economy was achieved by modulating precisely-timed push-offs for each step height. Least economy was achieved with hip power, which did not require as precise timing. This compares well with observations of humans on uneven terrain, showing similar near-normal push-off but with more variable step timing, and considerably more hip work. These analyses suggest how mechanical work and timing could be adjusted to compensate for real world environments.
Mathematical connection between short telomere induced senescence calculation and mortality rate data
Authors: Torrance Jerry B. , Goldband Steve
Published: June 2020

The last 20 years have seen a surge in scientific activity and promising results in the study of aging and longevity. Many researchers have focused on telomeres, which are composed of a series of TTAGGG repeat nucleotide sequences at the ends of each chromosome. Measurements of the length of these telomere strands show that they decrease in length with increasing age, leading many authors to propose that when the length of these telomere strands decreases sufficiently, the cells enter into a state of replicative senescence, eventually leading to disease and death. These ideas are supported by evidence that short telomere length is correlated with increased mortality. In this paper, we extend this idea to make an actual calculation of the predicted mortality rate caused by short telomere length induced senescence (STLIS). We derive a simple equation for the mathematical relationship between telomere length and mortality rate. Using only 3 parameters based on telomere length measurement data of Canadians, we have calculated both the magnitude and the age dependence of the mortality rate, for both men and women. We show that these calculated data are in good quantitative agreement with the actual number of Canadians that die. This agreement provides strong evidence (but not proof) that the mechanism of STLIS plays an important role in the major diseases of aging (e.g., cardiovascular disease, many cancers, and diabetes mellitus) which dominate human mortality. This result represents significant progress in our understanding the factors behind the cause of aging.
Cross talk between tumor stroma and cancer cells plays a critical role in progressive enrichment of cancer stem cell phenotype in primary breast tumors
Authors: Dhanota Ninjit , Bal Amanjit , Singh Gurpreet , Arora Sunil K
Published: June 2020

In order to delineate the underlying molecular mechanisms responsible for intra tumoral enrichment of BCSCs in aggressive breast tumors, firstly we evaluated the frequency and characteristics of breast cancer stem cells (BCSCs) within the tumor mass as well as in pathologically normal adjacent tissues in primary breast carcinomas of various clinical and histological grades. Then, we evaluated the expression profiles of various genes in non-cancer stem cells from these tumors to delineate the role played by cellular niche in de novo origin and/or expansion of intra-tumoral cancer stem cells.

The study included primary tumor and adjacent normal breast tissue specimens from chemotherapy-naïve breast carcinoma patients. The BCSCs, identified as Lin-CD44+CD24-and aldehyde dehydrogenase 1 A1 positive were enumerated. The frequency of intra-tumoral BCSCs was correlated with various clinicopathological parameters of breast cancer. The flow-cytometrically sorted stromal cells and cancer cells from treatment naïve primary breast tumors were processed for gene expression profiling using a custom designed PCR array of genes known to facilitate cancer cell proliferation and disease progression.

The frequency of BCSCs within the tumor mass as well as in the adjacent normal tissue correlated significantly with histopathological and molecular grades of tumors indicating a direct relationship of BCSC with aggressive behavior of breast cancer. A significantly higher number of BCSCs was also detected in metastatic LN group as compared to non-metastatic LN. Further, a significantly increased expression of the genes associated with growth factors, cytokines & matricellular proteins in tumors with high BCSCs content (> 5%; Hi-BCSCs tumors) as compared to Lo-BCSC tumors (with <5% intratumoral BCSC content) suggested the possible contribution of stromal cells and cancer cells in intra-tumoral expansion of CSCs. Similarly, a significant up-regulation of genes associated with hypoxia and angiogenesis in Hi-BCSCs tumors further supported the role of hypoxic environment. The expression levels of genes associated with epithelial to mesenchymal transition also followed a similar pattern. On the other hand, downregulated SNAI1 gene (generally upregulated in onset of EMT) in stromal cells of Hi-BCSCs tumors suggests a post EMT environment in Hi-BCSCs tumors.

The findings suggest that the molecular crosstalk between the non-BCSC niche cells and the cancer stem cells within the breast cancer microenvironment directly contribute to formation of biologically conducive conditions for expansion of cancer stem cells.
Yeast grown in continuous culture systems can detect mutagens with improved sensitivity relative to the Ames test
Authors: Ong Joseph Y , Pence Julia T , Molik David C , Goodson Holly V
Published: June 2020

Continuous culture systems allow for the controlled growth of microorganisms over a long period of time. Here, we develop a novel test for mutagenicity that involves growing yeast in continuous culture systems exposed to low levels of mutagen for a period of weeks. In contrast, most microorganism-based tests for mutagenicity expose the potential mutagen to the biological reporter at a high concentration of mutagen for a short period of time. Our test improves upon the sensitivity of the well-established Ames test by at least 20-fold for each of two mutagens that act by different mechanisms (the intercalator ethidium bromide and alkylating agent methylmethane sulfonate). To conduct the tests, cultures were grown in small, inexpensive continuous culture systems in media containing (potential) mutagen, and the resulting mutagenicity of the added compound was assessed via two methods: a canavanine-based plate assay and whole genome sequencing. In the canavanine-based plate assay, we were able to detect a clear relationship between the amount of mutagen and the number of canavanine-resistant mutant colonies over a period of one to three weeks of exposure. Whole genome sequencing of yeast grown in continuous culture systems exposed to MMS demonstrated that quantification of mutations is possible by identifying the number of unique variants across each strain but with lower sensitivity than the plate-based assay. In conclusion, we propose yeast grown in continuous culture systems can provide an improved and more sensitive test for mutagenicity.
Fast weight recovery, metabolic rate adjustment and gene-expression regulation define responses of cold-stressed honey bee brood
Authors: Ramirez Leonor , Luna Facundo , Mucci Claudio Andoni , Lamattina Lorenzo
Published: June 2020

In temperate climates, low ambient temperatures in late winter and in spring can result in cold stress conditions in brood areas of weakened honey bee colonies, leading to increased levels of developmental interruptions and death of the brood. Very little is known about the physiological and molecular mechanisms that regulate honey bee brood responses to acute cold-stress. Here, we hypothesized that central regulatory pathways mediated by insulin/insulin-like peptide signalling (IIS) and adipokinetic hormone (AKH) are linked to metabolic changes in cold-stressed honey bee brood.A. melliferabrood reared at suboptimal temperatures showed diminished growth rate and arrested development progress. Notably, cold-stressed brood rapidly recovers the growth in the first 24 h after returning at control rearing temperature, sustained by the induction of compensatory mechanisms. We determined fast changes in the expression of components of IIS and AKH pathways in cold-stressed brood supporting their participation in metabolic events, growth and stress responses. We also showed that metabolic rate keeps high in brood exposed to stress suggesting a role in energy supply for growth and cell repair. Additionally, transcript levels of the uncoupling protein MUP2 were elevated in cold-stressed brood, suggesting a role for heat generation through mitochondrial decoupling mechanisms and/or ROS attenuation. Physiological, metabolic and molecular mechanisms that shape the responses to cold-stress in honey bee brood are addressed and discussed.
Collective motion as a distinct behavioural state of the individual
Authors: Knebel Daniel , Sha-ked Ciona , Agmon Noa , Ariel Gil , Ayali Amir
Published: June 2020

The collective motion of swarms depends on adaptations at the individual level. We explored these and their effects on swarm formation and maintenance in locusts. The walking kinematics of individual insects were monitored under laboratory settings, before, as well as during collective motion in a group, and again after separation from the group. It was found that taking part in collective motion induced in the individual unique behavioural kinematics, suggesting the existence of a distinct behavioural mode that we term a “collective-motion-state”. This state, characterized by behavioural adaptation to the social context, is long lasting, not induced by crowding per-se, but only by experiencing collective motion. Utilizing computational models, we show that this adaptability increases the robustness of the swarm. Overall, our findings suggest that collective-motion is not only an emergent property of the group, but also depends on a behavioural mode, rooted in endogenous mechanisms of the individual.
Dendritic coincidence detection in Purkinje neurons of awake mice
Authors: Roome Christopher J. , Kuhn Bernd
Published: June 2020

Dendritic coincidence detection is thought fundamental to neuronal processing, yet the underlying dendritic voltage-calcium relationship remains unexplored in awake animals. Here, using simultaneous voltage and calcium two-photon imaging of Purkinje neuron spiny dendrites, we show how coincident sub- and suprathreshold synaptic inputs modulate dendritic calcium signaling during sensory stimulation in awake mice. Sensory stimulation evokes subthreshold excitatory and inhibitory post-synaptic potentials, that coincide with suprathreshold dendritic spikes triggered by climbing fiber and parallel fiber synaptic input. Purkinje neuron dendrites integrate these inputs in a time-dependent and non-linear fashion to enhance the sensory evoked dendritic calcium signal. Intrinsic supra-linear dendritic mechanisms, including voltage gated calcium channels and metabotropic glutamate receptors, are recruited cooperatively to expand the dynamic range of sensory evoked dendritic calcium signals. This establishes how dendrites use multiple interplaying mechanisms to perform coincidence detection, as a fundamental and ongoing feature of dendritic integration during behavior.
Miniaturized Devices for Bioluminescence Imaging in Freely Behaving Animals
Authors: Celinskis Dmitrijs , Friedman Nina , Koksharov Mikhail , Murphy Jeremy , Gomez-Ramirez Manuel , Borton David , Shaner Nathan , Hochgeschwender Ute , Lipscombe Diane , Moore Christopher
Published: June 2020

Fluorescence miniature microscopyin vivohas recently proven a major advance, enabling cellular imaging in freely behaving animals. However, fluorescence imaging suffers from autofluorescence, phototoxicity, photobleaching and non-homogeneous illumination artifacts. These factors limit the quality and time course of data collection. Bioluminescence provides an alternative kind of activity-dependent light indicator. Bioluminescent calcium indicators do not require light input, instead generating photons through chemiluminescence. As such, limitations inherent to the requirement for light presentation are eliminated. Further, bioluminescent indicators also do not require excitation light optics: the removal of this component should make lighter and lower cost microscope with fewer assembly parts. While there has been significant recent progress in making brighter and faster bioluminescence indicators, parallel advances in imaging hardware have not yet been realized. A hardware challenge is that despite potentially higher signal-to-noise of bioluminescence, the signal strength is lower than that of fluorescence. An open question we address in this report is whether fluorescent miniature microscopes can be rendered sensitive enough to detect bioluminescence. We demonstrate this possibilityin vitroandin vivoby implementing optimizations of the UCLA fluorescent miniscope. These optimizations yielded a miniscope (BLmini) which is 22% lighter in weight, has 45% fewer components, is up to 58% less expensive, offers up to 15 times stronger signal (as dichroic filtering is not required) and is sensitive enough to capture spatiotemporal dynamics of bioluminescence in the brain with a signal-to-noise ratio of 34 dB.
Extracellular GABA waves regulate coincidence detection in excitatory circuits
Authors: Sylantyev Sergiy , Savtchenko Leonid P. , O’Neill Nathanael , Rusakov Dmitri A.
Published: June 2020

Coincidence detection of excitatory inputs by principal neurons underpins the rules of signal integration and Hebbian plasticity in the brain. In the hippocampal circuitry, detection fidelity is thought to depend on the GABAergic synaptic input through a feed-forward inhibitory circuit also involving the hyperpolarization-activatedIhcurrent. However, afferent connections often bypass feed-forward circuitry, suggesting that a different GABAergic mechanism might control coincidence detection in such cases. To test whether fluctuations in the extracellular GABA concentration [GABA] could play a regulatory role here, we use a GABA ‘sniffer’ patch in acute hippocampal slices of the rat and document strong dependence of [GABA] on network activity. We find that blocking GABAergic signalling strongly reduces the coincidence detection window of direct excitatory inputs to pyramidal cells whereas increasing [GABA] through GABA uptake blockade expands it. The underlying mechanism involves membrane-shunting tonic GABAAreceptor current; it does not have to rely onIhbut depends strongly on the neuronal GABA transporter GAT-1. We use dendrite-soma dual patch-clamp recordings to show that the strong effect of membrane shunting on coincidence detection relies on nonlinear amplification of changes in the decay of dendritic synaptic currents when they reach the soma. Our results suggest that, by dynamically regulating extracellular GABA, brain network activity can optimise signal integration rules in local excitatory circuits.
Dissecting transcriptomic signatures of genotype x genotype interactions during the initiation of plant-rhizobium symbiosis
Authors: Fagorzi Camilla , Bacci Giovanni , Huang Rui , Cangioli Lisa , Checcucci Alice , Fini Margherita , Perrin Elena , Natali Chiara , diCenzo George Colin , Mengoni Alessio
Published: June 2020

Rhizobia are ecologically important, facultative plant symbiotic microbes. In nature there exists large variability in the association of rhizobial strains and host plant of the same species. Here, we evaluated whether plant and rhizobial genotypes influence the initial transcriptional response of rhizobium following perception of host plant. RNA-sequencing of the model rhizobiumSinorhizobium melilotiexposed to root exudates or luteolin was performed in a combination of threeS. melilotistrains and threeMedicago sativavarieties. The response to root exudates involved hundreds of changes in the rhizobium transcriptome. Of the differentially expressed genes, expression of 35% were influenced by strain genotype, 16% by the plant genotype, and 29% by strain x host plant genotype interactions. We also examined the response of a hybridS. melilotistrain, in which the symbiotic megaplasmid (~ 20% of the genome) was mobilized between two of the above-mentioned strains. Dozens of genes resulted up-regulated in the hybrid strain, indicative of nonadditive variation in the transcriptome. In conclusion, this study demonstrated that transcriptional responses of rhizobia upon perception of legumes is influenced by the genotypes of both symbiotic partners, and their interaction, suggesting a wide genetic spectrum of partner choice selection in plant-rhizobium symbiosis.
Predicting Mean Ribosome Load for 5’UTR of any length using Deep Learning
Authors: Karollus Alexander , Avsec Žiga , Gagneur Julien
Published: June 2020

The 5’ untranslated region plays a key role in regulating mRNA translation and consequently protein abundance. Therefore, accurate modeling of 5’UTR regulatory sequences shall provide insights into translational control mechanisms and help interpret genetic variants. Recently, a model was trained on a massively parallel reporter assay to predict mean ribosome load (MRL) - a proxy for translation rate - directly from 5’UTR sequence with a high degree of accuracy. However, this model is restricted to sequence lengths investigated in the reporter assay and therefore cannot be applied to the majority of human sequences without a substantial loss of information. Here, we introduced frame pooling, a novel neural network operation that enabled the development of an MRL prediction model for 5’UTRs of any length. Our model shows state-of-the-art performance on fixed length randomized sequences, while offering better generalization performance on longer sequences and on a variety of translation-related genome-wide datasets. Variant interpretation is demonstrated on a 5’UTR variant of the gene HBB associated with beta-thalassemia. Frame pooling could find applications in other bioinformatics predictive tasks. Moreover, our model, released open source, could help pinpoint pathogenic genetic variants.
Production and analysis of a mammalian septin hetero-octamer complex
Authors: DeRose Barry T. , Kelley Robert S. , Ravi Roshni , Kokona Bashkim , Spiliotis Elias T. , Padrick Shae B.
Published: June 2020

The septins are filament-forming proteins found in diverse eukaryotes from fungi to vertebrates, with roles in cytokinesis, shaping of membranes and modifying cytoskeletal organization. These GTPases assemble into rod-shaped soluble hetero-hexamers and hetero-octamers in mammals, which polymerize into filaments and higher order structures. While the cell biology and pathobiology of septins are advancing rapidly, mechanistic study of the mammalian septins is limited by a lack of recombinant hetero-octamer materials. We describe here the production and characterization of a recombinant mammalian septin hetero-octamer of defined stoichiometry, the SEPT2/SEPT6/SEPT7/SEPT3 complex. Using a fluorescent protein fusion to the complex, we observed filaments assembled from this complex. In addition, we used this novel tool to resolve recent questions regarding the organization of the soluble septin complex. Biochemical characterization of a SEPT3 truncation that disrupts SEPT3-SEPT3 interactions is consistent with SEPT3 occupying a central position in the complex while the SEPT2 subunits are at the ends of the rod-shaped octameric complexes. Consistent with SEPT2 being on the complex ends, we find that our purified SEPT2/SEPT6/SEPT7/SEPT3 hetero-octamer copolymerizes into mixed filaments with separately purified SEPT2/SEPT6/SEPT7 hetero-hexamer. We expect this new recombinant production approach to lay essential groundwork for future studies into mammalian septin mechanism and function.
New insights on the modelling of the molecular mechanisms underlying neural maps alignment in the midbrain
Authors: Savier Elise Laura , Dunbar James , Cheung Kyle , Reber Michael
Published: June 2020

We previously identified and modelled a principle of visual maps alignment in the midbrain involving the mapping of the retinal projections and concurrent transposition of retinal guidance cues into the superior colliculus providing positional information for the organization of cortical V1 projections onto the retinal map (Savier et al., 2017). This principle relies on mechanisms involving Epha/Efna signaling, correlated neuronal activity and axon competition. Here, using the 3-step map alignment computational model, we predict and validate in vivo the visual mapping defects in a well-characterized mouse model. Our results challenge previous hypotheses and provide an alternative, although complementary, explanation for the phenotype observed. In addition, we propose a new quantification method to assess the degree of alignment and organization between maps, allowing inter-model comparisons. This work generalizes the validity and robustness of the 3-step map alignment algorithm as a predictive tool and confirms the basic mechanisms of visual maps organization.
Depletion of cardiolipin induces major changes in energy metabolism inTrypanosoma bruceibloodstream forms
Authors: Serricchio Mauro , Hierro-Yap Carolina , Schädeli David , Hamidane Hisham Ben , Hemphill Andrew , Graumann Johannes , Zíková Alena , Bütikofer Peter
Published: June 2020

Cardiolipin (CL) is a mitochondrial inner membrane glycerophospholipid that associates with mitochondrial proteins to promote their activities and to facilitate protein complex and super-complex formation. Loss of CL leads to destabilized respiratory complexes and mitochondrial dysfunction. The role of CL in an organism lacking a conventional electron transport chain (ETC) has not been elucidated so far. We now report that inTrypanosoma bruceibloodstream forms, in which the ETC is truncated and composed of alternative oxidase and glycerol-3-phosphate dehydrogenase, and the mitochondrial membrane potential is generated by the hydrolytic action of the FoF1-ATP synthase, the inducible depletion of cardiolipin synthase (TbCls) is essential for parasite survival. Loss of TbCls and CL caused a rapid drop in ATP levels and a decline in the mitochondrial membrane potential. Unbiased proteomic analyses revealed a reduction in the levels of many mitochondrial proteins, most notably of FoF1-ATP synthase subunits and of the alternative oxidase, resulting in a strong decline of glycerol-3-phosphate-stimulated oxygen consumption. Interestingly, the changes in cellular respiration preceded the observed decrease in FoF1-ATPase stability, suggesting that the truncated ETC is the first pathway responding to the decline in CL. In addition, proteomic and metabolomic analyses revealed that select proteins and pathways involved in glucose and amino acid transport and metabolism are up-regulated during CL depletion, possibly as a stress response to restore cellular ATP levels.
Reward-based invigoration of sequential reaching
Authors: Sporn Sebastian , Chen Xiuli , Galea Joseph M
Published: June 2020

Seeking reward is a powerful tool for shaping human behaviour. While it has been demonstrated that reward invigorates performance of simple movements, its effect on more complex sequential actions is less clear. In addition, it is unknown why reward-based improvements for discrete actions are transient, i.e. performance gains are lost once reward is removed, but appear long lasting for sequential actions. We show across three experiments that reward invigorates sequential reaching performance. Driven by a reward-based increase in speed, movements also exhibited greater coarticulation, smoothness and a closer alignment to a minimum jerk trajectory. Critically, these performance gains were maintained across multiple days even after the removal of reward. We propose that coarticulation, the blending together of sub-movements into a single continuous action, provides a mechanism by which reward can invigorate sequential performance whilst also increasing efficiency. This change in efficiency appears essential for the retention of reward-based improvements in motor behaviour.
Protein tyrosine phosphatase-PEST (PTP-PEST) mediates hypoxia-induced endothelial autophagy and angiogenesis through AMPK activation
Authors: Chandel Shivam , Manikandan Amrutha , Mehta Nikunj , Nathan Abel Arul , Tiwari Rakesh Kumar , Mohapatra Samar Bhallabha , Chandran Mahesh , Jaleel Abdul , Manoj Narayanan , Dixit Madhulika
Published: June 2020

Global and endothelial loss of PTP-PEST is associated with impaired cardiovascular development and embryonic lethality. Although hypoxia is implicated in vascular morphogenesis and remodelling, its effect on PTP-PEST remains unexplored. Here we report that hypoxia (1% oxygen)increases protein levels and catalytic activity of PTP-PEST in primary endothelial cells. Immunoprecipitation followed by mass spectrometry (LC/MS/MS) revealed that AMP-activated protein kinase alpha subunits (AMPK α1and α2) interact with PTP-PEST under normoxia but not in hypoxia. Co-immunoprecipitation experiments confirmed this observation and determined that AMPK α subunits interact with the catalytic domain of PTP-PEST. Knock-down of PTP-PEST abrogated hypoxia mediated tyrosine dephosphorylation and activation of AMPK (Thr172phosphorylation). Absence of PTP-PEST also blocked hypoxia-induced autophagy (measured as LC3 degradation and puncta formation) which was rescued by AMPK activator, metformin (500µM). Since endothelial autophagy is a pre-requisite for angiogenesis, knock-down of PTP-PEST also attenuated endothelial cell migration and capillary tube formation with autophagy inducer rapamycin (200nM) rescuing these effects. In conclusion, this work identifies for the first time PTP-PEST as a regulator of hypoxia-induced AMPK activation and endothelial autophagy to promote angiogenesis.
Passive Novel Isodamping Dynamometer for Mobile Measurement of Plantar Flexor Function
Authors: Drazan John F. , Hullfish Todd J , Baxter Josh R.
Published: June 2020

Isokinetic dynamometers are the gold standard tools used to assessin vivojoint and muscle function in human subjects, however, the large size and high cost of these devices prevents their widespread use outside of biomechanics lab. In this study, we developed a mobile dynamometer to allow for field measurements of joint level function. To ensure subject safety, we designed a new “isodamping” dynamometer that acted as passive energy sink which constrains velocity by forcing incompressible oil through an orifice with an adjustable diameter. We validated the performance of this device by testing plantar flexor function in six healthy adults on both a commercial isokinetic dynamometer and this novel device at three velocities/damper settings and at three different effort levels. During maximal effort contraction, measurements of peak moment and velocity at peak moment of the novel device and the commercial device were strongly correlated along the predicted quadratic line (R2> 0.708,p≤ 0.008). The setting of the damper prescribed the relationship between peak moment and velocity at peak moment across all subjects and effort levels (R2> 0.91,p< 0.001). The novel device was significantly smaller (0.75 m2footprint), lighter (30 kg), and lower cost (~$2,200 US) than commercial devices compared to commercially-available isokinetic dynamometers (5.95 m2footprint, 450 kg, and ~$40,000 US respectively).
Stick Stippling for Joint 3D Visualization of Diffusion MRI Fiber Orientations and Density
Authors: Cabeen Ryan P. , Laidlaw David H. , Toga Arthur W.
Published: June 2020

This paper investigates a stick stippling approach for glyph-based visualization of complex neural fiber architecture derived from diffusion magnetic resonance imaging. The presence of subvoxel crossing fibers in the brain has prompted the development of advanced modeling techniques; however, there remains a need for improved visualization techniques to more clearly convey their rich structure. While tractography can illustrate large scale anatomy, visualization of diffusion models can provide a more complete picture of local anatomy without the known limitations of tracking. We identify challenges and evaluate techniques for visualizing multi-fiber models and identified techniques that improve on existing methods. We conducted experiments to compare these representations and evaluated them within vivodiffusion MR datasets that vary in voxel resolution and anisotropy. We found that stick rendering as 3D tubes increased legibility of fiber orientation and that encoding fiber density by tube radius reduced clutter and reduced dependence on viewing orientation. Furthermore, we identified techniques to reduce the negative perceptual effects of voxel gridding through a jittering and re-sampling approach to produce a stippling effect. Looking forward, this approach provides a new way to explore diffusion MRI datasets that may aid in the visual analysis of white matter fiber architecture and microstructure. Our software implementation is available in the Quantitative Imaging Toolkit (QIT).
Papiliotrema maritimif.a. sp. nov., a new tremellaceous yeast species associated to macrophytes in a Marshland of South Brazil
Authors: Ramírez-Castrillón Mauricio , Gomes Fernanda Fraga , de Souza Andrea Formoso , Leite Belize Rodrigues , Pagani Danielle Machado , Valente Patricia
Published: June 2020

One new yeast species,Papiliotrema maritimisp. nov., is being proposed to be suitable into the Rhynchogastremataceae family, belonging to the Tremellales clade. This new species is related to six others from thePapiliotremagenus:P. taeanensis, P. siamense, P. perniciosus, P. nemorosus, P. bandonii, P. japonicaandP. fuscus. The novel species is proposed based on the phylogenetic species concept through analysis of the D1/D2 region, part of the large subunit (LSU) rRNA gene and the internal transcribed spacer (ITS) region. A total of 11 strains ofPapiliotrema maritimisp. nov. were obtained from macrophytes leaves collected in south Brazil.Papiliotrema maritimisp. nov. differs by 12, 15, 25, 25, 25 and 29 substitutions in the D1/D2 domain from the relatedspecies P. fuscus, P. japonica, P. siamense, P. nemorosus, P. bandonii, and P. perniciosus, respectively. Concerning the ITS region, there are 11 substitutions and 52 or more substitutions when compared toP. teanensisand its closest relatives. The type strain ofPapiliotrema maritimisp. nov. is UFMG-CM-Y6048. The MycoBank number forPapiliotrema maritimisp. nov. is MB 835603.
Synthetic Turing patterns in engineered microbial consortia
Authors: Duran-Nebreda Salva , Pla Jordi , Vidiella Blai , Piñero Jordi , Conde Nuria , Solé Ricard
Published: June 2020

Multicellular entities are characterized by exquisite spatial patterns, intimately related to the functions they perform. Oftentimes these patterns emerge as periodic structures with a well-defined characteristic scale. A candidate mechanism to explain their origins was early introduced by Alan Turing through the interaction and diffusion of two so calledmorphogens. Unfortunately, most available evidence for Turing patterns in biology is usually obscured by the tangled nature of regulatory phenomena, making difficult to validate Turing’s proposal in developmental processes. Here we follow a different approach, by designing synthetic genetic circuits in engineeredE. colistrains that implement the essential activator-inhibitor motif (AIM) using a two-cell consortium. The two diffusible compartments are one cell type (activator, small-diffusion component) and a small signal molecule (a homoserine lactone, acting as the fast-diffusing inhibitor). Using both experimental results, we show that the AIM is capable of generating diffusion-induced instabilities leading to regular spatial patterns. The artificial construction taken here can help validate developmental theories and identify universal properties underpinning biological pattern formation. The implications of the work for the area of synthetic developmental biology are outlined.
Chemical Systems Biology Reveals Mechanisms of Glucocorticoid Receptor Signaling
Authors: Bruno Nelson E. , Nwachukwu Jerome C. , Srinivasan Sathish , Nettles Charles C. , Izard Tina , Jin Zhuang , Boregowda Siddaraju V. , Phinney Donald G. , Elemento Olivier , Liu Xu , Ortlund Eric A. , Houtman René , Stavreva Diana A. , Hager Gordon L. , Kamenecka Theodore M. , Kojetin Douglas J. , Nettles Kendall W.
Published: June 2020

Glucocorticoids display remarkable anti-inflammatory activity, but their use is limited by on-target adverse effects including insulin resistance and skeletal muscle atrophy. We used a chemical systems biology approach, Ligand Class Analysis (LCA), to examine ligands designed to modulate glucocorticoid receptor activity through distinct structural mechanisms. These ligands displayed diverse activity profiles, providing the variance required to identify target genes and coregulator interactions that were highly predictive of their effects on myocyte glucose disposal and protein balance. Their anti-inflammatory effects were linked to glucose disposal but not muscle atrophy. This approach also predicted selective modulationin vivo, identifying compounds that were muscle sparing or anabolic for protein balance and mitochondrial potential. LCA defined the mechanistic links between the ligand-receptor interface and ligand-driven physiological outcomes, a general approach that can be applied to any ligand-regulated allosteric signaling system.
Surprising amount of stasis in repetitive genome content across the Brassicales
Authors: Beric Aleksandra , Mabry Makenzie E. , Harkess Alex E. , Schranz M. Eric , Conant Gavin C. , Edger Patrick P. , Meyers Blake C. , Pires J. Chris
Published: June 2020

Genome size of plants has long piqued the interest of researchers due to the vast differences among organisms. However, the mechanisms that drive size differences have yet to be fully understood. Two important contributing factors to genome size are expansions of repetitive elements, such as transposable elements (TEs), and whole-genome duplications (WGD). Although studies have found correlations between genome size and both TE abundance and polyploidy, these studies typically test for these patterns within a genus or species. The plant order Brassicales provides an excellent system to test if genome size evolution patterns are consistent across larger time scales, as there are numerous WGDs. This order is also home to one of the smallest plant genomes,Arabidopsis thaliana- chosen as the model plant system for this reason - as well as to species with very large genomes. With new methods that allow for TE characterization from low-coverage genome shotgun data and 71 taxa across the Brassicales, we find no correlation between genome size and TE content, and more surprisingly we identify no significant changes to TE landscape following WGD.
Morphogenesis of the islets of Langerhans is guided by extra-endocrine Slit2/3 signals
Authors: Gilbert Jennifer M. , Adams Melissa T. , Sharon Nadav , Jayaraaman Hariharan , Blum Barak
Published: June 2020

The spatial architecture of the islets of Langerhans is vitally important for their correct function, and alterations in islet morphogenesis often result in diabetes mellitus. We have previously reported that Roundabout (Robo) receptors are required for proper islet morphogenesis. As part of the Slit-Robo signaling pathway, Robo receptors work in conjunction with Slit ligands to mediate axon guidance, cell migration, and cell positioning in development. However, the role of Slit ligands in islet morphogenesis has not yet been determined. Here we report that Slit ligands are expressed in overlapping and distinct patterns in both endocrine and non-endocrine tissues in late pancreas development. We show that function of either Slit2 or Slit3, which are predominantly expressed in the pancreatic mesenchyme, is required and sufficient for islet morphogenesis, while Slit1, which is predominantly expressed in the β cells, is dispensable for islet morphogenesis. We further show that Slit functions as a repellent signal to β cells. These data suggest that clustering of endocrine cells during islet morphogenesis is guided, at least in part, by repelling Slit2/3 signals from the pancreatic mesenchyme.
Cellular debris, not mucilage polysaccharides, dominate extracts ofPlantago ovataandPlantago lanceolatacalli grownin vitro
Authors: Cowley James M. , Herliana Lina , Betts Natalie S. , Burton Rachel A.
Published: June 2020

Mucilage is a hydrophilic mixture of polysaccharides produced by seeds of many species, and used in research, industrial processes and as human health supplements. As such, demand often outweighs supply. In recent years, several researchers have reported that mucilage can be produced efficiently fromin vitro-cultured calli as a direct ‘plant-less’ alternative to seed mucilage; however, this mucilage has not been rigorously characterised. Here we replicate previously published culturing and extraction procedures and couple them with compositional analysis to determine whether the mucilage produced fromPlantago ovataandP. lanceolatacalli are similar to seed mucilage. Our monosaccharide profiling and microscopy show that, while calli derived from either seedling hypocotyls or roots yield more material than seeds using the same extraction techniques, the majority of extract mass is cellular debris. Debris polysaccharide composition was significantly different to seed mucilage from both species. Plant tissue culture as an alternative source of high yields of useful mucilage polysaccharides, at least by these and similar methods, is likely to not be possible.
GlypNirO: An automated workflow for quantitativeN- andO-linked glycoproteomic data analysis
Authors: Phung Toan K. , Pegg Cassandra L. , Schulz Benjamin L.
Published: June 2020

Mass spectrometry glycoproteomics is rapidly maturing, allowing unprecedented insights into the diversity and functions of protein glycosylation. However, quantitative glycoproteomics remains challenging. We developed GlypNirO, an automated software pipeline which integrates the complementary outputs of Byonic and Proteome Discoverer to allow high-throughput automated quantitative glycoproteomic data analysis. The output of GlypNirO is clearly structured, allowing manual interrogation, and is also appropriate for input into diverse statistical workflows. We used GlypNirO to analyse a published plasma glycoproteome dataset and identified changes in site-specificN- andO-glycosylation occupancy and structure associated with hepatocellular carcinoma as putative biomarkers of disease.
Integrated analysis of glycan and RNA in single cells
Authors: Minoshima Fumi , Ozaki Haruka , Odaka Haruki , Tateno Hiroaki
Published: June 2020

Single-cell sequencing has emerged as an indispensable technology to dissect cellular heterogeneity but never been applied to the simultaneous analysis of glycan and RNA. Using oligonucleotide-labeled lectins, we first established lectin-based glycan profiling of single cells by sequencing (scGlycan-seq). We then combined the scGlycan-seq with single-cell transcriptome profiling (scRNA-seq) for joint analysis of glycan and RNA in single cells (scGR-seq). Using scGR-seq, we analyzed the two modalities in human induced pluripotent stem cells (hiPSCs) before and after differentiation into neural progenitor cells at the single cell resolution. The combination of RNA and glycan separated the two cell types clearer than either one of them. Furthermore, integrative analysis of glycan and RNA modalities in single cells found known and novel lectins that were specific to hiPSCs and coordinated with neural differentiation. Taken together, we demonstrate that scGR-seq can reveal the cellular heterogeneity and biological roles of glycans across multicellular systems.
The Rab11 effectors Fip5 and Fip1 regulate zebrafish intestinal development
Authors: Jewett Cayla E. , Appel Bruce H. , Prekeris Rytis
Published: June 2020

The Rab11 apical recycling endosome pathway is a well-established regulator of polarity and lumen formation; however, Rab11-vesicular trafficking also directs a diverse array of other cellular processes, raising the question of how Rab11 vesicles achieve specificity in space, time, and content of cargo delivery. In part, this specificity is achieved through effector proteins, yet the role of Rab11 effector proteinsin vivoremains vague. Here, we use CRISPR/Cas9 gene editing to study the role of the Rab11 effector Fip5 during zebrafish intestinal development. Zebrafish contain two paralogous genes,fip5aandfip5b, that are orthologs of humanFIP5. We find thatfip5aandfip5bmutant fish show phenotypes characteristic of microvillus inclusion disease, including microvilli defects, inclusion bodies, and lysosomal accumulation. Single and double mutant analysis suggest thatfip5aandfip5bfunction in parallel and regulate apical trafficking pathways required for assembly of keratin at the terminal web. Remarkably, in some genetic backgrounds, the absence of Fip5 triggers protein upregulation of a closely related family member, Fip1. This compensation mechanism occurs both during zebrafish intestinal development and in tissue culture models of lumenogenesis. In conclusion, our data implicate the Rab11 effectors Fip5 and Fip1 in a trafficking pathway required for apical microvilli formation.
A multiple ion-uptake phenotyping platform reveals shared mechanisms that affect nutrient uptake by maize roots
Authors: Griffiths Marcus , Roy Sonali , Guo Haichao , Seethepalli Anand , Huhman David , Ge Yaxin , Sharp Robert E. , Fritschi Felix B. , York Larry M.
Published: June 2020

Nutrient uptake is critical for crop growth and determined by root foraging in soil. Growth and branching of roots lead to effective root placement to acquire nutrients, but relatively less is known about absorption of nutrients at the root surface from the soil solution. This knowledge gap could be alleviated by understanding sources of genetic variation for short-term nutrient uptake on a root length basis. A new modular platform for high-throughput phenotyping of multiple ion uptake kinetics was designed to determine nutrient uptake rates inZea mays. Using this system, uptake rates were characterized for the crop macronutrients nitrate, ammonium, potassium, phosphate and sulfate among the Nested Association Mapping (NAM) population founder lines. The data revealed that substantial genetic variation exists for multiple ion uptake rates in maize. Interestingly, specific nutrient uptake rates (nutrient uptake rate per length of root) were found to be both heritable and distinct from total uptake and plant size. The specific uptake rates of each nutrient were positively correlated with one another and with specific root respiration (root respiration rate per length of root), indicating that uptake is governed by shared mechanisms. We selected maize lines with high and low specific uptake rates and performed an RNA-seq analysis, which identified key regulatory components involved in nutrient uptake. The high-throughput multiple ion uptake kinetics pipeline will help further our understanding of nutrient uptake, parameterize holistic plant models, and identify breeding targets for crops with more efficient nutrient acquisition.

Significance Statement

Nutrient uptake is among the most limiting factors for plant growth and yet has not been used as a selection criterion in breeding. This is partly due to the lack of high-throughput phenotyping methods for measuring nutrient uptake. Here we describe a novel high-throughput phenotyping pipeline for quantification of multiple ion uptake rates. Using this new phenotyping system, our results demonstrate that specific ion uptake performance by maize plants is positively correlated among the macronutrients nitrogen, phosphorus, potassium and sulfur, and that substantial variation exists within a genetically diverse population. The findings reveal components of regulatory pathways possibly related with enhanced uptake, and confirm that nutrient uptake itself is a potential target for breeding of nutrient-efficient crops.
Transforming the Language of Life: Transformer Neural Networks for Protein Prediction Tasks
Authors: Nambiar Ananthan , Liu Simon , Hopkins Mark , Heflin Maeve , Maslov Sergei , Ritz Anna
Published: June 2020

Abstract

The scientific community is rapidly generating protein sequence information, but only a fraction of these proteins can be experimentally characterized. While promising deep learning approaches for protein prediction tasks have emerged, they have computational limitations or are designed to solve a specific task. We present a Transformer neural network that pre-trains task-agnostic sequence representations. This model is fine-tuned to solve two different protein prediction tasks: protein family classification and protein interaction prediction. Our method is comparable to existing state-of-the art approaches for protein family classification, while being much more general than other architectures. Further, our method outperforms all other approaches for protein interaction prediction. These results offer a promising framework for fine-tuning the pre-trained sequence representations for other protein prediction tasks.