bluuebunny/crossref_metadata_2025 huggingface dataset:
Role and patterns of butterflies and hawkmoths in plant-pollinator networks at different elevations and seasons in tropical rainforests of Mount Cameroon
Authors: Mertens Jan E.J. , Brisson Lucas , Janeček Štěpán , Klomberg Yannick , Maicher Vincent , Sáfián Szabolcs , Delabye Sylvain , Potocký Pavel , Kobe Ishmeal N. , Pyrcz Tomasz , Tropek Robert
Published: February 2021

Butterflies and moths are well-visible flower visitors. Nevertheless, almost no quantification of their role in plant-pollinator interactions exists at a community level, especially from tropical rainforests. Moreover, we have virtually no knowledge on environmental and other factors affecting lepidopteran flower visits.

We focused on the role of butterflies and hawkmoths as flower visitors in tropical rainforests of Mount Cameroon, especially on its elevational and seasonal changes. We also analysed their preferences to selected floral traits, with a specific focus on pollination syndromes.

We video-recorded flower visitors of 1,115 specimens of 212 plant species (>26,000 recording hrs) along the complete elevational gradient of rainforests in two main seasons, and compared frequencies of flower-visiting lepidopterans to other visitors. We compared characteristics of plant-lepidopteran networks among elevations and seasons, and analysed patterns of selected lepidopteran traits. Finally, we analysed inter-family differences in their floral preferences.

Altogether, we recorded 734 flower visits by 80 butterflies and 27 hawkmoth species, representing only ~4% of all 18,439 flower visits. Although lepidopterans visited only a third species, they appeared key visitors of several plants. The most flower visits by lepidopterans were recorded in mid-elevations and dry season, mirroring the general patterns of lepidopteran diversity. The networks showed no apparent elevational or seasonal patterns, probably because of the surprisingly high specialisation of interactions in all networks. Significant non-linear changes of proboscis and forewing lengths were found along elevation, and long-proboscid hesperiid butterflies visited flowers with longer tubes or spurs. Substantial differences in floral preferences were found between sphingids, and papilionid, nymphalid and lycaenid butterflies, revealing importance of nectar production, floral size and shape for sphingids, and floral colour for butterflies.

Butterflies and hawkmoths were confirmed as relatively minor visitors of tropical forest flowers, although they seemed crucial for pollination of some plant species. Moreover, the revealed floral preferences and trait-matchings confirmed a potential of some lepidopteran families to drive floral evolution in tropical ecosystems.
Optical Estimation of Absolute Membrane Potential Using One- and Two-Photon Fluorescence Lifetime Imaging Microscopy
Authors: Lazzari-Dean Julia R. , Miller Evan W.
Published: February 2021

Background

Membrane potential (Vmem) exerts physiological influence across a wide range of time and space scales. To study Vmemin these diverse contexts, it is essential to accurately record absolute values of Vmem, rather than solely relative measurements.

Materials & Methods

We use fluorescence lifetime imaging of a small molecule voltage sensitive dye (VF2.1.Cl) to estimate mV values of absolute membrane potential.

Results

We test the consistency of VF2.1.Cl lifetime measurements performed on different single photon counting instruments and find that they are in striking agreement (differences of <0.5 ps/mV in the slope and <50 ps in the y-intercept). We also demonstrate that VF2.1.Cl lifetime reports absolute Vmemunder two-photon (2P) illumination with better than 20 mV of Vmemresolution, a nearly 10-fold improvement over other lifetime-based methods.

Conclusions

We demonstrate that VF-FLIM is a robust and portable metric for Vmemacross imaging platforms and under both one-photon and two-photon illumination. This work is a critical foundation for application of VF-FLIM to record absolute membrane potential signals in thick tissue.
Sec17/Sec18 can support membrane fusion without help from completion of SNARE zippering
Authors: Song Hongki , Torng Thomas , Orr Amy , Brunger Axel T. , Wickner William
Published: February 2021

Membrane fusion requires R-, Qa-, Qb-, and Qc-family SNAREs that zipper into RQaQbQc coiled coils, driven by the sequestration of apolar amino acids. Zippering has been thought to provide all the force driving fusion. Sec17/SNAP can form an oligomeric assembly with SNAREs with the Sec17 C-terminus bound to Sec18/NSF, the central region bound to SNAREs, and a crucial apolar loop near the N-terminus poised to insert into membranes. Though Sec17 aids zippering, we now report that Sec17 and Sec18 will drive robust fusion without requiring zippering completion. Zippering-driven fusion is blocked by deleting the C-terminal quarter of any Q-SNARE domain or by replacing the apolar amino acids of the Qa-SNARE which face the center of the 4-SNARE coiled coils with polar residues. These blocks to fusion, singly or combined, are bypassed by Sec17 and Sec18, and SNARE-dependent fusion is restored without help from completing zippering.
AirLift: A Fast and Comprehensive Technique for Remapping Alignments between Reference Genomes
Authors: Kim Jeremie S. , Firtina Can , Cavlak Meryem Banu , Cali Damla Senol , Hajinazar Nastaran , Alser Mohammed , Alkan Can , Mutlu Onur
Published: February 2021

AirLift is the first read remapping tool that enables users to quickly and comprehensively map a read set, that had been previously mapped to one reference genome, to another similar reference. Users can then quickly run downstream analysis of read sets for each latest reference release. Compared to the state-of-the-art method for remapping reads (i.e., full mapping), AirLift reduces the overall execution time to remap read sets between two reference genome versions by up to 27.4×. We validate our remapping results with GATK and find that AirLift provides high accuracy in identifying ground truth SNP/INDEL variants.

Code Availability

AirLift source code and readme describing how to reproduce our results are available athttps://github.com/CMU-SAFARI/AirLift.
Synthesizing VERDICT maps from standard DWI data using GANs
Authors: Chiou Eleni , Valindria Vanya , Giganti Francesco , Punwani Shonit , Kokkinos Iasonas , Panagiotaki Eleftheria
Published: February 2021

VERDICT maps have shown promising results in clinical settings discriminating normal from malignant tissue and identifying specific Gleason grades non-invasively. However, the quantitative estimation of VERDICT maps requires a specific diffusion-weighed imaging (DWI) acquisition. In this study we investigate the feasibility of synthesizing VERDICT maps from standard DWI data from multi-parametric (mp)- MRI by employing conditional generative adversarial networks (GANs). We use data from 67 patients who underwent both standard DWI-MRI and VERDICT MRI and rely on correlation analysis and mean squared error to quantitatively evaluate the quality of the synthetic VERDICT maps. Quantitative results show that the mean values of tumour areas in the synthetic and the real VERDICT maps were strongly correlated while qualitative results indicate that our method can generate realistic VERDICT maps that could supplement mp-MRI assessment for better diagnosis.
Molecular effects of mannanase-hydrolyzed coprameal to intestinal immunity in the Pacific white shrimp(Litopenaeus vannamei)
Authors: Rungrassamee Wanilada , Arayamethakorn Sopacha , Karoonuthaisiri Nitsara , Chen Shih-Chu , Chang Eric , Chan Samu , Yoshida Yasuhiko , Maebuchi Motohiro , Ibuki Masahisa
Published: February 2021

To mitigate disease outbreak, an alternative approach through enhancing shrimp immunity was explored. Mannan oligosaccharides (MOS) have been previously reported to enhance shrimp immune system. Here, coprameal samples were digested with mannanase to yield MOS, namely, mannanase-hydrolyzed coprameal (MCM) and feasibility of MCM as shrimp immunostimulant in grow-out ponds was determined. Pacific white shrimp (Litopenaeus vannamei) were fed with the commercial diet containing 1% MCM as the MCM-supplemented group and compared to the non-MCM control diet. There was no significant difference in survival rates between the MCM-supplemented and the control groups throughout the 4-month-period of the trial (p> 0.05). Gene expression analysis in shrimp intestines revealed that the transcript levels of antimicrobial peptides (anti-lipopolysaccharide factor isoform 1(alf1),penaeidin (pen3a)andcrustin (crus))and lysozymes(lyz)were not significantly different in the MCM-supplemented group. Meanwhile,C-type lectinandtoll-like receptortranscript levels, whose gene products play roles as pattern recognition proteins, were significantly higher in a group fed with MCM for 2- and 4-month periods than those of the control group (p< 0.05). The increased transcript levels ofC-type lectinandtoll-like receptorprovide evidence for potential implementation of MCM as feed supplement to modulate shrimp immune system.
Shades of grey: Coat-colour dependent effect of urbanization on the bacterial microbiome of a wild mammal
Authors: Stothart Mason R. , Newman Amy E.M.
Published: February 2021

Background

Host-associated microbiota can be fundamental to the ecology of their host and may even help wildlife species colonize novel niches or cope with rapid environmental change. Urbanization is a globally replicated form of severe environmental change which we can leverage to better understand wildlife microbiomes. Does the colonization of separate cities result in parallel changes in the intestinal microbiome of wildlife, and if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, we quantified the effect of urbanization on the microbiome of eastern grey squirrels (Sciurus carolinensis). Eastern grey squirrels are ubiquitous in both rural and urban environments throughout their native range, across which they display an apparent coat colour polymorphism (agouti, black, intermediate).

Results

Grey squirrel microbiomes differed between rural and city environments; however, comparable variation was explained by habitat heterogeneity within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure was more strongly influenced by local environmental conditions (rural and city forests versus human built habitats) than urbanization of the broader landscape (city versus rural). Many of the bacterial genera identified as characterizing the microbiomes of built-environment squirrels are though to specialize on host-derived products and have been linked in previous research to low fibre diets. However, despite an effect of urbanization at fine spatial scales, phylogenetic patterns in the microbiome were coat colour phenotype dependent. City and built environment agouti squirrels displayed greater phylogenetic beta-dispersion than those in rural or forest environments, and null modelling results indicated that the phylogenetic structure of urban agouti squirrels did not differ greatly from stochastic phylogenetic expectations.

Conclusions

Habitat heterogeneity at fine spatial scales affects host-associated microbiomes, however, we found little evidence that this pattern was the result of similar selective pressures acting on the microbiome within environments. Further, this result, those of phylogeny-independent analyses, and patterns of beta-dispersion lead us to suggest that microbiota dispersal and ecological drift are integral to shaping the inter-environmental differences we observed. These patterns were partly mediated by squirrel coat colour phenotype, and therefore putatively, host physiology. Given a well-known urban cline in squirrel coat colour melanism, grey squirrels provide an ideal free-living system with which to study how host genetics mediate environment x microbiome interactions.
Early Dynamics of Chronic Myeloid Leukemia on Nilotinib Predicts Deep Molecular Response
Authors: Okamoto Yuji , Hirano Mitsuhito , Morino Kai , Kajita Masashi K. , Nakaoka Shinji , Tsuda Mayuko , Sugimoto Kei-ji , Tamaki Shigehisa , Hisatake Junichi , Yokoyama Hisayuki , Igarashi Tadahiko , Shinagawa Atsushi , Sugawara Takeaki , Hara Satoru , Fujikawa Kazuhisa , Shimizu Seiichi , Yujiri Toshiaki , Wakita Hisashi , Nishiwaki Kaichi , Tojo Arinobu , Aihara Kazuyuki
Published: February 2021

Chronic myeloid leukemia (CML) is a myeloproliferative disorder caused by theBCR-ABL1tyrosine kinase1,2.ABL1-selective tyrosine kinase inhibitors (TKIs) including nilotinib have dramatically improved the prognosis of patients with CML3–7. The ultimate goal of CML treatment is likely to be TKI-free maintenance of deep molecular response (DMR), which is defined by quantitative measurement ofBCR-ABL1transcripts on the international scale (IS)8, and durable DMR is a prerequisite to reach this goal9. Thus, an algorithm to enable the early prediction of DMR achievement on TKI therapy is quite valuable. Here, we show that our mathematical framework based on a clinical trial dataset10can accurately predict the response to frontline nilotinib. We found that our simple dynamical model can predict nilotinib response by using two common laboratory findings (observation values): IS11,12and white blood cell (WBC) count. Furthermore, our proposed method identified patients who failed to achieve DMR with high fidelity according to the data collected only at three initial time points during nilotinib therapy. Since our model relies on the general properties of TKI response, our framework would be applicable to CML patients who receive frontline nilotinib or other TKIs in clinical practice.

Significance Statement

Chronic myeloid leukemia (CML) is a myeloproliferative disorder caused by the BCR-ABL1 tyrosine kinase. The goal of this treatment is the sequential achievement of deep molecular response (DMR). Tyrosine kinase inhibitors (TKIs) are effective in the reduction because they inhibit CML cell proliferation. However, because of individual differences in the TKI efficacy, some patients are unable to achieve DMR, so that early prediction of DMR reachability is necessary for personalized medicine. By combining time series analysis and mathematical modeling, we developed a mathematical method that accurately predicts patients who do not achieve DMR in the early stages of TKI administration. Our prediction method gives a basis of effective personalized treatments for CML patients.
Hierarchical reactivation of transcription during mitosis-to-G1 transition by Brn2 and Ascl1 in neural stem cells
Authors: Soares Mário A. F. , Soares Diogo S. , Teixeira Vera , Bressan Raul Bardini , Pollard Steven M. , Oliveira Raquel A. , Castro Diogo S.
Published: February 2021

During mitosis, chromatin condensation is accompanied by a global arrest of transcription. Recent studies suggest transcriptional reactivation upon mitotic exit occurs in temporally coordinated waves, but the underlying regulatory principles have yet to be elucidated. In particular, the contribution of sequence-specific transcription factors (TFs) remains poorly understood. Here we report that Brn2, an important regulator of neural stem cell identity, associates with condensed chromatin throughout cell division, as assessed by live-cell imaging of proliferating neural stem cells. By contrast, the neuronal fate determinant Ascl1 dissociates from mitotic chromosomes. ChIP-seq analysis reveals that Brn2 mitotic-chromosome binding does not result in sequence-specific interactions prior to mitotic exit, relying mostly on electrostatic forces. Nevertheless, surveying active transcription using single-molecule RNA-FISH against immature transcripts, indicates the differential presence of TF near chromatin when exiting mitosis is associated with early (anaphase) versus late (early G1) reactivation of key targets of Brn2 and Ascl1, respectively. Moreover, by using a mitotic-specific dominant negative approach, we show that competing with Brn2 binding during mitotic exit reduces the transcription of its target gene Nestin. Our study shows an important role for differential binding of TFs to mitotic chromosomes, governed by their electrostatic properties, in defining the temporal order of transcriptional reactivation during mitosis-to-G1 transition.
ATLASx: a computational map for the exploration of biochemical space
Authors: Mohammadi-Peyhani Homa , Hafner Jasmin , Sveshnikova Anastasia , Viterbo Victor , Hatzimanikatis Vassily
Published: February 2021

Metabolic “dark matter” describes currently unknown metabolic processes, which form a blind spot in our general understanding of metabolism and slow down the development of biosynthetic cell factories and naturally derived pharmaceuticals. Mapping the dark matter of metabolism remains an open challenge that can be addressed globally and systematically by existing computational solutions. In this work, we use 490 generalized enzymatic reaction rules to map both known and unknown metabolic processes around a biochemical database of 1.5 million biological compounds. We predict over 5 million reactions and integrate nearly 2 million naturally and synthetically-derived compounds into the global network of biochemical knowledge, named ATLASx. ATLASx is available to researchers as a powerful online platform that supports the prediction and analysis of novel biochemical pathways and evaluates the biochemical vicinity of molecule classes (https://lcsbdatabases.epfl.ch/Atlas2).
Delayed induction of type I and III interferons mediates nasal epithelial cell permissiveness to SARS-CoV-2
Authors: Hatton Catherine F , Botting Rachel A , Dueñas Maria Emilia , Haq Iram J , Verdon Bernard , Thompson Benjamin J , Spegarova Jarmila Stremenova , Gothe Florian , Stephenson Emily , Gardner Aaron I , Murphy Sandra , Scott Jonathan , Garnett James P , Carrie Sean , Powell Jason , Khan C M Anjam , Huang Lei , Hussain Rafiqul , Coxhead Jonathan , Davey Tracey , Simpson A John , Haniffa Muzlifah , Hambleton Sophie , Brodlie Malcolm , Ward Chris , Trost Matthias , Reynolds Gary , Duncan Christopher J A
Published: February 2021

The nasal epithelium is a plausible entry point for SARS-CoV-2, a site of pathogenesis and transmission, and may initiate the host response to SARS-CoV-2. Antiviral interferon (IFN) responses are critical to outcome of SARS-CoV-2. Yet little is known about the interaction between SARS-CoV-2 and innate immunity in this tissue. Here we applied single-cell RNA sequencing and proteomics to a primary cell model of human nasal epithelium differentiated at air-liquid interface. SARS-CoV-2 demonstrated widespread tropism for nasal epithelial cell types. The host response was dominated by type I and III IFNs and interferon-stimulated gene products. This response was notably delayed in onset relative to viral gene expression and compared to other respiratory viruses. Nevertheless, once established, the paracrine IFN response began to impact on SARS-CoV-2 replication. When provided prior to infection, recombinant IFNβ or IFNλ1 induced an efficient antiviral state that potently restricted SARS-CoV-2 viral replication, preserving epithelial barrier integrity. These data suggest that the IFN-I/III response to SARS-CoV-2 initiates in the nasal airway and suggest nasal delivery of recombinant IFNs to be a potential chemoprophylactic strategy.
Gram-negative outer membrane proteins with multiple β-barrel domains
Authors: Solan Ron , Pereira Joana , Lupas Andrei N. , Kolodny Rachel , Ben-Tal Nir
Published: February 2021

Outer membrane beta barrels (OMBBs) are found in the outer membrane of Gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel β-sheets that close onto themselves, forming pores that traverse the membrane. Currently known structures include only one barrel, of 8-36 strands, per chain. The lack of multi-OMBB chains is surprising, as most OMBBs form oligomers and some function only in this state. Using a combination of sensitive sequence-comparison methods and co-evolutionary analysis tools, we identify many proteins combining multiple beta barrels within a single chain; combinations that include 8-stranded barrels prevail. These multi-barrels seem to be the result of independent, lineage-specific fusion and amplification events. The absence of multi-barrels that are universally conserved in bacteria with an outer membrane, coupled with their frequentde novogenesis suggests that their functions are not essential, but rather beneficial in specific environments. Adjacent barrels of complementary function within the same chain may allow for new functions beyond those of the individual barrels.
Deletion of CD73 increases exercise power in mice
Authors: Aguiar Aderbal S , Speck Ana Elisa , Canas Paula M. , Cunha Rodrigo A.
Published: February 2021

Ecto-5’-nucleotidase or CD73 is the main source of extracellular adenosine involved in the activation of adenosine A2Areceptors, responsible for the ergogenic effects of caffeine. We now investigated the role of CD73 in exercise by comparing female wild-type (WT) and CD73 knockout (KO) mice in a treadmill graded test to evaluate running power, oxygen uptake, and respiratory exchange ratio (RER) – the gold standards characterizing physical performance. Spontaneous locomotion in the open field and submaximal running power andin the treadmill were similar between CD73-KO and WT mice;also demonstrated equivalent aerobic power, but CD73-KO mice displayed a 43.7±4.2% larger critical power (large effect size, P<0.05) and 3.8±0.4% increase of maximum RER (small effect size, P<0.05). Thus, KO of CD73 was ergogenic, i.e., it increased physical performance.
Bioengineering of genetically encoded gene promoter repressed by flavonoids for constructing intracellular sensor for molecular events
Authors: Desmet Nicole M. , Dhusia Kalyani , Qi Wenjie , Doseff Andrea I. , Bhattacharya Sudin , Gilad Assaf A.
Published: February 2021

In recent years, Synthetic Biology has emerged as a new discipline where functions that were traditionally performed by electronic devices are replaced by “cellular devices”. Those are genetically encoded circuits, constructed of DNA that are built from biological parts (aka bio-parts). The cellular devices can be used for sensing and responding to natural and artificial signals. However, a major challenge in the field is that the crosstalk between many cellular signaling pathways use the same signaling endogenous molecules that can result in undesired activation. To overcome this problem, we utilized a specific promoter that can activate genes with a natural, non-toxic ligand at a highly-induced transcription level with low background or undesirable off-target expression. Here we used the orphan aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor that upon activation binds to specific AHR response elements (AHRE) of the Cytochrome P450, family 1, subfamily A, polypeptide 1 (CYP1A1) promoter. Flavonoids have been identified as AHR ligands. Data presented here shows successful creation of a synthetic gene “off” switch that can be monitored directly using an optical reporter gene. This is the first step towards bioengineering of a synthetic, nanoscale bio-part for constructing a sensor for molecular events.
Human breast milk enhances intestinal mucosal barrier function and innate immunity in a pediatric human enteroid model
Authors: Noel Gaelle , In Julie G. , Lemme-Dumit Jose M. , DeVine Lauren R. , Cole Robert N. , Guerrerio Anthony L. , Kovbasnjuk Olga , Pasetti Marcela F.
Published: February 2021

Breastfeeding has been associated with long lasting health benefits. Nutrients and bioactive components of human breast milk promote cell growth, immune development, and shield the infant gut from insults and microbial threats. The molecular and cellular events involved in these processes are ill defined. We have established human pediatric enteroids and interrogated maternal milk’s impact on epithelial cell maturation and function in comparison with commercial infant formula. Colostrum applied apically to pediatric enteroid monolayers reduced ion permeability, stimulated epithelial cell differentiation, and enhanced tight junction function by upregulating occludin expression. Breast milk heightened the production of antimicrobial peptide α-defensin 5 by goblet and Paneth cells, and modulated cytokine production, which abolished apical release of pro-inflammatory GM-CSF. These attributes were not found in commercial infant formula. Epithelial cells exposed to breast milk elevated apical and intracellular pIgR expression and enabled maternal IgA translocation. Proteomic data revealed a breast milk-induced molecular pattern associated with tissue remodeling and homeostasis. Using a novelex vivopediatric enteroid model, we have identified cellular and molecular pathways involved in human milk-mediated improvement of human intestinal physiology and immunity.
Force-Correction Analysis Method for Derivation of Multidimensional Free Energy Landscapes from Adaptively Biased Replica Simulations
Authors: Marinelli Fabrizio , Faraldo-Gómez José D.
Published: February 2021

A methodology is proposed for the calculation of multidimensional free-energy landscapes of molecular systems, based on analysis of multiple Molecular Dynamics trajectories wherein adaptive biases have been applied to enhance the sampling of different collective variables. In this approach, which we refer to as Force Correction Analysis Method (FCAM), local averages of the total and biasing forces are evaluated post-hoc, and the latter are subtracted from the former to obtain unbiased estimates of the mean force across collective-variable space. Multidimensional free-energy surfaces and minimum free-energy pathways are then derived from integration of the mean force landscape through kinetic Monte Carlo algorithm. To evaluate the proposed method, a series of numerical tests and comparisons with existing approaches were carried out for small molecules, peptides, and proteins, based on all-atom trajectories generated with standard, concurrent and replica-exchange Metadynamics in collective-variable spaces ranging from one- to six-dimensional. The tests confirm the correctness of the FCAM formulation and demonstrate that calculated mean forces and free energies converge rapidly and accurately, outperforming other methods used to unbias this kind of simulation data.

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The P3b differentiates parallel physical and rule-based updating of a sensory model
Authors: Schwartze Michael , Bellotti Francesca I. , Kotz Sonja A.
Published: February 2021

The capacity to form and update mental representations of the type and timing of sensory events is a central tenet of adaptive behavior in a dynamically changing environment. An internal model of stimulus contingencies provides a means to optimize behavior through predictive adjustments based on past to future events. To this end, neural and cognitive processes rely on systematic relations between events and use these rules to optimize information processing. The P3 complex of the event-related potential of the electroencephalogram (ERP/EEG) is a well-established and extensively tested index of such mechanisms. Here we investigated the P3b sensitivity to auditory stimulus deviations associated with two updating operations: physical change (switching stimulus pitches) and rule change (switching additive and subtractive target stimulus counting). Participants listened to a variant of the classical oddball sequence consisting of frequent standard (600 Hz) and two equally probable less frequent deviant tones (660 Hz, 540 Hz), keeping count of the deviant tones and switching between addition and subtraction with a pitch change. The results indicate specific amplitude modulations, confirming the P3b as a context-sensitive marker of physical and cognitive components of an internal model. This suggests that the P3b can be used as a differential marker of predictive coding mechanisms.
Phagocytosed polyhedrin-cytokine co-crystal nanoparticles provide sustained secretion of bioactive cytokines from macrophages
Authors: Wendler Astrid , James Nicholas , Jones Michael H , Pernstich Christian
Published: February 2021

Many cells possess the ability to engulf and incorporate particles by phagocytosis. This active process is characteristic of microorganisms as well as higher order species. In mammals, monocytes, macrophages and microglia are among so-called professional phagocytes. In addition, cells such as fibroblast and chondrocytes are classified as non-professional phagocytes. Professional phagocytes play important roles in both the innate and adaptive immune response, wound healing and tissue homeostasis. Consequently, these cells are increasingly studied as targets and vectors of therapeutic intervention to treat a range of diseases. Professional phagocytes are notoriously difficult to transfect limiting their study and manipulation. Consequently, efforts have shifted towards the development of nanoparticles to deliver a cargo to phagocytic cells via phagocytosis. However, this approach carries significant technical challenges, particularly for protein cargos. We have focused on the development of nanoscale co-crystalline protein depots, known as PODS®, that contain protein cargos, including cytokines. Here, we show that PODS are readily phagocytosed by non-professional as well as professional phagocytic cells and have attributes, such as highly sustained release of cargo, that suggest potential utility for the study and exploitation of phagocytic cells for drug delivery. Monocytes and macrophages that ingest PODS retain normal characteristics including a robust chemotactic response. Moreover, the PODS-cytokine cargo is secreted by the loaded cell at a level sufficient to modulate the behavior of surrounding non-phagocytic cells. The results presented here demonstrate the potential of PODS nanoparticles as a novel molecular tool for the study and manipulation of phagocytic cells and for the development of Trojan horse immunotherapy strategies to treat cancer and other diseases.
A genome-scale metabolic model ofSaccharomyces cerevisiaethat integrates expression constraints and reaction thermodynamics
Authors: Oftadeh Omid , Salvy Pierre , Masid Maria , Curvat Maxime , Miskovic Ljubisa , Hatzimanikatis Vassily
Published: February 2021

Eukaryotic organisms play an important role in industrial biotechnology, from the production of fuels and commodity chemicals to therapeutic proteins. To optimize these industrial systems, a mathematical approach can be used to integrate the description of multiple biological networks into a single model for cell analysis and engineering. One of the current most accurate models of biological systems include metabolism and expression (ME-models), and Expression and Thermodynamics FLux (ETFL) is one such formulation that efficiently integrates RNA and protein synthesis with traditional genome-scale metabolic models. However, ETFL is so far only applicable forE. coli. To therefore adapt this ME-model forSaccharomyces cerevisiae, we herein developed yETFL. To do this, we augmented the original formulation with additional considerations for biomass composition, the compartmentalized cellular expression system, and the energetic costs of biological processes. We demonstrated the predictive ability of yETFL to capture maximum growth rate, essential genes, and the phenotype of overflow metabolism. We envision that the extended ETFL formulation can be applied to ME-model development for a wide range of eukaryotic organisms. The utility of these ME-models can be extended into academic and industrial research.
TuMV infection alters miR168/AGO1 and miR403/AGO2 systems regulation in Arabidopsis
Authors: Manacorda Carlos Augusto , Tasselli Sabrina , Marano María Rosa , Asurmendi Sebastian
Published: February 2021

Plant Argonaute proteins, chiefly AGO1 and 2, restrict viral infections. AGO1/2 also participate in developmental processes and are tightly regulated by microRNAs. Under viral infections, the regulatory loop comprising miR168/AGO1 is well studied, but much less so the miR403/AGO2 system. We studied both regulatory systems in TuMV-infected Arabidopsis plants. TuMV downregulated miRNAs precursor molecules, but mature miRNAs overaccumulated, without evidence of transcriptional alteration. AGO1 protein remained at basal levels whereas AGO2 overaccumulated. These results are in line with previous reports studying abiotic and biotic impact on microRNA biogenesis and AGO-dependent antiviral defense, expanding our knowledge of the miR403/AGO2 regulatory system.
Structural effects driven by rare point mutations in amylin hormone, the type II diabetes-associated peptide
Authors: Mendes Wendy S. , Franco Octavio L. , Alencar Sergio A. , Porto William F.
Published: February 2021

Background

Amylin is a 37-amino-acid peptide hormone co-secreted with insulin, which participates in glucose homeostasis. This hormone is able to aggregate in a β-sheet conformation and deposit in islet amyloids, a hallmark in type II diabetes. Since amylin is a gene-encoded hormone, this peptide has variants caused by point mutations that can impact its functions.

Methods

Here, we analyzed the structural effects caused by S20G and G33R point mutations which, according to the 1000 Genomes Project, have frequency in East Asian and European populations, respectively. The analyses were performed by means of aggrescan server, SNP functional effect predictors, and molecular dynamics.

Results

We found that both mutations have aggregation potential and cause changes in the monomeric forms when compared with wild-type amylin. Furthermore, comparative analyses with pramlintide, an amylin drug analogue, allowed us to infer that second α-helix maintenance may be related to the aggregation potential.

Conclusions

The S20G mutation has been described as pathologically related, which is in agreement with our findings. In addition, our data suggest that the G33R mutation might have a deleterious effect. The data presented here also provide new therapy opportunities, whether for creating more effective drugs for diabetes or implementing specific treatment for patients with these mutations.

General Significance

Our data could help to better understand the impact of mutations on the wild-type amylin sequence, as a starting point for the evaluation and characterization of other variations. Moreover, these findings could improve the health of patients with type II diabetes.
Morphogenesis and cell ordering in confined bacterial biofilms
Authors: Zhang Qiuting , Li Jian , Nijjer Japinder , Lu Haoran , Kothari Mrityunjay , Alert Ricard , Cohen Tal , Yan Jing
Published: February 2021

Biofilms are aggregates of bacterial cells surrounded by an extracellular matrix. Much progress has been made in studying biofilm growth on solid substrates; however, little is known about the biophysical mechanisms underlying biofilm development in three-dimensional confined environments, in which the biofilm-dwelling cells must push against and even damage the surrounding environment to proliferate. Here, combining single-cell imaging, mutagenesis, and rheological measurement, we reveal the key morphogenesis steps ofVibrio choleraebiofilms embedded in hydrogels as they grow by four orders of magnitude from their initial size. We show that the morphodynamics and cell ordering in embedded biofilms are fundamentally different from those of biofilms on flat surfaces. Treating embedded biofilms as inclusions growing in an elastic medium, we quantitatively show that the stiffness contrast between the biofilm and its environment determines biofilm morphology and internal architecture, selecting between spherical biofilms with no cell ordering and oblate ellipsoidal biofilms with high cell ordering. When embedded in stiff gels, cells self-organize into a bipolar structure that resembles the molecular ordering in nematic liquid crystal droplets.In vitrobiomechanical analysis shows that cell ordering arises from stress transmission across the biofilm-environment interface, mediated by specific matrix components. Our imaging technique and theoretical approach are generalizable to other biofilm-forming species, and potentially to biofilms embedded in mucus or host tissues as during infection. Our results open an avenue to understand how confined cell communities grow by means of a compromise between their inherent developmental program and the mechanical constraints imposed by the environment.

Significance Statement

Biofilms are microbial cities in which bacterial cells reside in a polymeric matrix. They are commonly found inside soft confining environments such as food matrices and host tissues, against which bacteria must push to proliferate. Here, by combining single-cell live imaging and mechanical characterization, we show that the confining environment determines the dynamics of biofilm shape and internal structure. This self-organized evolution of biofilm architecture is caused by force transmission between the environment and the biofilm, mediated by the extracellular matrix secreted by the cells. Our findings lead to new ways to understand how bacterial communities develop under mechanical constraints, and potentially to new strategies for preventing and controlling biofilm growth in three-dimensional environments.
Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain
Authors: Rafiei Atefeh , Lee Linda , Crowder D. Alex , Saltzberg Daniel J. , Sali Andrej , Brouhard Gary J. , Schriemer David C.
Published: February 2021

Doublecortin (DCX) is a microtubule (MT) associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX remain poorly resolved. Here, we describe the molecular architecture of the DCX-MT complex through an integrative modeling approach that combines data from X-ray crystallography, cryo-EM and a high-fidelity chemical crosslinking method. We demonstrate that DCX interacts with MTs through its N-terminal domain and induces a lattice-dependent self-association involving both the C-terminal structured domain and the C-tails, in a conformation that favors an open, domain-swapped state. The networked state can accommodate multiple different attachment points on the MT lattice, all of which orient the C-tails away from the lattice. As numerous disease mutations cluster in the C-terminus, and regulatory phosphorylations cluster in the C-tail, our study shows that lattice-driven self-assembly is an important property of DCX.
Genomic architecture of 5S rDNA cluster and its variations within and between species
Authors: Ding Qiutao , Li Runsheng , Ren Xiaoliang , Chan Lu-yan , Ho Vincy W. S. , Xie Dongying , Ye Pohao , Zhao Zhongying
Published: February 2021

Ribosomal genes (rDNAs) are arranged in purely tandem repeats, preventing them from being reliably assembled onto chromosome. The uncertainty of rDNA genomic structure presents a significant barrier for studying their function and evolution. Here, we generate ultra-long Nanopore and short NGS reads to delineate the architecture and variation of the 5S rDNA cluster in the different strains ofC. elegansandC. briggsae. We classify the individual rDNA units into 25 types based on the unique sequence variations in each unit ofC. elegans(N2). We next perform manual assembly of the cluster using the long reads that carry these units, which led to an assembly of rDNA cluster consisting of up to 167 5S rDNA units. The ordering and copy number of various rDNA units are indicative of separation time between strains. Surprisingly, we observed a drastically lower level of variation in the 5S rDNA cluster in theC. elegansCB4856 andC. briggsaeAF16 strains thanC. elegansN2 strain, suggesting a unique mechanism in maintaining the rDNA cluster stability in the N2. Single-copy transgenes landed into the rDNA cluster shows the expected expression in the soma, supporting that rDNA genomic environment is transcriptionally compatible with RNA polymerase II. Delineating the structure and variation of rDNA cluster paves the way for its functional and evolutionary studies.
Pyrazinamide action is driven by the cell envelope stress response in Mycobacterium tuberculosis
Authors: Thiede Joshua M. , Dillon Nicholas A. , Howe Michael D. , Aflakpui Ranee , Modlin Samuel J. , Hoffner Sven E. , Valafar Faramarz , Minato Yusuke , Baughn Anthony D.
Published: February 2021

Pyrazinamide (PZA) plays a crucial role in first-line tuberculosis drug therapy. Unlike other antimicrobial agents, PZA is only active against Mycobacterium tuberculosis at low pH. The basis for this conditional drug susceptibility remains undefined. In this study, we utilized a genome-wide approach to interrogate potentiation of PZA action. We find that mutations in numerous genes involved in central metabolism as well as cell envelope maintenance and stress response are associated with PZA resistance. Further, we demonstrate that constitutive activation of the cell envelope stress response can drive PZA susceptibility independent of environmental pH. Consequently, treatment with peptidoglycan synthesis inhibitors, such as beta-lactams and D-cycloserine, potentiate PZA action through triggering this response. These findings illuminate a regulatory mechanism for conditional PZA susceptibility and reveals new avenues for enhancing potency of this important drug through targeting activation of the cell envelope stress response.
Sensitive, reliable, and robust circRNA detection from RNA-seq with CirComPara2
Authors: Gaffo Enrico , Buratin Alessia , Molin Anna Dal , Bortoluzzi Stefania
Published: February 2021

Circular RNAs (circRNAs) are a large class of covalently closed RNA molecules that originate by a process called back-splicing. CircRNAs are emerging as functional RNAs involved in the regulation of biological processes as well as in disease and cancer mechanisms. Current computational methods for circRNA identification from RNA-seq experiments are characterised by low discovery rates and performance dependent on the analysed data set. We developed a new automated computational pipeline, CirComPara2 (https://github.com/egaffo/CirComPara2), that consistently achieves high recall rates without losing precision by combining multiple circRNA detection methods. In our benchmark analysis, CirComPara2 outperformed state-of-the-art circRNA discovery tools and proved to be a reliable and robust method for comprehensive transcriptomics characterisation.
Dynamic selective auditory attention detection using RNN and reinforcement learning
Authors: Geravanchizadeh Masoud , Roushan Hossein
Published: February 2021

The cocktail party phenomenon describes the ability of the human brain to focus auditory attention on a particular stimulus while ignoring other acoustic events. Selective auditory attention detection (SAAD) is an important issue in the development of brain-computer interface systems and cocktail party processors. This paper proposes a new dynamic attention detection system to process the temporal evolution of the input signal. The proposed dynamic SAAD is modeled as a sequential decision-making problem, which is solved by recurrent neural network (RNN) and reinforcement learning methods of Q-learning and deep Q-learning. Among different dynamic learning approaches, the evaluation results show that the deep Q-learning approach with RNN as agent provides the highest classification accuracy (94.2%) with the least detection delay. The proposed SAAD system is advantageous, in the sense that the detection of attention is performed dynamically for the sequential inputs. Also, the system has the potential to be used in scenarios, where the attention of the listener might be switched in time in the presence of various acoustic events.
TransPi – a comprehensive TRanscriptome ANalysiS PIpeline forde novotranscriptome assembly
Authors: Rivera-Vicéns R.E. , Garcia-Escudero C.A. , Conci N. , Eitel M. , Wörheide G.
Published: February 2021

The use of RNA-Seq data and the generation ofde novotranscriptome assemblies have been pivotal for studies in ecology and evolution. This is distinctly true for non-model organisms, where no genome information is available. Nevertheless, studies of differential gene expression, DNA enrichment baits design, and phylogenetics can all be accomplished with the data gathered at the transcriptomic level. Multiple tools are available for transcriptome assembly, however, no single tool can provide the best assembly for all datasets. Therefore, a multi assembler approach, followed by a reduction step, is often sought to generate an improved representation of the assembly. To reduce errors in these complex analyses while at the same time attaining reproducibility and scalability, automated workflows have been essential in the analysis of RNA-Seq data. However, most of these tools are designed for species where genome data is used as reference for the assembly process, limiting their use in non-model organisms. We present TransPi, a comprehensive pipeline forde novotranscriptome assembly, with minimum user input but without losing the ability of a thorough analysis. A combination of different model organisms, k-mer sets, read lengths, and read quantities were used for assessing the tool. Furthermore, a total of 49 non-model organisms, spanning different phyla, were also analyzed. Compared to approaches using single assemblers only, TransPi produces higher BUSCO completeness percentages, and a concurrent significant reduction in duplication rates. TransPi is easy to configure and can be deployed seamlessly using Conda, Docker and Singularity.
Development of distance education in Chinese higher education in perspectives of accessibility, quality and equity under COVID-19
Authors: Chen Ying , Hou Angela Yung Chi , Huang Lei
Published: February 2021

Purpose

This paper aimed to explore the development of distance education (DE) in Chinese higher education as well as the three significant themes: accessibility, quality and equity in Chinese DE and the performance of these three themes in Chinese DE.

Design/methodology/approach

Document analysis was used as the major research method in this study to examine the development and challenges in terms of accessibility, quality and equity in Chinese DE. In this study, national-level official policy documents and reports from the Chinese government were collected and analyzed. Also, scientific articles from CNKI were analyzed to find out the evolution of the Frontier topics on Chinese DE in accessibility, quality and equity.

Findings

There are three major findings. First, the Chinese government has shown its positive attitude toward DE in higher education. Second, compared with the other two themes: quality and equity; the number of articles in the accessibility of DE was lower than the other two themes and the problems of accessing online courses were insufficiently caused by two reasons due to lack of basic ICT literacy and poor Internet infrastructure. Third, there was a gap between Chinese policies and research articles mainly because of the unbalanced development of accessibility in policy management and research articles.

Research limitations/implications

Although this paper has summarized the development of the DE in Chinese higher education, it was clear that accessibility, quality and equity were three critical issues in DE. However, there are still other essential factors that contribute to the development of DE that requires further investigation, such as learner satisfaction, different features of learning platforms and instructional strategy.

Practical implications

The findings of this paper can be used to identify the attitude toward the DE of the Chinese government. Besides, the accessibility could be a research and practical focus for Chinese DE in the future.

Originality/value

This study showed some significant policies released by the Chinese government toward DE in higher education and revealed the achievements, trends and challenges in the accessibility, quality and equity of Chinese DE.