### Recent Submissions

• #### RNA-Sequencing And Mass-Spectrometry Proteomic Time-Series Analysis of T-Cell Differentiation Identified Multiple Splice Variants Models That Predicted Validated Protein Biomarkers In Inflammatory Diseases

(Research Square Platform LLC, 2021-09-17) [Preprint]
Background Profiling of mRNA expression is an important method to identify biomarkers but complicated by limited correlations between mRNA expression and protein abundance. We hypothesized that these correlations could be improved by mathematical models based on measuring splice variants and time delay in protein translation. Methods We characterized time-series of primary human naïve CD4+ T cells during early T-helper type 1 differentiation with RNA-sequencing and mass-spectrometry proteomics. We then performed computational time-series analysis in this system and in two other key human and murine immune cell types. Linear mathematical mixed time-delayed splice variant models were used to predict protein abundances, and the models were validated using out-of-sample predictions. Lastly, we re-analysed RNA-Seq datasets to evaluate biomarker discovery in five T-cell associated diseases, further validating the findings for multiple sclerosis (MS) and asthma.Results The new models significantly out-performing models not including the usage of multiple splice variants and time-delays, as shown in cross-validation tests. Our mathematical models provided more differentially expressed proteins between patients and controls in all five diseases. Moreover, analysis of these proteins in asthma and MS supported their relevance. One marker, sCD27, was clinically validated in MS using two independent cohorts, for treatment response and prognosis.Conclusion Our splice variant and time-delay models substantially improved the prediction of protein abundance from mRNA data in three immune cell-types. The models provided valuable biomarker candidates, which were validated in clinical studies of MS and asthma. We propose that our strategy is generally applicable for biomarker discovery.
• #### Cancer-associated mutations in the p85α N-terminal SH2 domain activate a spectrum of receptor tyrosine kinases.

(Proceedings of the National Academy of Sciences of the United States of America, 2021-09-11) [Article]
The phosphoinositide 3-kinase regulatory subunit p85α is a key regulator of kinase signaling and is frequently mutated in cancers. In the present study, we showed that in addition to weakening the inhibitory interaction between p85α and p110α, a group of driver mutations in the p85α N-terminal SH2 domain activated EGFR, HER2, HER3, c-Met, and IGF-1R in a p110α-independent manner. Cancer cells expressing these mutations exhibited the activation of p110α and the AKT pathway. Interestingly, the activation of EGFR, HER2, and c-Met was attributed to the ability of driver mutations to inhibit HER3 ubiquitination and degradation. The resulting increase in HER3 protein levels promoted its heterodimerization with EGFR, HER2, and c-Met, as well as the allosteric activation of these dimerized partners; however, HER3 silencing abolished this transactivation. Accordingly, inhibitors of either AKT or the HER family reduced the oncogenicity of driver mutations. The combination of these inhibitors resulted in marked synergy. Taken together, our findings provide mechanistic insights and suggest therapeutic strategies targeting a class of recurrent p85α mutations.
• #### Aridity modulates belowground bacterial community dynamics in olive tree

(Environmental Microbiology, Wiley, 2021-09-07) [Article]
Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlate with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.
• #### Generation of human blastocyst-like structures from pluripotent stem cells

(Cell Discovery, Springer Science and Business Media LLC, 2021-09-07) [Article]
Human blastocysts are comprised of the first three cell lineages of the embryo: trophectoderm, epiblast and primitive endoderm, all of which are essential for early development and organ formation. However, due to ethical concerns and restricted access to human blastocysts, a comprehensive understanding of early human embryogenesis is still lacking. To bridge this knowledge gap, a reliable model system that recapitulates early stages of human embryogenesis is needed. Here we developed a three-dimensional (3D), two-step induction protocol for generating blastocyst-like structures (EPS-blastoids) from human extended pluripotent stem (EPS) cells. Morphological and single-cell transcriptomic analyses revealed that EPS-blastoids contain key cell lineages and are transcriptionally similar to human blastocysts. Furthermore, EPS-blastoids are similar with human embryos that were cultured for 8 or 10 days in vitro, in terms of embryonic structures, cell lineages and transcriptomic profiles. In conclusion, we developed a scalable system to mimic human blastocyst development, which can potentially facilitate the study of early implantation failure that induced by developmental defects at early stage.
• #### The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptions to host-switching

(NCBI, 2021-09-05) [Bioproject, Dataset]
Plasmodium simium, a parasite of various species of Platyrrhini monkeys whose range is restricted to the Atlantic Forest of Brazil, is genetically and morphologically similar to P. vivax. Based on this similarity, it appears likely that P. simium originated as a parasite of monkeys in Brazil following a host switch from humans carrying P. vivax. The 2015 outbreak of P. simium in the local human population raised questions about the degree of divergence that has occurred between P. vivax and P. simium, and whether adaptation to monkeys has led to the evolution of a parasite with clinical relevance to human health that differs from that of P. vivax. The degree and nature of adaptation to a non-human primate host and a sylvatic transmission cycle that has occurred in P. simium following its anthroponotic origin is of relevance to the understanding of how malaria parasites adapt to new hosts. It is also of interest to determine whether the current, human-infecting P. simium parasites have recently undergone changes at the genomic level that have allowed them to infect people in this region, as it has previously been suggested that P. simium has historically lacked the ability to infect man.
• #### Sustainable and Eco-Friendly Coral Restoration through 3D Printing and Fabrication

(ACS Sustainable Chemistry & Engineering, American Chemical Society (ACS), 2021-09-02) [Article]
Coral reef degradation is a rising problem, driven by marine heatwaves, the spread of coral diseases, and human impact by overfishing and pollution. Our capacity to restore coral reefs lags behind in terms of scale, effectiveness, and cost-efficiency. While common restoration efforts rely on the formation of carbonate skeletons on structural frames for supported coral growth, this technique is a rate-limiting step in the growth of scleractinian corals. Reverse engineering and additive manufacturing technologies offer an innovative shift in approach from the use of concrete blocks and metal frames to sophisticated efforts that use scanned geometries of harvested corals to fabricate artificial coral skeletons for installation in coral gardens and reefs. Herein, we present an eco-friendly and sustainable approach for coral fabrication by merging three-dimensional (3D) scanning, 3D printing, and molding techniques. Our method, 3D CoraPrint, exploits the 3D printing technology to fabricate artificial natural-based coral skeletons, expediting the growth rate of live coral fragments and quickening the reef transplantation process while minimizing nursery costs. It allows for flexibility, customization, and fast return time with an enhanced level of accuracy, thus establishing an environmentally friendly, scalable model for coral fabrication to boost restorative efforts around the globe.
• #### Machine Learning and Deep Learning Methods that use Omics Data for Metastasis Prediction

(Computational and Structural Biotechnology Journal, Elsevier BV, 2021-09) [Article]
Knowing metastasis is the primary cause of cancer-related deaths, incentivized research directed towards unraveling the complex cellular processes that drive the metastasis. Advancement in technology and specifically the advent of high-throughput sequencing provides knowledge of such processes. This knowledge led to the development of therapeutic and clinical applications, and is now being used to predict the onset of metastasis to improve diagnostics and disease therapies. In this regard, predicting metastasis onset has also been explored using artificial intelligence approaches that are machine learning, and more recently, deep learning-based. This review summarizes the different machine learning and deep learning-based metastasis prediction methods developed to date. We also detail the different types of molecular data used to build the models and the critical signatures derived from the different methods. We further highlight the challenges associated with using machine learning and deep learning methods, and provide suggestions to improve the predictive performance of such methods.
• #### Reversible Electrochemical Charging of n-Type Conjugated Polymer Electrodes in Aqueous Electrolytes

(Journal of the American Chemical Society, American Chemical Society (ACS), 2021-09-01) [Article]
Conjugated polymers achieve redox activity in electrochemical devices by combining redox-active, electronically conducting backbones with ion-transporting side chains that can be tuned for different electrolytes. In aqueous electrolytes, redox activity can be accomplished by attaching hydrophilic side chains to the polymer backbone, which enables ionic transport and allows volumetric charging of polymer electrodes. While this approach has been beneficial for achieving fast electrochemical charging in aqueous solutions, little is known about the relationship between water uptake by the polymers during electrochemical charging and the stability and redox potentials of the electrodes, particularly for electron-transporting conjugated polymers. We find that excessive water uptake during the electrochemical charging of polymer electrodes harms the reversibility of electrochemical processes and results in irreversible swelling of the polymer. We show that small changes of the side chain composition can significantly increase the reversibility of the redox behavior of the materials in aqueous electrolytes, improving the capacity of the polymer by more than one order of magnitude. Finally, we show that tuning the local environment of the redox-active polymer by attaching hydrophilic side chains can help to reach high fractions of the theoretical capacity for single-phase electrodes in aqueous electrolytes. Our work shows the importance of chemical design strategies for achieving high electrochemical stability for conjugated polymers in aqueous electrolytes.
• #### Functional Crypto-Adenylate Cyclases Operate in Complex Plant Proteins.

(Frontiers in plant science, Frontiers Media SA, 2021-08-30) [Article]
Adenylyl cyclases (ACs) and their catalytic product cAMP are regulatory components of many plant responses. Here, we show that an amino acid search motif based on annotated adenylate cyclases (ACs) identifies 12 unique $\textit{Arabidopsis thaliana}$ candidate ACs, four of which have a role in the biosynthesis of the stress hormone abscisic acid (ABA). One of these, the 9-cis-epoxycarotenoid dioxygenase (NCED3 and At3g14440), was identified by sequence and structural analysis as a putative AC and then tested experimentally with two different methods. Given that the $\textit{in vitro}$ activity is low (fmoles cAMP pmol$^{-1}$ protein min$^{-1}$), but highly reproducible, we term the enzyme a crypto-AC. Our results are consistent with a role for ACs with low activities in multi-domain moonlighting proteins that have at least one other distinct molecular function, such as catalysis or ion channel activation. We propose that crypto-ACs be examined from the perspective that considers their low activities as an innate feature of regulatory ACs embedded within multi-domain moonlighting proteins. It is therefore conceivable that crypto-ACs form integral components of complex plant proteins participating in intra-molecular regulatory mechanisms, and in this case, potentially linking cAMP to ABA synthesis.
• #### Decoding Electrophysiological Signals with Organic Electrochemical Transistors

(Macromolecular Bioscience, Wiley, 2021-08-30) [Article]
The organic electrochemical transistor (OECT) has unique characteristics that distinguish it from other transistors and make it a promising electronic transducer of biological events. High transconductance, flexibility, and biocompatibility render OECTs ideal for detecting electrophysiological signals. Device properties such as transconductance, response time, and noise level should, however, be optimized to adapt to the needs of various application environments including in vitro cell culture, human skin, and inside of a living system. This review includes an overview of the origin of electrophysiological signals, the working principles of OECTs, and methods for performance optimization. While covering recent research examples of the use of OECTs in electrophysiology, a perspective is provided for next-generation bioelectric sensors and amplifiers for electrophysiology applications.
• #### Functional Crypto-Adenylate Cyclases Operate in Complex Plant Proteins.

(Frontiers in plant science, Frontiers Media SA, 2021-08-30) [Article]
Adenylyl cyclases (ACs) and their catalytic product cAMP are regulatory components of many plant responses. Here, we show that an amino acid search motif based on annotated adenylate cyclases (ACs) identifies 12 unique $\textit{Arabidopsis thaliana}$ candidate ACs, four of which have a role in the biosynthesis of the stress hormone abscisic acid (ABA). One of these, the 9-cis-epoxycarotenoid dioxygenase (NCED3 and At3g14440), was identified by sequence and structural analysis as a putative AC and then tested experimentally with two different methods. Given that the $\textit{in vitro}$ activity is low (fmoles cAMP pmol$^{-1}$ protein min$^{-1}$), but highly reproducible, we term the enzyme a crypto-AC. Our results are consistent with a role for ACs with low activities in multi-domain moonlighting proteins that have at least one other distinct molecular function, such as catalysis or ion channel activation. We propose that crypto-ACs be examined from the perspective that considers their low activities as an innate feature of regulatory ACs embedded within multi-domain moonlighting proteins. It is therefore conceivable that crypto-ACs form integral components of complex plant proteins participating in intra-molecular regulatory mechanisms, and in this case, potentially linking cAMP to ABA synthesis.
• #### Seasonal and annual changes in the microbial communities of Ofunato Bay, Japan, based on metagenomics.

(Scientific reports, 2021-08-27) [Article]
Five years of datasets from 2015 to 2019 of whole genome shotgun sequencing for cells trapped on 0.2-µm filters of seawater collected monthly from Ofunato Bay, an enclosed bay in Japan, were analysed, which included the 2015 data that we had reported previously. Nucleotide sequences were determined for extracted DNA from three locations for both the upper (1 m) and deeper (8 or 10 m) depths. The biotic communities analysed at the domain level comprised bacteria, eukaryotes, archaea and viruses. The relative abundance of bacteria was over 60% in most months for the five years. The relative abundance of the SAR86 cluster was highest in the bacterial group, followed by Candidatus Pelagibacter and Planktomarina. The relative abundance of Ca. Pelagibacter showed no relationship with environmental factors, and those of SAR86 and Planktomarina showed positive correlations with salinity and dissolved oxygen, respectively. The bacterial community diversity showed seasonal changes, with high diversity around September and low diversity around January for all five years. Nonmetric multidimensional scaling analysis also revealed that the bacterial communities in the bay were grouped in a season-dependent manner and linked with environmental variables such as seawater temperature, salinity and dissolved oxygen.
• #### l-Lactate: Food for Thoughts, Memory and Behavior.

(Metabolites, MDPI AG, 2021-08-26) [Article]
More and more evidence shows how brain energy metabolism is the linkage between physiological and morphological synaptic plasticity and memory consolidation. Different types of memory are associated with differential inputs, each with specific inputs that are upstream diverse molecular cascades depending on the receptor activity. No matter how heterogeneous the response is, energy availability represents the lowest common denominator since all these mechanisms are energy consuming and the brain networks adapt their performance accordingly. Astrocytes exert a primary role in this sense by acting as an energy buffer; glycogen granules, a mechanism to store glucose, are redistributed at glance and conveyed to neurons via the Astrocyte-Neuron Lactate Shuttle (ANLS). Here, we review how different types of memory relate to the mechanisms of energy delivery in the brain.
• #### Estimations of Integrated Information Based on Algorithmic Complexity and Dynamic Querying

(World Scientific, 2021-08-22) [Book Chapter]
Integrated information has been introduced as a metric to quantify the amount of information generated by a system beyond the information generated by its individual elements. While the metrics associated with the Greek letter ϕ require the calculation of the interaction of an exponential number of sub-divisions of the system, most of these numerical approaches related to the metric are based on the basics of classical information theory and perturbation analysis. Here we introduce and sketch alternative approaches to connect algorithmic complexity and integrated information based on the concept of algorithmic perturbation rooted in algorithmic information dynamics and its concept of programmability. We hypothesize that if an object is algorithmic random or algorithmic simple, algorithmic random perturbations will have little to no effect to the internal capabilities of a system to produce integrated information but when an object is more integrated the object will also display elements able to perturb the object and increase or decrease its algorithmic randomness. We sketch some of these ideas related to an object integrated information value and its algorithmic information content. We propose that such an algorithmic perturbation test quantifying compression sensitivity may provide a system with a means to extract explanations–causal accounts–of its own behavior hence making IIT and associated measure ϕ more explainable and interpretable. Our technique may reduce the number of calculations to arrive at some estimations with algorithmic perturbation guiding a more efficient search. Our work sets the stage for a systematic exploration and further investigation of the connections between algorithmic complexity and integrated information at the level of both theory and practice.
• #### Integration of Organic Electrochemical Transistors with Implantable Probes

(Advanced Materials Technologies, Wiley, 2021-08-19) [Article]
Organic electrochemical transistors (OECTs) are widely used as amplifying transducers of biological signals due to their high transconductance and biocompatibility. For implantable applications that penetrate into tissue, OECTs need to be integrated onto narrow probes. The scarcity of real estate necessitates the use of small local gate electrodes and narrow interconnects. This work shows that both of these factors lead to a decrease in the maximum transconductance and an increase in gate voltage required to attain this maximum. This work further shows that coating the gate electrode with a thick conducting polymer improves performance. These findings help guide the development of efficient OECTs on implantable probes.
• #### Complexation of uranyl (UO2)2+ with bidentate ligands: XRD, spectroscopic, computational, and biological studies.

(PloS one, Public Library of Science (PLoS), 2021-08-19) [Article]
Three new uranyl complexes [(UO2)(OAc)2(CMZ)], [(UO2)(OAc)2(MP)] and [(UO2)(OAc)2(SCZ)] were synthesized and characterized by elemental analysis, FT-IR, UV-Vis spectroscopy, powder XRD analysis, and molar conductivity. The IR analysis confirmed binding to the metal ion by the sulfur and ethoxy oxygen atoms in the carbimazole (CMZ) ligand, while in the 6-mercaptopurine (MP) ligand, the sulfur and the N7 nitrogen atom of a purine coordinated binding to the metal ion. The third ligand showed a 1:1 molar ratio and bound via sulfonamide oxygen and the nitrogen of the pyrimidine ring. Analysis of the synthesized complexes also showed that acetate groups had monodentate binding to the (UO22+). Density Functional Theory (DFT) calculations at the B3LYP level showed similar structures to the experimental results. Theoretical quantum parameters predicted the reactivity of the complexes in the order, [(UO2)(OAc)2(SCZ)] > [(UO2)(OAc)2(MP)]> [(UO2)(OAc)2(CMZ)]. DNA binding studies revealed that [(UO2)(OAc)2(SCZ)] and [(UO2)(OAc)2(CMZ)] have the highest binding constant (Kb) among the uranyl complexes. Additionally, strong binding of the MP and CMZ metal complexes to human serum albumin (HSA) were observed by both absorbance and fluorescence approaches. The antibacterial activity of the complexes was also evaluated against four bacterial strains: two gram-negative; Escherichia coli and Klebsiella pneumonia, and two gram-positive; Staphylococcus aureus and Streptococcus mutans. [(UO2)(OAc)2(MP)] had the greatest antibacterial activity against Klebsiella pneumonia, the gram-positive bacteria, with even higher activity than the standard antibiotic. In vitro cytotoxicity tests were also performed against three human cancer lines, and revealed the most cytotoxic complexes to be [(UO2)(OAc)2(SCZ)], which showed moderate activity against a colon cancer cell line. Thus, uranyl addition enhances the antibacterial and anticancer properties of the free ligands.
• #### Mesomorphic Behaviour and DFT Insight of Arylidene Schiff Base Liquid Crystals and Their Pyridine Impact Investigation

(Crystals, MDPI AG, 2021-08-18) [Article]
A new series of Schiff base liquid crystal have been prepared and studied. Schiff bases of p-alkyl aniline derivatives and 4-phenyl pyridine-4′-carbaldehyde were prepared. The terminal alkyl groups substituting aniline are of varied chain length, namely C8, C12 and C14. The structures of the compounds were elucidated by 1H NMR and 13C NMR. The mesomorphic thermal and optical characteristics of the samples were determined via differential thermal analysis (DSC) and polarization optical microscopy (POM). All compounds exhibit enantiotropic dimorphic mesophase behaviour, referred to as smectic X1 (SmX1) and smectic X2 (Sm A). Experimental results obtained for the mesophases were correlated with density functional theory (DFT) theoretical calculations. The results of the new series are further compared to two series of compounds bearing pyridine (two ring Schiff bases) and biphenyl, respectively, in their mesogens. The series of compounds of one pyridine ring are generally not mesomorphic. The results indicate that the alkyl chain length has a strong impact on the mesomorphic characteristics and thermal stabilities of the different mesophases. As a trend, the temperature ranges of both of smectic mesophases of all compounds are higher in new compounds bearing the 4-phenyl pyridine moiety. In addition, the total mesophase range is generally higher in the new compounds when compared to their biphenyl analogues. Finally, theoretical DFT calculations were performed to illustrate the experimental finding of the mesomorphic behaviour in terms of the molecular geometry and aromaticity, π–π stacking and LOL-π.
• #### A prevalent neglect of environmental control in mammalian cell culture calls for best practices

(Nature Biomedical Engineering, Springer Science and Business Media LLC, 2021-08-13) [Article]
Human cell lines, first cultured in the 1950s1, are indispensable in biomedical research. Today, a wide range of cell types are available, and sophisticated advanced ‘omics’ and visualization techniques allow for the routine assessment of cell identity and cellular responses2. However, the culture methods have remained relatively unchanged. Major advances in culture systems were made over three decades ago3,4, yet the old standard approach of batch cell culture — the culture of cells either in suspension or as adherent monolayers of cells in standard media5,6,7 — remains the predominant method in biomedical research.
• #### Digital Reconstruction of the Neuro-Glia-Vascular Architecture.

(Cerebral cortex (New York, N.Y. : 1991), Oxford University Press (OUP), 2021-08-13) [Article]
Astrocytes connect the vasculature to neurons mediating the supply of nutrients and biochemicals. They are involved in a growing number of physiological and pathophysiological processes that result from biophysical, physiological, and molecular interactions in this neuro-glia-vascular ensemble (NGV). The lack of a detailed cytoarchitecture severely restricts the understanding of how they support brain function. To address this problem, we used data from multiple sources to create a data-driven digital reconstruction of the NGV at micrometer anatomical resolution. We reconstructed 0.2 mm3 of the rat somatosensory cortex with 16 000 morphologically detailed neurons, 2500 protoplasmic astrocytes, and its microvasculature. The consistency of the reconstruction with a wide array of experimental measurements allows novel predictions of the NGV organization, allowing the anatomical reconstruction of overlapping astrocytic microdomains and the quantification of endfeet connecting each astrocyte to the vasculature, as well as the extent to which they cover the latter. Structural analysis showed that astrocytes optimize their positions to provide uniform vascular coverage for trophic support and signaling. However, this optimal organization rapidly declines as their density increases. The NGV digital reconstruction is a resource that will enable a better understanding of the anatomical principles and geometric constraints, which govern how astrocytes support brain function.
• #### Molecular Basis for Environment Sensing by a Nucleoid-Structuring Bacterial Protein Filament

(The Journal of Physical Chemistry Letters, American Chemical Society (ACS), 2021-08-12) [Article]
The histone-like nucleoid structuring (H-NS) protein controls the expression of hundreds of genes in Gram-positive bacteria through its capability to coat and condense DNA. This mechanism requires the formation of superhelical H-NS protein filaments that are sensitive to temperature and salinity, allowing H-NS to act as an environment sensor. We use multiscale modeling and simulations to obtain detailed insights into the mechanism of H-NS filament's sensitivity to environmental changes. Through the simulations of the superhelical H-NS filament, we reveal how different environments induce heterogeneity of H-NS monomers. Further, we observe that transient self-association within the H-NS filament creates temperature-inducible strain and might mildly oppose DNA binding. We also probe different H-NS-DNA complex architectures and show that complexation enhances the stability of both DNA and H-NS superhelices. Overall, our results provide unprecedented molecular insights into the environmental sensing and DNA interactions of a prototypical nucleoid-structuring bacterial protein filament.