bluuebunny/crossref_metadata_2025 huggingface dataset:
Automatic Generation of Personalised Skeletal Models of the Lower Limb from Three-Dimensional Bone Geometries
Authors: Modenese Luca , Renault Jean-Baptiste
Published: June 2020

The generation of personalised and patient-specific musculoskeletal models is currently a cumbersome and time-consuming task that normally requires several processing hours and trained operators. We believe that this aspect discourages the use of computational models even when appropriate data are available and personalised biomechanical analysis would be beneficial. In this paper we present a computational tool that enables the fully automatic generation of skeletal models of the lower limb from three-dimensional bone geometries, normally obtained by segmentation of medical images. This tool was evaluated against four manually created lower limb models finding remarkable agreement in the computed joint parameters, well within human operator repeatability. The coordinate systems origins were identified with maximum differences between 0.5 mm (hip joint) and 5.9 mm (subtalar joint), while the joint axes presented discrepancies between 1° (knee joint) to 11° (subtalar joint). To prove the robustness of the methodology, the models were built from four datasets including both genders, anatomies ranging from juvenile to elderly and bone geometries reconstructed from high-quality computed tomography as well as lower-quality magnetic resonance imaging scans. The entire workflow, implemented in MATLAB scripting language, executed in seconds and required no operator intervention, creating lower extremity models ready to use for kinematic and kinetic analysis or as baselines for more advanced musculoskeletal modelling approaches, of which we provide some practical examples. We auspicate that this technical advancement, together with upcoming progress in medical image segmentation techniques, will promote the use of personalised models in larger-scale studies than those hitherto undertaken.
ReCodLiver0.9: Overcoming challenges in genome-scale metabolic reconstruction of a non-model species
Authors: Hanna Eileen Marie , Zhang Xiaokang , Eide Marta , Fallahi Shirin , Furmanek Tomasz , Yadetie Fekadu , Zielinski Daniel Craig , Goksøyr Anders , Jonassen Inge
Published: June 2020

The availability of genome sequences, annotations and knowledge of the biochemistry underlying metabolic transformations has led to the generation of metabolic network reconstructions for a wide range of organisms in bacteria, archaea, and eukaryotes. When modeled using mathematical representations, a reconstruction can simulate underlying genotype-phenotype relationships. Accordingly, genome-scale models (GEMs) can be used to predict the response of organisms to genetic and environmental variations. A bottom-up reconstruction procedure typically starts by generating a draft model from existing annotation data on a target organism. For model species, this part of the process can be straightforward, due to the abundant organism-specific biochemical data. However, the process becomes complicated for non-model less-annotated species. In this paper, we present a draft liver reconstruction, ReCodLiver0.9, of Atlantic cod (Gadus morhua), a non-model teleost fish, as a practicable guide for cases with comparably few resources. Although the reconstruction is considered a draft version, we show that it already has utility in elucidating metabolic response mechanisms to environmental toxicants by mapping gene expression data of exposure experiments to the resulting model.

Author summary

Genome-scale metabolic models (GEMs) are constructed based upon reconstructed networks that are carried out by an organism. The underlying biochemical knowledge in such networks can be transformed into mathematical models that could serve as a platform to answer biological questions. The availability of high-throughput biological data, including genomics, proteomics, and metabolomics data, supports the generation of such models for a large number of organisms. Nevertheless, challenges arise for non-model species which are typically less annotated. In this paper, we discuss these challenges and possible solutions in the context of generation of a draft liver reconstruction of Atlantic cod (Gadus morhua). We also show how experimental data, here gene expression data, can be mapped to the resulting model to understand the metabolic response of cod liver to environmental toxicants.
Anisotropic random walks reveal chemotaxis signaling output in run-reversing bacteria
Authors: Antani Jyot D. , Sumali Anita X. , Lele Tanmay P. , Lele Pushkar P.
Published: June 2020

The bias for a particular direction of rotation of the flagellar motor is a sensitive readout of chemotaxis signaling, which mediates bacterial migration towards favorable chemical environments. The rotational bias has not been characterized inHelicobacter pylori, which limits our understanding of the signaling dynamics. Here, we determined thatH. pyloriswim faster (slower) whenever their flagella rotate counterclockwise (clockwise) by analyzing their hydrodynamic interactions with bounding surfaces. The anisotropy in swimming speeds helped quantify the fraction of the time that the cells swam slower to report the first measurements of the bias. A stochastic model of run-reversals indicated that the anisotropy promotes faster spread compared to isotropic swimmers. The approach further revealed that the diffuse spread ofH. pyloriis likely limited at the physiological temperature due to increased reversal frequencies. Thus, anisotropic run-reversals make it feasible to study signal-response relations in the chemotaxis network in non-model bacterial species.

Impact Statement

Anisotropy in run and reversal swimming speeds promotes the spread ofH. pyloriand reveals temperature-dependent behavior of the flagellar switch.
13C Electron Nuclear Double Resonance Spectroscopy Shows Acetyl-CoA Synthase Binds Two Substrate CO in Multiple Binding Modes and Reveals the Importance of a CO-Binding ‘Alcove’
Authors: James Christopher D. , Wiley Seth , Ragsdale Stephen W. , Hoffman Brian M.
Published: June 2020

EPR and Electron Nuclear Double Resonance spectroscopies here characterize CO binding to the active-site A cluster of wild-type (WT) Acetyl-CoA Synthase (ACS) and two variants, F229W and F229A. The A-cluster binds CO to a proximal Ni (Nip) that bridges a [4Fe-4S] cluster and distal Nid. An alcove seen in the ACS crystal-structure near the A-cluster, defined by hydrophobic residues including F229, forms a cage surrounding a Xe mimic of CO and is suggested to ‘cradle’ this CO. Previously, we only knew WT ACS bound a single CO in the Ared-CO intermediate, here seen as forming Nip(I)-CO with CO on-axis of the dz2odd-electron orbital (g⊥>g‖∼2). The two-dimensional field-frequency pattern of 2K-35 GHz13C-ENDOR spectra collected across the Ared-CO EPR envelope now reveals a second CO bound in the dz2orbital’s equatorial plane. This WT A-cluster conformer dominates the nearly-conservative F229W variant, but13C-ENDOR reveals a minority “A” conformation with (g‖>g⊥∼2) characteristic of a ‘cloverleaf’ (eg. dx2-y2) odd-electron orbital, and with Nipbinding two, apparently ‘in-plane’ CO. Disruption of the alcove through introduction of the smaller alanine residue in the F229A variant diminishes conversion to Ni(I) ∼tenfold and introduces extensive cluster flexibility.13C-ENDOR shows the F229A cluster is mostly (60%) in the “A” conformation, but with ∼20% each of the WT conformer and an “O” state in which dz2Nip(I) (g⊥>g‖∼2) surprisingly lacks CO. This paper thus demonstrates the importance of an intact alcove in forming and stabilizing the Ni(I)-CO intermediate in the Wood-Ljungdahl pathway of anaerobic CO and CO2fixation.
Spatially explicit modelling of kelp-grazer interactions: a seascape approach for effective habitat enhancement using artificial reefs
Authors: Filippo Ferrario , Suskiewicz Thew , Johnson Ladd Erik
Published: June 2020

Artificial structures are sprawling along the coast affecting the aspect and the functioning of shallow coastal seascapes. For years, the ecology of artificial structures has been investigated mainly in contrast to natural coastal habitats. However, it is increasingly emerging that structuring processes, such as trophic interactions, can depend on properties of the surrounding landscape. Heterogeneity of coastal seafloor and habitats could thus play a major role in determining the variability of ecological outcomes on artificial structures.

Artificial reefs are being used in coastal areas in attempts to restore and enhance marine habitats and communities, including large brown seaweed (“kelp”), to offset habitat loss and mitigate coastal development impacts. The outcome of enhancement projects using artificial reefs have not always been either consistent or positive. Overlooking the effect of strong ecological interactions adds a high level of uncertainty and can undermine the success of these efforts.

In Eastern Canada, top-down control exerted by green sea urchins (Strongylocentrotus droebachiensis) can seriously compromise the success of artificial reefs for kelp enhancement. Importantly, urchin interactions with macroalgae are likely to be influenced by the bottom composition. A seascape approach could thus integrate behavior and habitat heterogeneity.

We investigated whether the local seascape could create zones of differential grazing risk for kelp outplanting kelp (Alaria esculenta) on artificial blocks on an heterogenous bottom. Adopting a spatially explicit framework, we determined how seascape affected the urchin use of the habitat and used this information to map the grazing risk throughout the area.

Kelp survival was a function of frequency of urchin presence throughout the study site. While urchins avoided sandy patches, bottom composition and algal cover modulated the within-patch urchin use of the habitat. This translated in the heterogeneity of grazing risk intensity.

Synthesis and applications. The presence of discrete seascape features locally increased the grazing risk for kelp by differentially affecting the urchin’s usage of the habitat, even within the same bottom patch. Incorporating this information when planning artificial reefs could minimize the detrimental grazing risk thus increasing the rate of success and ensuring lasting results.
Modeling the effect of COVID-19 disease on the cardiac function: a computational study
Authors: Regazzoni Francesco , Vergara Christian , Dede’ Luca , Zunino Paolo , Guglielmo Marco , Scrofani Roberto , Fusini Laura , Cogliati Chiara , Pontone Gianluca , Quarteroni Alfio
Published: June 2020

Background

The effect of COVID-19 on the cardiac function and on the vascular system increases the morbidity and mortality of infected subjects with cardiovascular diseases.

Objectives

To provide preliminary results on cardiac global outcomes (such as cardiac output, ventricular pressures) obtained by means of computational models in plausible scenarios characterized by COVID-19.

Methods

We considered a lumped parameters computational model of the cardiovascular system, which models, from the mechanical point of view, the systemic and pulmonary circulations, the four cardiac valves and the four heart chambers, through mathematical equations of the underlying physical processes. To study the effect of COVID-19, we varied the heart rate, the contractility and the pulmonary resistances in suitable ranges.

Results

Our computations on individuals with both otherwise normal and impaired cardiac functions revealed that COVID-19 worsen cardiac function, as shown by a decrease of some cardiac biomarkers values such as cardiac output and ejection fraction. In the case of existing impaired cardiac function, the presence of COVID-19 lead to values outside the normal ranges.

Conclusions

Computational models revealed to be an effective tool to study the effect of COVID-19 on the cardiovascular system. Such effect could be significant for patients with impaired cardiac function. This is especially useful to perform a sensitivity analysis of the hemodynamics for different conditions.

CONDENSED ABSTRACT

Emerging studies address how COVID-19 infection might impact the cardiovascular system. This relates particularly to the development of myocardial injury, acute coronary syndrome, myocarditis, arrhythmia, and heart failure. Prospective treatment approach is advised for these patients. By the assessment of conventional important biomarkers obtained with new sources as a 0-dimentional computational model, we propose a new study protocol as an effective method to evaluate short-term prognosis. The clinical protocol proposed will help to rapidly identify which patients require intensive monitoring, diagnostic strategy and most adequate therapy.
The crystal structure of the Ca2+-ATPase 1 fromListeria monocytogenesreveals a pump primed for dephosphorylation
Authors: Hansen Sara Basse , Dyla Mateusz , Neumann Caroline , Hoegh Quistgaard Esben Meldgaard , Andersen Jacob Lauwring , Kjaergaard Magnus , Nissen Poul
Published: June 2020

Many bacteria export intracellular calcium using active transporters homologous to the sarco/endoplasmic reticulum Ca2+-ATPase (SERCA). Here we present three crystal structures of Ca2+-ATPase 1 from Listeria monocytogenes (LMCA1). Structures with BeF3-mimicking a phosphoenzyme state reveal a closed state, which is intermediate between the outward-open E2P and the proton-occluded E2-P* conformations known for SERCA. It suggests that LMCA1 in the E2P state is pre-organized for dephosphorylation upon Ca2+release, consistent with the rapid dephosphorylation observed in single-molecule studies. An arginine side-chain occupies the position equivalent to calcium binding site I in SERCA, leaving a single Ca2+-binding site in LMCA1, corresponding to SERCA site II. Observing no putative transport pathways dedicated to protons, we infer a direct proton counter transport through the Ca2+exchange pathways. The LMCA1 structures provide insight into the evolutionary divergence and conserved features of this important class of ion transporters.
Diversity of mosquitoes (Diptera: Culicidae) collected in different types of larvitraps in an Amazon rural settlement
Authors: Feijó Almeida Jessica , Matos Belchior Heliana Christy , Ríos-Velásquez Claudia María , Costa Pessoa Felipe Arley
Published: June 2020

Anthropogenic environments provide favorable conditions for some species, which are especially suitable for mosquitoes that present eclecticism at the moment of choice for the site of oviposition. The present study, the diversity of mosquitoes in plastic container, bamboo internode, and tire placed in forest, the forest edge, and peridomicile environments in a rural settlement area was assessed. Eighteen sampling points were chosen, delimited by a buffer 200 m, placed in environments: forest, forest edge, and peridomicile. In each environment, larvitraps were installed, separated by a minimum distance of 7 m and 1 m from the ground. A total of 10,131 immature mosquitoes of 20 species were collected. The most abundant species wasCulex urichii(29.5%), followed byTrichoprosopom digitatum(27.1%), andCx. (Melanoconion) sp. (10,4%). There was a difference in the composition of immature mosquito populations between larvitraps (p<0.0005), and the plastic container hosted a greater diversity of species, whereas tires presented a greater abundance of individuals. The forest, forest edge, and peridomicile environments were also significantly different with regard to diversity of immature mosquito populations (p<0.0010). The forest edge was the environment with the greatest diversity of species, followed by the peridomicile and forest environments. In the forest and peridomicile, plastic container larvitraps had the greatest diversity, whereas the forest edge tire presented the largest number of individuals. Further, tire larvitraps collected the largest number of individuals in all environments. We identified 10 species associated with the bamboo internode and tire. We also observed the preference of species for artificial larvitraps, such as the plastic container and tire, even in wild environments. These artificial objects may represent a risk factor for the population living in this region, as all vector species found in the study were present in plastic containers and tires.
Correlation Coefficient Based Automatic Optic Disc Detection from Retinal Images
Authors: Anand S. , Prabhadevi R. , Rini D.
Published: June 2020

In this paper an algorithm to detect the optic disc (OD) automatically is described. The proposed method is based on the circular brightness of the OD and its correlation coefficient. At first the peak intensity points are taken, a mask is generated for the given image which gives the circular bright regions of the image. To locate the OD accurately, a pattern is generated which is similar to the OD. By correlating the retinal image with the pattern generated, the maximum correlation of the pattern with the OD is obtained. On locating the coordinates of maximum correlation, the exact location of the OD is detected. The proposed algorithm has been tested with DRIVE database images and an average OD detection accuracy of 95% was obtained for healthy and pathological retinas respectively.
One score to rule them all: severity assessment in laboratory mice
Authors: Talbot Steven R. , Struve Birgitta , Wassermann Laura , Heider Miriam , Weegh Nora , Knape Tilo , Hofmann Martine C. J. , von Knethen Andreas , Jirkof Paulin , Keubler Lydia , Bleich André , Häger Christine
Published: June 2020

Animal welfare and the refinement of experimental procedures are fundamental aspects of biomedical research. They provide the basis for robust experimental designs and reproducibility of results. In many countries, the determination of welfare is a mandatory legal requirement and implies the assessment of the degree of the severity that an animal experiences during an experiment. However, for an effective severity assessment, an objective and exact approach/system/strategy is needed. In light of these demands, we have developed the Relative Severity Assessment (RELSA) score.

This comprehensive composite score was established on the basis of physiological and behavioral data from a surgical mouse study. Body weight, the Mouse Grimace Scale score, burrowing behavior, and the telemetry-derived parameters heart rate, heart rate variability, temperature, and general activity were used to investigate the quality of indicating severity during postoperative recovery. The RELSA scores not only revealed individual severity levels but also allowed a comparison of severity in distinct mouse models addressing colitis, sepsis, and restraint stress using ak-means clustering approach with the maximum achieved RELSA scores.

We discriminated and classified data from sepsis nonsurvivors into the highest relative severity level. Data from mice after intraperitoneal transmitter implantation and sepsis survivor al were located in the next lower cluster, while data from mice subjected to colitis and restraint stress were placed in the lowest severity cluster. Analysis of individual variables and their combinations revealed model- and time-dependent contributions to severity levels.

In conclusion, we propose the RELSA score as a validated tool for objective real-time applicability in severity assessment and as a first step towards a unified and accessible risk assessment tool in biomedical research. As an effective severity assessment system, it will fundamentally improve animal welfare, as well as data quality and reproducibility.
Revealing grand-paternal programming of lipid metabolism using a novel computational tool
Authors: Furse Samuel , Watkins Adam J. , Chiarugi Davide , Hojat Nima , Smith James , Williams Huw E. L. , Koulman Albert
Published: June 2020

While the consequences of poor maternal diet on the offspring’s cardio-metabolic health have been studied in detail, the role of the father’s diet on the health of his offspring is poorly understood. We used a known mouse model to establish the impact of an isocaloric paternal low-protein high-carbohydrate diet on the offspring’s lipid metabolism. Detailed lipid profiles were acquired from F1 neonate (3 weeks), F1 adult (16 weeks) and F2 neonate male and female offspring, in serum, liver, brain, heart and abdominal adipose tissues by Mass Spectrometry and Nuclear Magnetic Resonance. Using a purpose-built computational tool for analysing lipid metabolism as a network, we characterised the number, type and abundance of lipid variables in and between tissues (Lipid Traffic Analysis), finding a variety of alterations associated with paternal diet. These elucidate a mechanism for the defective physiological behaviour of systems at risk of cardio-metabolic disease.
Biochemical evidence of furin specificity and potential for phospho-regulation at Spike protein S1/S2 cleavage site in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV
Authors: Örd Mihkel , Faustova Ilona , Loog Mart
Published: June 2020

The Spike protein of the novel coronavirus SARS-CoV2 contains an insertion680SPRRAR↓SV687forming a cleavage motif RxxR for furin-like enzymes at the boundary of S1/S2 subunits. Cleavage at S1/S2 is important for efficient viral entry into target cells. The insertion is absent in other CoV-s of the same clade, including SARS-CoV1 that caused the 2003 outbreak. However, an analogous insertion was present in the Spike protein of the more distant Middle East Respiratory Syndrome coronavirus MERS-CoV. We show that a crucial third arginine at the left middle position, comprising a motif RRxR is required for furin recognitionin vitro, while the general motif RxxR in common with MERS-CoV is not sufficient for cleavage. Further, we describe a surprising finding that the two serines at the edges of the insertSPRRAR↓SV can be efficiently phosphorylated by proline-directed and basophilic protein kinases. Both phosphorylations switch off furin’s ability to cleave the site. Although phosphoregulation of secreted proteins is still poorly understood, further studies, supported by a recent report of tenin vivophosphorylated sites in the Spike protein of SARS-CoV2, could potentially uncover important novel regulatory mechanisms for SARS-CoV2.
Deconstructing glucose-mediated catabolite repression of thelacoperon ofEscherichia coli: II. Positive feedback exists and drives the repression
Authors: Aggarwal Ritesh K. , Narang Atul
Published: June 2020

The expression of thelacoperon ofE. coliis subject to positive feedback during growth in the presence of gratuitous inducers, but its existence in the presence of lactose remains controversial. The key question in this debate is: Do the lactose enzymes, Lac permease and β-galactosidase, promote accumulation of allolactose? If so, positive feedback exists since allolactose does stimulate synthesis of the lactose enzymes. Here, we addressed the above question by developing methods for determining the intracellular allolactose concentration as well as the kinetics of enzyme induction and dilution. We show that duringlacinduction in the presence of lactose, the intracellular allolactose concentration increases with the lactose enzyme level, which implies that lactose enzymes promote allolactose accumulation, and positive feedback exists. We also show that duringlacrepression in the presence of lactose + glucose, the intracellular allolactose concentration decreases with the lactose enzyme levels, which suggests that under these conditions, the positive feedback loop turns in the reverse direction. The induction and dilution rates derived from the transient data show that the positive feedback loop is reversed due to a radical shift of the steady state induction level. This is formally identical to the mechanism driving catabolite repression in the presence of TMG + glucose.
Regulation of the activity of an antimicrobial peptide by sterols or hopanoids: possible role in cell recognition
Authors: Alvares Dayane S. , Monti Mariela R. , Neto João Ruggiero , Wilke Natalia
Published: June 2020

It is now accepted that hopanoids act as sterol-surrogates in membranes of some sterol-lacking bacteria. Here we inquiry whether the hopanoid diplopterol (DP) could attenuate the activity of the antimicrobial peptide Polybia-MP1 (MP1) similarly to cholesterol (CHO). Survival ofP. aeruginosaexposed to MP1 was lower for cells incubated with DP than those incubated with CHO, and the affinity and subsequent effect of the peptide on lipid bilayers were different in the presence of DP than in the presence of CHO. Membrane properties showed a non-monotonic behavior as the peptide adsorbed, penetrated, and translocated bilayers with DP suggesting a reorganization of MP1 during these processes. We conclude that MP1 selectivity is finely tuned by lipid composition, and propose the differential interaction and consequent effect promoted by the peptide in membranes with diplopterol as a promising starting point for targeting antimicrobial peptides to hopanoid-containing bacterial membranes.
Predicting lapses of attention with sleep-like slow waves
Authors: Andrillon Thomas , Burns Angus , MacKay Teigane , Windt Jennifer , Tsuchiya Naotsugu
Published: June 2020

Attentional lapses are ubiquitous and can negatively impact performance. They correlate with mind wandering, or thoughts that are unrelated to ongoing tasks and environmental demands. In other cases, the stream of consciousness itself comes to a halt and the mind goes blank. What is happening in the brain that leads to these mental states? To understand the neural mechanisms underlying attentional lapses, we cross-analysed the behaviour, subjective experience and neural activity of healthy participants performing a task. Random interruptions prompted participants to indicate their mental states as task-focused, mind-wandering or mind-blanking. High-density electroencephalography revealed the occurrence of spatially and temporally localized slow waves, a pattern of neural activity characteristic of the transition toward sleep. These slow waves accompanied behavioural markers of lapses and preceded reports of mind wandering and mind blanking. Furthermore, the location of slow waves distinguished sluggish versus impulsive behaviours, mind wandering versus mind blanking. Our results suggest attentional lapses share a common physiological origin: the emergence of local sleep-like activity within the awake brain.
RAAS blockade, kidney disease, and expression ofACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells
Authors: Subramanian Ayshwarya , Vernon Katherine A , Slyper Michal , Waldman Julia , Luecken Malte D , Gosik Kirk , Dubinsky Dan , Cuoco Michael S , Keller Keith , Purnell Jason , Nguyen Lan , Dionne Danielle , Rozenblatt-Rosen Orit , Weins Astrid ,   Human Cell Atlas Lung Biological Network, Regev Aviv , Greka Anna
Published: June 2020

SARS-CoV-2, the coronavirus that causes COVID-19, binds to angiotensin-converting enzyme 2 (ACE2) on human cells. Beyond the lung, COVID-19 impacts diverse tissues including the kidney. ACE2 is a key member of the Renin-Angiotensin-Aldosterone System (RAAS) which regulates blood pressure, largely through its effects on the kidney. RAAS blockers such as ACE inhibitors (ACEi) and Angiotensin Receptor Blockers (ARBs) are widely used therapies for hypertension, cardiovascular and chronic kidney diseases, and therefore, there is intense interest in their effect on ACE2 expression and its implications for SARS-CoV-2 pathogenicity. Here, we analyzed single-cell and single-nucleus RNA-seq of human kidney to interrogate the association of ACEi/ARB use withACE2expression in specific cell types. First, we performed an integrated analysis aggregating 176,421 cells across 49 donors, 8 studies and 8 centers, and adjusting for sex, age, donor and center effects, to assess the relationship ofACE2with age and sex at baseline. We observed a statistically significant increase inACE2expression in tubular epithelial cells of the thin loop of Henle (tLoH) in males relative to females at younger ages, the trend reversing, and losing significance with older ages.ACE2expression in tLoH increases with age in females, with an opposite, weak effect in males. In an independent cohort, we detected a statistically significant increase inACE2expression with ACEi/ARB use in epithelial cells of the proximal tubule and thick ascending limb, and endothelial cells, but the association was confounded in this small cohort by the underlying disease. Our study illuminates the dynamics ofACE2expression in specific kidney cells, with implications for SARS-CoV-2 entry and pathogenicity.
Constraints on the Efficiency of Electromicrobial Production
Authors: Salimijazi Farshid , Kim Jaehwan , Schmitz Alexa , Grenville Richard , Bocarsly Andrew , Barstow Buz
Published: June 2020

Electromicrobial production technologies (EMP) aim to combine renewable electricity and microbial metabolism. We have constructed molecular to reactor scale models of EMP systems using H2-oxidation and extracellular electron transfer (EET). We predict the electrical-to-biofuel conversion efficiency could rise to ≥ 52% with in vivo CO2-fixation. H2 and EET-mediated EMP both need reactors with high surface areas. H2-diffusion at ambient pressure requires areas 20 to 2,000 times that of the solar photovoltaic (PV) supplying the system. Agitation can reduce this to less than the PV area, and the power needed becomes negligible when storing ≥ 1.1 megawatts. EET-mediated systems can be built that are ≤ 10 times the PV area and have minimal resistive energy losses if a conductive extracellular matrix (ECM) with a resistivity and height seen in natural conductive biofilms is used. The system area can be reduced to less than the PV area if the ECM conductivity and height are increased to those of conductive artificial polymers. Schemes that use electrochemical CO2-fixation could achieve electrical-to-fuel efficiencies of almost 50% with no complications of O2-sensitivity.
The buds ofOscarella lobularis(Porifera): a new convenient model for sponge cell and developmental biology
Authors: Caroline Rocher , Amélie Vernale , Laura Fierro-Constaín , Nina Séjourné , Sandrine Chenesseau , Christian Marschal , Emilie Le Goff , Morgan Dutilleul , Cédric Matthews , Florent Marschal , Nicolas Brouilly , Dominique Massey-Harroche , Alexander Ereskovsky , André Le Bivic , Carole Borchiellini , Emmanuelle Renard
Published: June 2020

The comparative study of the four non-bilaterian phyla (Cnidaria, Placozoa, Ctenophora, Porifera) should provide insights into the origin of bilaterian traits. Except for Cnidaria, present knowledge on the cell biology and development of these animals is so far limited. Non-bilaterian models are needed to get further into cell architecture and molecular mechanisms.

Given the developmental, histological, ecological and genomic differences between the four sponge classes, we develop a new sponge model: the buds of theOscarella lobularis(class Homoscleromorpha). This experimental model supplements the two other most famous sponge modelsAmphimedon queenslandicaandEphydatia muelleri, both belonging to the class Demospongiae.

Budding is a natural and spontaneous asexual reproduction mean, but budding can be triggeredin vitroensuring availability of biological material all year long. We provide a full description of buds, from their formation to their development into juveniles. Their transparency enables fluorescent and live imaging, and their abundance allows for experimental replicates. Moreover, regeneration and cell reaggregation capabilities provide interesting experimental morphogenetic contexts. The numerous techniques now mastered on these buds make it a new suitable sponge model.

Summary statement

Studying sponge biology is needed to understand the evolution of metazoans. We developed a new model suitable for experimental biology that allows to study morphogenetic processes with modern tools.
Sphingosine 1-phosphate activates the MAP3K1-JNK pathway to promote epithelial movement and morphogenesis
Authors: Wang Jingjing , Mongan Maureen , Chun Jerold , Xia Ying
Published: June 2020

MAP 3 kinase 1 (MAP3K1) plays an essential role in embryonic eyelid development. It regulates epithelial morphogenesis through the spatial-temporal activation of Jun N-terminal kinases (JNKs), resulting in forward progression of the embryonic eyelid epithelial cells to enable eyelid closure. The developmental signals that activate the MAP3K1-JNK pathway are still unknown, mainly due to the lack of suitable keratinocyte lines to elucidate the mechanisms of pathway regulation. To address this deficiency, we developed a straightforward method for long-term culture of mouse keratinocytes in feeder-free conditions using Ca2+-free media. Cells grown under these conditions displayed characteristic basal epithelial morphology and keratin 14 expression, but did not form tight- or adherens-junctions. Increased extracellular Ca2+levels restored the formation of cell-cell junctions. Using keratinocyte lines derived from wild type andMap3k1-deficient mice, we found that sphingosine 1-phosphate (S1P) activated the JNK-c-JUN pathways in a manner dependent on MAP3K1 kinase activity and that this MAP3K1-mediated signaling led to epithelial cell migration. Thein vivoroles of this pathway were examined through crossing of genetic mutant mice. Loss-of-function of the S1P receptor(S1pr) 2/3 became haploinsufficient only when combined withMap3k1andJnk1mutations such that the compound mutants displayed eyelid closure defects, suggesting these gene products cooperated in eye morphogenesis. Results of this work establish the S1PR-MAP3K1-JNK pathway as a crucial signaling mechanism for epithelial cell movement and morphogenesis.
Two classes of active transcription sites and their roles in developmental regulation
Authors: Robinson-Thiewes Sarah , McCloskey John , Kimble Judith
Published: June 2020

Genes encoding powerful developmental regulators are exquisitely controlled, often at multiple levels. Here, we use single molecule FISH (smFISH) to investigate nuclear active transcription sites (ATS) and cytoplasmic mRNAs of three key regulatory genes along theC. elegans germline developmental axis. The genes encode ERK/MAP kinase and core components of the Notch-dependent transcription complex. Using differentially-labeled probes spanning either a long first intron or downstream exons, we identify two ATS classes that differ in transcriptional progression: iATS harbor partial nascent transcripts while cATS harbor full-length nascent transcripts. Remarkably, the frequencies of iATS and cATS are patterned along the germline axis in a gene-, stage- and sex-specific manner. Moreover, regions with more frequent iATS make fewer full-length nascent transcripts and mRNAs, whereas those with more frequent cATS produce more of them. We propose that the regulated balance of these two ATS classes has a major impact on transcriptional output during development.
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions
Authors: Zarin Taraneh , Strome Bob , Peng Gang , Pritišanac Iva , Forman-Kay Julie D , Moses Alan M
Published: June 2020

Previously, we showed that intrinsically disordered regions in proteins (IDRs) contain multiple sequence-distributed molecular features that are conserved over evolution, despite little sequence similarity that can be detected in alignments (Zarin et al. 2019). Here, we aim to use these molecular features to make specific functional predictions for individual IDRs and identify the molecular features within them that are responsible for specific functions. We find that the predictable functions are diverse, identifying previously known associated molecular features, as well as features that were previously not known to be associated with these functions. We experimentally confirm that elevated isoelectric point and hydrophobicity, features that are positively associated with mitochondrial localization, are necessary for mitochondrial targeting function. Remarkably, increasing isoelectric point in a synthetic IDR restores weak mitochondrial targeting. We believe feature analysis represents a new systematic approach to understand how biological functions of IDRs are specified by their protein sequences.
Recalcitrance ofCannabis sativatode novoregeneration; a multi-genotype replication study
Authors: Monthony Adrian S. , Kyne Sean T. , Grainger Christopher M. , Jones A. Maxwell P.
Published: June 2020

1

Cannabis sativais relatively recalcitrant to regeneration from somatic tissues, but several reports have been published demonstrating a response. Most reports show low levels of regeneration from somatic tissues, but a landmark publication by Lataet al. in 2010 reported regeneration from leaf explants with a 96% response rate, producing an average of 12.3 shoots per explant in a single, high-THC genotype. Despite the importance regeneration plays in plant biotechnology this protocol has not been used in subsequent papers in the decade since it was published, raising the concern that it is not reproducible. Many researchers are looking to build research programmes in this growing field, and it is important that the reproducibility and robustness of single-genotypeC. sativaregeneration protocols undergo multi-lab validations to ensure they are reproducible across the species. Replication studies in this burgeoning field will help research groups avoid lost time and resources which arise from pursuing protocols that are not reproducible. Here we test the replicability of this protocol across 10 drug-typeC. sativagenotypes. This protocol successfully induced callus in all 10 genotypes. Callus size and appearance substantially differed among cultivars, with the most responsive genotype producing 6-fold more callus than the least responsive genotype. However, the most successful shoot induction medium developed in the 2010 paper failed to induce regeneration in any of the cultivars tested, resulting in the eventual necrosis of the calli. Based on this replication study, it is evident that the existing regeneration protocol is not robust and could not be replicated in any of the 10 genotypes tested.
Parabrachial Opioidergic Projections to Preoptic Hypothalamus Mediate Behavioral and Physiological Thermal Defenses
Authors: Norris Aaron J. , Shaker Jordan R. , Cone Aaron L. , Ndiokho Imeh B. , Bruchas Michael R
Published: June 2020

Maintaining stable body temperature through environmental thermal stressors requires detection of temperature changes, relay of information, and coordination of physiological and behavioral responses. Studies have implicated areas in the preoptic hypothalamic area (POA) and the parabrachial nucleus (PBN) as nodes in the thermosensory neural circuitry and indicate the opioid system within the POA is vital in regulating body temperate. In the present study we identify neurons projecting to the POA from PBN expressing the opioid peptides Dynorphin (Dyn) and Enkephalin (Enk). We determine that warm-activated PBN neuronal populations overlap with both Dyn and Enk expressing PBN populations. We demonstrate that Dyn and Enk expressing neurons are partially overlapping subsets of a glutamatergic population in the PBN. Using optogenetic approaches we selectively activate projections in the POA from PBN Dyn, Enk, and VGLUT2 expressing neurons. Our findings demonstrate that Dyn, Enk, and VGLUT2 expressing PBN neurons are critical for physiological and behavioral heat defense.
A Live-Cell Assay for the Detection of pre-microRNA-Protein Interactions
Authors: Rosenblum Sydney L. , Lorenz Daniel A. , Garner Amanda L.
Published: June 2020

Recent efforts in genome-wide sequencing and proteomics have revealed the fundamental roles that RNA-binding proteins (RBPs) play in the life cycle and function of both coding and non-coding RNAs. While these methodologies provide a systems-level view of the networking of RNA and proteins, approaches to enable the cellular validation of discovered interactions are lacking. Leveraging the power of bioorthogonal chemistry- and split-luciferase-based assay technologies, we have devised a conceptually new assay for the live-cell detection of RNA-protein interactions (RPIs), RNA interaction with Protein-mediated Complementation Assay, or RiPCA. As proof-of-concept, we have utilized the interaction of the pre-microRNA, pre-let-7, with its binding partner, Lin28. Using this system, we have demonstrated the selective detection of the pre-let-7-Lin28 RPI in both the cytoplasm and nucleus. Furthermore, we determined this technology can be used to discern relative affinities for specific sequences as well as of individual RNA binding domains. Thus, RiPCA has the potential to serve as a useful tool in supporting the investigation of cellular RPIs.
In VivoMechanisms of Chemotherapy-Induced Acute Follicle Loss in the Human Ovary: An Individual-Oocyte Transcriptomic Analysis from Human Ovarian Xenografts
Authors: Titus S. , Szymanska K.J. , Musul B. , Turan V. , Taylan E. , Garcia-Milian R. , Mehta S. , Oktay K.
Published: June 2020

Gonadotoxic chemotherapeutics, such as cyclophosphamide, cause early menopause and infertility in women. Earlier histological studies showed ovarian reserve depletion via severe DNA damage and apoptosis, but others suggested activation of PI3K/PTEN/Akt pathway and follicle ‘burn-out’ as a cause. Using a human ovarian xenograft model, we performed single-cell RNA-sequencing on laser-captured individual primordial follicle oocytes 12h after a single cyclophosphamide injection to determine the mechanisms of acute follicle loss after gonadotoxic chemotherapy. RNA-sequencing showed 190 differentially expressed genes between the cyclophosphamide- and vehicle-exposed oocytes. Ingenuity Pathway Analysis predicted a significant decrease in the expression of anti-apoptotic pro-AktPECAM1(p=2.13E-09),IKBKE(p=0.0001), andANGPT1(p=0.003), and reduced activation of PI3K/PTEN/Akt after cyclophosphamide. The qRT-PCR and immunostaining confirmed that in primordial follicle oocytes, cyclophosphamide did not change the expressions ofAkt(p=0.9),rpS6(p=0.3),Foxo3a(p=0.12) and anti-apoptoticBcl2(p=0.17), nor affect their phosphorylation status. There was significantly increased DNA damage by γH2AX (p=0.0002) and apoptosis by active-caspase-3 (p=0.0001) staining in the primordial follicles and no change in the growing follicles 12h after chemotherapy. These data suggest that the mechanism of acute follicle loss by cyclophosphamide is via apoptosis, rather than growth activation of primordial follicle oocytes in the human ovary.

One Sentence Summary

Single-cell transcriptomic interrogation of primordial follicles in human ovarian xenografts reveals that chemotherapy causes acute ovarian reserve depletion by inducing a pro-apoptotic state rather than activating pathways that result in follicle growth initiation.
Zebrafishfollistatin-like 1bregulates cardiac contraction during early development
Authors: Zeng Xin-Xin I. , Ocorr Karen , Ensberg Erik J. , Dong P. Duc si
Published: June 2020

Extracellular glycoprotein Follistatin-like protein 1 (FSTL1) has been reported to be involved in multiple signaling pathways and biological processes during development and disease. In addition, some mouse studies have suggested an inhibitory role of FSTL1 in BMP signaling, in certain context. Yet, whether FSTL1 has biological functions in early heart development are largely unknown. In our functional studies, CRISPR/Cas9 genome editing was used to createfstl1aandfstl1binsertion/deletion mutations in zebrafish and our results suggest thatfstl1bis important in regulating heart development during early embryogenesis.in situhybridization revealed thatfstl1btranscripts are expressed in the developing zebrafish heart, andfstl1bhomozygous (-/-) mutant exhibited pericardial edema and showed significantly reduced contractility in the ventricle, with incomplete penetrance. We found that zebrafishfstl1b (-/-)mutant hearts formed a collapsed ventricle with strong reductions in the sarcomere structure protein alpha-actinin, although the number of cardiomyocytes was comparable to wild type control siblings. Further, normal levels offstl1bseems to prevent the expansion of Bmp signaling into ventricular myocytes, which is consistent with the previously established model of Bmp-dependent cardiac contraction. Together these results reveal the zebrafish orthologfstl1bregulates sarcomere structure and cardiac contractile function. In vertebrate developing heart, it might function as a key component in a novel pathway that constrains Bmp signaling from ventricular myocytes.
Diverse scientific benchmarks for implicit membrane energy functions
Authors: Alford Rebecca F. , Gray Jeffrey J.
Published: June 2020

Energy functions are fundamental to biomolecular modeling. Their success depends on robust physical formalisms, efficient optimization, and high-resolution data for training and validation. Over the past 20 years, progress in each area has advanced soluble protein energy functions. Yet, energy functions for membrane proteins lag behind due to sparse and low-quality data, leading to overfit tools. To overcome this challenge, we assembled a suite of 12 tests on independent datasets varying in size, diversity, and resolution. The tests probe an energy function’s ability to capture membrane protein orientation, stability, sequence, and structure. Here, we present the tests and use thefranklin2019energy function to demonstrate them. We then present a vision for transforming these “small” datasets into “big data” that can be used for more sophisticated energy function optimization. The tests are available through the Rosetta Benchmark Server (https://benchmark.graylab.jhu.edu/) and GitHub (https://github.com/rfalford12/Implicit-Membrane-Energy-Function-Benchmark).
Remote homology search with hidden Potts models
Authors: Wilburn Grey W. , Eddy Sean R.
Published: June 2020

Most methods for biological sequence homology search and alignment work with primary sequence alone, neglecting higher-order correlations. Recently, statistical physics models called Potts models have been used to infer all-by-all pairwise correlations between sites in deep multiple sequence alignments, and these pairwise couplings have improved 3D structure predictions. Here we extend the use of Potts models from structure prediction to sequence alignment and homology search by developing what we call a hidden Potts model (HPM) that merges a Potts emission process to a generative probability model of insertion and deletion. Because an HPM is incompatible with efficient dynamic programming alignment algorithms, we develop an approximate algorithm based on importance sampling, using simpler probabilistic models as proposal distributions. We test an HPM implementation on RNA structure homology search benchmarks, where we can compare directly to exact alignment methods that capture nested RNA base-pairing correlations (stochastic context-free grammars). HPMs perform promisingly in these proof of principle experiments.

Author summary

Computational homology search and alignment tools are used to infer the functions and evolutionary histories of biological sequences. Most widely used tools for sequence homology searches, such as BLAST and HMMER, rely on primary sequence conservation alone. It should be possible to make more powerful search tools by also considering higher-order covariation patterns induced by 3D structure conservation. Recent advances in 3D protein structure prediction have used a class of statistical physics models called Potts models to infer pairwise correlation structure in multiple sequence alignments. However, Potts models assume alignments are given and cannot build new alignments, limiting their use in homology search. We have extended Potts models to include a probability model of insertion and deletion so they can be applied to sequence alignment and remote homology search using a new model we call a hidden Potts model (HPM). Tests of our prototype HPM software show promising results in initial benchmarking experiments, though more work will be needed to use HPMs in practical tools.