bluuebunny/crossref_metadata_2025 huggingface dataset:
Supervised machine learning with feature selection for prioritization of targets related to time-based cellular dysfunction in aging
Authors: Truter Nina , van Rensburg Zuné Jansen , Oudrhiri Radouane , Singh Raminderpal , Louw Carla
Published: June 2022

Background

Global life expectancy has been increasing without a corresponding increase in health span and with greater risk for aging-associated diseases such as Alzheimer’s disease (AD). An urgent need to delay the onset of aging-associated diseases has arisen and a dramatic increase in the number of potential molecular targets has led to the challenge of prioritizing targets to promote successful aging. Here, we developed a pipeline to prioritize aging-related genes which integrates the plethora of publicly available genomic, transcriptomic, proteomic and morphological data of C. elegans by applying a supervised machine learning approach. Additionally, a unique biological post-processing analysis of the computational output was performed to better reveal the prioritized gene’s function within the context of pathways and processes involved in aging across the lifespan of C. elegans.

Results

Four known aging-related genes — daf-2, involved in insulin signaling; let-363 and rsks-1, involved in mTOR signaling; age-1, involved in PI3 kinase signaling — were present in the top 10% of 4380 ranked genes related to different markers of cellular dysfunction, validating the computational output. Further, our ranked output showed that 91% of the top 438 ranked genes consisted of known genes on GenAge, while the remaining genes had thus far not yet been associated with aging-related processes.

Conclusion

These ranked genes can be translated to known human orthologs potentially uncovering previously unknown information about the basic aging processes in humans. These genes (and their downstream pathways) could also serve as targets against aging-related diseases, such as AD.
Photografted zwitterionic hydrogel coating durability for reduced foreign body response to cochlear implants
Authors: Peel Adreann , Bennion Douglas M. , Horne Ryan , Hansen Marlan R. , Guymon C. Allan
Published: June 2022

Objective

Durability of photografted zwitterionic hydrogel coatings on cochlear implant biomaterials was examined to determine viability of these antifouling surfaces during insertion and long-term implant usage. Approach: Tribometry was used to determine the effect of zwitterionic coatings on lubricity of surfaces with varying hydration level, applied normal force, and timeframe. Additionally, flexural resistance was investigated using mandrel bending.Ex vivodurability was assessed by determining coefficient of friction between tissues and treated surfaces. Furthermore, cochlear implantation force was measured using cadaveric human cochleae. Main results: Hydrated zwitterionic hydrogel coatings reduced frictional resistance approximately 20-fold compared to uncoated PDMS, which importantly led to significantly lower mean force experienced by coated cochlear implants during insertion compared to uncoated systems. Under flexural force, zwitterionic films resisted failure for up to 60 minutes of desiccation. The large increase in lubricity was maintained for 20 hours under continual force while hydrated. For loosely crosslinked systems, films remained stable and lubricious even after rehydration following complete drying. All films remained hydrated and functional under frictional force for at least 30 minutes in ambient conditions while drying, with lower crosslink densities showing the greatest longevity. Moreover, photografted zwitterionic hydrogel samples showed no evidence of degradation and nearly identical lubricity before and after implantation. Significance: This work demonstrates that photografted zwitterionic hydrogel coatings are sufficiently durable to maintain viability before, during, and after implantation. Mechanical properties, including greatly increased lubricity, are preserved after complete drying and rehydration for various applied forces. Additionally, this significantly enhanced lubricity translates to significantly decreased force during insertion of implants which should result in less trauma and scarring.
Expression Microdissection for use in qPCR based analysis of miRNA in a single cell type
Authors: Jenike Ana E. , Bunkelman Brady , Perzel Mandell Kira A. , Oduor Cliff , Chin Deborah , Mair Devin , Jenike Katharine M. , Kim Deok-Ho , Bailey Jeffrey A. , Rafailovich Miriam H. , Rosenberg Avi Z. , Halushka Marc K.
Published: June 2022

Cell-specific microRNA (miRNA) expression estimates are important in characterizing the localization of miRNA signaling within tissues. Much of this data is obtained from cultured cells, a process known to significantly alter miRNA expression levels. Thus, our knowledge of in vivo cell miRNA expression estimates is poor. We previously demonstrated expression microdissection-miRNA-sequencing (xMD-miRNA-seq) as a means to acquire in vivo estimates, directly from formalin fixed tissues, albeit with limited yield. Here we optimized each step of the xMD process including tissue retrieval, tissue transfer, film preparation, and RNA isolation to increase RNA yields and ultimately show strong enrichment for in vivo miRNA expression by qPCR array. These method improvements, including the development of a non-crosslinked ethylene vinyl acetate (EVA) membrane, resulted in a 23-45 fold increase in miRNA yield, depending on cell type. By qPCR, miR-200a was increased 14-fold in xMD-derived small intestine epithelial cells, with a concurrent 336-fold reduction in miR-143, relative to the matched non-dissected duodenal tissue. xMD is now an optimized method to obtain robust in vivo miRNA expression estimates from cells.
Mapping the semi-nested community structure of 3D chromosome contact networks
Authors: Bernenko Dolores , Lee Sang Hoon , Stenberg Per , Lizana Ludvig
Published: June 2022

Mammalian DNA folds into 3D structures that facilitate and regulate genetic processes such as transcription, DNA repair, and epigenetics. Several insights derive from chromosome capture methods, such as Hi-C, which allow researchers to construct contact maps depicting 3D interactions among all DNA segment pairs. These maps show a complex cross-scale organization spanning megabase-pair compartments to short-ranged DNA loops. To better understand the organizing principles, several groups analyzed Hi-C data assuming a Russian-doll-like nested hierarchy where DNA regions of similar sizes merge into larger and larger structures. Apart from being a simple and appealing description, this model explains, e.g., the omnipresent chequerboard pattern seen in Hi-C maps, known as A/B compartments, and foreshadows the co-localization of some functionally similar DNA regions. However, while successful, this model is incompatible with the two competing mechanisms that seem to shape a significant part of the chromosomes’ 3D organization: loop extrusion and phase separation. This paper aims to map out the chromosome’s actual folding hierarchy from empirical data. To this end, we take advantage of Hi-C experiments and treat the measured DNA-DNA interactions as a weighted network. From such a network, we extract 3D communities using the generalized Louvain algorithm. This algorithm has a resolution parameter that allows us to scan seamlessly through the community size spectrum, from A/B compartments to topologically associated domains (TADs). By constructing a hierarchical tree connecting these communities, we find that chromosomes are more complex than a perfect hierarchy. Analyzing how communities nest relative to a simple folding model, we found that chromosomes exhibit a significant portion of nested and non-nested community pairs alongside considerable randomness. In addition, by examining nesting and chromatin types, we discovered that nested parts are often associated with active chromatin. These results highlight that crossscale relationships will be essential components in models aiming to reach a deep understanding of the causal mechanisms of chromosome folding.
Learning to learn online with neuromodulated synaptic plasticity in spiking neural networks
Authors: Schmidgall Samuel , Hays Joe
Published: June 2022

We propose that in order to harness our understanding of neuroscience toward machine learning, we must first have powerful tools for training brain-like models of learning. Although substantial progress has been made toward understanding the dynamics of learning in the brain, neuroscience-derived models of learning have yet to demonstrate the same performance capabilities as methods in deep learning such as gradient descent. Inspired by the successes of machine learning using gradient descent, we demonstrate that models of neuromodulated synaptic plasticity from neuroscience can be trained in Spiking Neural Networks (SNNs) with a framework of learning to learn through gradient descent to address challengingonlinelearning problems. This framework opens a new path toward developing neuroscience inspired online learning algorithms.
PhysiCell training apps: A case study for creating interactive training materials for scientific software packages
Authors: Sundus Aneequa , Kurtoglu Furkan , Konstantinopoulos Kali , Chen Mary , Willis Drew , Heiland Randy , Macklin Paul
Published: June 2022

Cell-based tissue simulations require not only the ability to write new code in a simulation framework, but also an understanding of underlying mathematical models, background biology, and parameters for each behavior of an agent. This can entail a steep learning curve for interdisciplinary researchers joining computational biology research. We have created a suite of cloud-hosted open-source tools to separately explore and learn key components of an agent-based cellular simulation framework. This creates an self-contained environment to learn and test functions of cells and the micro-environment in a modular fashion before creating more detailed, research-focused simulation models.
Are cell wall traits a component of the succulent syndrome?
Authors: Fradera-Soler Marc , Leverett Alistair , Mravec Jozef , Jørgensen Bodil , Borland Anne M. , Grace Olwen M.
Published: June 2022

Succulence is an adaptation to low water availability characterised by the presence of water-storage tissues that alleviate water stress under low water availability. The succulent syndrome has evolved convergently in over 80 plant families and is associated with anatomical, physiological and biochemical traits. Despite the alleged importance of cell wall traits in drought responses, their significance in the succulent syndrome has long been overlooked. Here, by analysing published pressure–volume curves, we show that elastic adjustment, whereby plants change cell wall elasticity, is uniquely beneficial to succulents for avoiding turgor loss. In addition, we used comprehensive microarray polymer profiling (CoMPP) to assess the biochemical composition of cell walls in leaves. Across phylogenetically diverse species, we uncover several differences in cell wall biochemistry between succulent and non-succulent leaves, pointing to the existence of a ‘succulent glycome’. We also highlight the glycomic diversity among succulent plants, with some glycomic features being restricted to certain succulent lineages. In conclusion, we suggest that cell wall biomechanics and biochemistry should be considered among the characteristic traits that make up the succulent syndrome.
Renal ischemia-reperfusion injury attenuated by exosomes extracted from splenic ischemic preconditioning
Authors: Hongtao Liu , Ye Shen
Published: June 2022

Objective

To investigate the protective effects of the exosomes extracted from splenic ischemic preconditioning (sIPC) on renal ischemia-reperfusion (IR) injury.

Materials and methods

Splenic ischemic preconditioning(sIPC)was conducted on mice in vivo 24 hours before the start of renal ischemia-reperfusion (IR) injury experiment, and serum exosomes derived from sIPC mice were infused into the mice model of renal ischemia-reperfusion injury. The kidney tissue and serum were collected 24 hours later. The morphological changes and inflammation in ischemia-reperfusion kidneys were determined by hematoxylin-eosin (HE) staining.Then the apoptosis of kidney tissue sections were detected by TUNEL staining, Ki-67 immunohistochemical staining was used to assess the proliferation.In addition, the levels of pro-inflammatory cytokines including TNF-α, IL-1β and SCr in serum were measured by ELISA.

In vitro, we extracted exosomes from mouse spleen fibroblasts pretreated with hypoxia and reoxygenation (H/R) and administered them to mouse renal epithelial cells.Furthermore, for the hypoxia-reoxygenation model of renal epithelial cells, TUNEL and flow cytometry were used to evalutaed cell apoptosis;Then ELISA was used to measure the levels of TNF-α and IL-1β in the cell supernatant, Bax and Bcl-2 were measured by Western Blotting.

Results

HE staining showed that the renal injury caused by ischemia-reperfusion attenuated after sIPC. TUNEL staining showed that renal tissue apoptosis was greatly reduced after sIPC or injection of exosomes extracted from splenic fibroblast hypoxia-reoxygenation model. Ki-67 staining showed that the positive rates of IRI+sIPC group, IRI+mSF(H/R)-exo group, IRI+mSF(H/R+PBS)-exo group were close, higher than IRI group but lower than sham group. ELISA test of kidney tissue showed that the serum creatinine, TNF-α and IL-1β induced by IRI decreased with sIPC and addition of the above-mentioned exosomes.In vitro, the exosomes extracted from the hypoxia-reoxygenation model of splenic fibroblasts had the same protective effect on hypoxia-reoxygenated mouse renal epithelial cells model, and this protective effect disappears after the addition of exosome inhibitors.TUNEL and flow cytometry showed that the exosomes reduced the apoptosis. The ELISA test results showed that the levels of TNF-α and IL-1β in the H/R group increased significantly, but decreased due to the splenic fibroblast exosomes treated with starvation.While the exosome inhibitors inhibited the effects of exosomes.Western blot results showed that the Bax expression level of the H/R group increased, and the Bcl-2 decreased.While the starvation-treated splenic fibroblast exosomes decreased the Bax level and increased the Bcl-2 level.

Conclusions

The exosomes extracted from splenic ischemic preconditioning exerted a protective capacity to attenuate renal IR injury.
A topological method of generating action potentials and EEG oscillations in a surface network
Authors: Sen Siddhartha
Published: June 2022

A wide variety of electrical activities are observed to occur in the brain. They include one dimensional voltage pulses (action potentials) that propagate along nerve fibers, transient localized oscillations, and persistent surface waveforms oscillating in five distinct frequency bands, called EEG waveforms. However, although a satisfactory theory for propagating pulses exists a unified theoretical framework for modeling all its excitations is lacking. In this paper we construct a special surface network in which all observed brain-like signals can be generated by topological means. The network has surface electrons,is, as we will prove, an exact topological surface representation of the unknown intricate connectivity architecture of the brain’s nerve fibers, and its surface has a mathematical representation. A dynamical law which requires that all input and out put signals of the network respect the mathematical structure of the surface is used to study the network. Using this law it is shown that all brain-like signals can be generated by input signals that locally deform the surface of a subunit of the network, transiently, reducing its topology to that of a sphere. The topological spheres thus produced have surface voltage oscillating waveforms in five theoretically determined frequencies bands and are identified as EEG waveforms. Methods for analyzing these waveforms are developed and used to explain their observed deep sleep structures and determine their properties.
Accurate and efficient protein sequence design through learning concise local environment of residues
Authors: Huang Bin , Fan Tingwen , Wang Kaiyue , Zhang Haicang , Yu Chungong , Nie Shuyu , Qi Yangshuo , Zheng Wei-Mou , Han Jian , Fan Zheng , Sun Shiwei , Ye Sheng , Yang Huaiyi , Bu Dongbo
Published: June 2022

Protein sequence design has been widely applied in rational protein engineering and increasing the design accuracy and efficiency is highly desired. Here we present ProDESIGN-LE, an accurate and efficient design approach, which adopts a concise but informative representation of residue’s local environment and trains a transformer to select an appropriate residue at a position from its local environment. ProDESIGN-LE iteratively applies the transformer on the positions in the target structure, eventually acquiring a designed sequence with all residues fitting well with their local environments. ProDESIGN-LE designed sequences for 68 naturally occurring and 129 hallucinated proteins within 20 seconds per protein on average, and the predicted structures from the designed sequences perfectly resemble the target structures with state-of-the-art average TM-score exceeding 0.80. We further experimentally validated ProDESIGN-LE by designing five sequences for an enzyme, chloramphenicol O-acetyltransferase type III (CAT III), and recombinantly expressing the proteins in E. coli. Of these proteins, three exhibited excellent solubility, and one yielded monomeric species with circular dichroism spectra consistent with the natural CAT III protein.
Accurate background reduction in adaptive optical 3D-STED nanoscopy by dynamic phase switching
Authors: Tu Shijie , Liu Xin , Yuan Difu , Tao Wenli , Han Yubing , Shi Yan , Li Yanghui , Kuang Cuifang , Liu Xu , Yao Yufeng , Xu Yesheng , Hao Xiang
Published: June 2022

Stimulated emission depletion (STED) fluorescence nanoscopy allows the three-dimensional (3D) visualization of nanoscale subcellular structures, providing unique insights into their spatial organization. However, 3D-STED imaging and quantification of dense features are obstructed by the low signal-to-background ratio (SBR), resulting from optical aberrations and out-of-focus background. Here, combining with adaptive optics, we present an easy-to-implement and flexible method to improve SBR by dynamic phase switching. By switching to a counterclockwise vortex phase mask and a top-hat one with an incorrect inner radius, the depletion pattern features a nonzero-intensity center, enabling accurate background recordings. When the recorded background is subtracted from the aberration-corrected 3D-STED image, the SBR in dense sample areas can be improved by a factor of 3–6 times. We demonstrate our method on various dense subcellular structures, showing more advantages than the software-based background subtraction algorithms.

Abstract Figure
Intense sexual conflict affects the female choice strategy in the gregarious desert locust
Authors: Golov Y. , Lavy O. , Halon E. , Rillich J. , Ayali A. , Harari A
Published: June 2022

Disclaimer statement

The authors have withdrawn their manuscript due to disagreement of several aspects regarding the interpretation of the results reported in this paper. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Chronic infection control relies on T cells with lower foreign antigen binding strength generated by N-nucleotide diversity
Authors: Jamaleddine Hassan , Rogers Dakota , Perreault Geneviève , Mandl Judith N. , Khadra Anmar
Published: June 2022

The pathogens to which T cells respond is determined by the T cell receptors (TCRs) present in an individual’s repertoire. Although more than 90% of the TCR repertoire is generated by terminal deoxynucleotidyl transferase (TdT)-mediated N-nucleotide addition during V(D)J recombination, the benefit of TdT-modified TCRs remains unclear. Here, we computationally and experimentally investigated whether TdT systematically modifies the affinity distribution of a TCR repertoire in ways that impacts acute or chronic infection. Our computational model predicts a shift toward low-affinity T cells over time during chronic, but not acute, infections. Elimination of low-affinity T cellsin silicosubstantially delayed chronic infection clearance. Corroborating an affinity-centric benefit for TCR diversity, we showed that infection of TdT-deficient mice delayed the clearance of a chronic viral pathogen, while acute viral control was unaffected. Our data thus suggest that TdT-mediated TCR diversity is of particular benefit in the control of prolonged pathogen replication.
Intrinsic Neural Timescales in Autism Spectrum Disorder and Schizophrenia. A Replication and Direct Comparison Study
Authors: Uscătescu Lavinia Carmen , Kronbichler Martin , Said-Yürekli Sarah , Kronbichler Lisa , Calhoun Vince , Corbera Silvia , Bell Morris , Pelphrey Kevin , Pearlson Godfrey , Assaf Michal
Published: June 2022

Intrinsic neural timescales (INT) reflect the duration for which brain areas store information. A posterior – anterior hierarchy of increasingly longer INT has been revealed in both typically developed individuals (TD), as well as patients diagnosed with autism spectrum disorder (ASD) and schizophrenia (SZ), though INT are, overall, shorter in both patient groups. In the present study, we attempted to replicate previously reported group differences by comparing INT of TD to ASD and SZ. We replicated the previously reported result showing reduced INT in the left lateral occipital gyrus and the right post-central gyrus in SZ compared to TD. For the first time, we also directly compared the INT of the two patient groups and found that these same two areas show significantly reduced INT in SZ compared to ASD. In ASD, significant correlations were found between INT and their clinical and phenotypic characteristics. Our results point to the left lateral occipital gyrus and the right post-central gyrus as holding potential for further diagnostic refinement of SZ.
Mechanism of the ANT-mediated transport of fatty acid anions across the inner mitochondrial membrane
Authors: Kreiter Jürgen , Brkljača Zlatko , Škulj Sanja , Bardakji Sarah , Vazdar Mario , Pohl Elena E.
Published: June 2022

The additional protonophoric function of the mitochondrial adenine nucleotide translocase (ANT1) is now recognized. However, the molecular mechanism remains controversial. Fatty acid (FA) cycling hypothesis postulates that FAs transport protons across the inner mitochondrial membrane to the matrix by a flip-flop, whereas ANT1 facilitates the translocation of FA anions (FA-) back to the intermembrane space. By a combined approach involving measurements of current through the planar lipid bilayers reconstituted with recombinant ANT1, site-directed mutagenesis and molecular dynamics simulations, we show that FA- is initially caught by R59 on the matrix side of ANT1, then moves along the positively charged protein-lipid interface, and binds to R79, where it is protonated in the hydrated cavity in the presence of D134. R79 is crucial for the competitive binding of ANT1 substrates (ATP and ADP) and inhibitors (carboxyatractyloside, bongkrekic acid). The binding sites are well-conserved in mitochondrial SLC25 members, implying a general transporting mechanism for FA anions.
Epo-IGF1R crosstalk expands stress-specific progenitors in regenerative erythropoiesis and myeloproliferative neoplasm
Authors: Hsieh Hsi-Hsien , Yao Huiyu , Ma Yue , Zhang Yuannyu , Xiao Xue , Stephens Helen , Chung Stephen S. , Xu Lin , Xu Jian , Rampal Raajit K. , Huang Lily Jun-shen
Published: June 2022

We find that in regenerative erythropoiesis, the erythroid progenitor landscape is reshaped, and a previously undescribed progenitor population with CFU-E activity (stress CFU-E/sCFU-E) is markedly expanded to restore the erythron. sCFU-E are targets of erythropoietin (Epo) and sCFU-E expansion requires signaling from the Epo receptor (EpoR) cytoplasmic tyrosines. Molecularly, Epo promotes sCFU-E expansion via JAK2/STAT5-dependent expression of IRS2, thus engaging the pro-growth signaling from the IGF1 receptor (IGF1R). Inhibition of IGF1R/IRS2 signaling impairs sCFU-E cell growth, whereas exogenous IRS2 expression rescues cell growth in sCFU-E expressing truncated EpoR lacking cytoplasmic tyrosines. This sCFU-E pathway is the major pathway involved in erythrocytosis driven by the oncogenic JAK2 mutant, JAK2(V617F), in myeloproliferative neoplasm. Inability to expand sCFU-E cells by truncated EpoR protects against JAK2(V617F)-driven erythrocytosis. In myeloproliferative neoplasm patient samples, the number of sCFU-E like cells increases, and inhibition of IGR1R/IRS2 signaling blocks Epo-hypersensitive erythroid cell colony formation. In summary, we identify a new stress-specific erythroid progenitor cell population that links regenerative erythropoiesis to pathogenic erythrocytosis.

Key Points

Epo-induced IRS2 allows engagement of IGF1R signaling to expand a previously unrecognized progenitor population in erythropoietic stress.

Truncated EpoR does not support stress CFU-E expansion and protects against JAK2(V617F)-driven erythrocytosis in MPN.
fimpera: drastic improvement of Approximate Membership Query data-structures with counts
Authors: Robidou Lucas , Peterlongo Pierre
Published: June 2022

Motivation

High throughput sequencing technologies generate massive amounts of biological sequence datasets as costs fall. One of the current algorithmic challenges for exploiting these data on a global scale consists in providing efficient query engines on these petabyte-scale datasets. Most methods indexing those datasets rely on indexing words of fixed lengthk, calledk-mers. Many applications, such as metagenomics, require the abundance of indexedk-mers as well as their simple presence or absence, but no method scales up to petabyte-scaled datasets. This deficiency is primarily because storing abundance requires explicit storage of thek-mers in order to associate them with their counts. Using counting Approximate Membership Queries (cAMQ) data structures, such as counting Bloom filters, provides a way to index large amounts ofk-mers with their abundance, but at the expense of a sensible false positive rate.

Results

We propose a novel algorithm, calledfimpera, that enables the improvement of any cAMQ performance. Applied to counting Bloom filters, our proposed algorithm reduces the false positive rate by two orders of magnitude and it improves the precision of the reported abundances. Alternatively, fimpera allows for the reduction of the size of a counting Bloom filter by two orders of magnitude while maintaining the same precision.fimperadoes not introduce any memory overhead and may even reduces the query time.

Availability

https://github.com/lrobidou/fimpera

Supplementary information

Supplementary data are available atBioinformaticsonline.
Modeling and inference of spatial intercellular communications and multilayer signaling regulations using stMLnet
Authors: Cheng Jinyu , Yan Lulu , Nie Qing , Sun Xiaoqiang
Published: June 2022

Multicellular organisms require intercellular and intracellular signaling to coordinately regulate different cell functions. Although many methods of cell-cell communication (CCC) inference have been developed, they seldom account for both the intracellular signaling responses and global spatial information. The recent advancement of spatial transcriptomics (ST) provides unprecedented opportunities to better decipher CCC signaling and functioning. In this paper, we propose anST-basedmultilayernetwork method, stMLnet, for inferring spatial intercellular communication and multilayer signaling regulations by quantifying distance-weighted ligand–receptor signaling activity based on diffusion and mass action models and mapping it to intracellular targets. We benchmark stMLnet with existing methods using simulation data and 8 real datasets of cell type-specific perturbations. Furthermore, we demonstrate the applicability of stMLnet on six ST datasets acquired with four different technologies (e.g., seqFISH+, Slide-seq v2, MERFIS and Visium), showing its effectiveness and reliability on ST data with varying spatial resolutions and gene coverages. Finally, stMLnet identifies positive feedback circuits between alveolar epithelial cells, macrophages, and monocytes via multilayer signaling pathways within a COVID-19 microenvironment. Our proposed method provides an effective tool for predicting multilayer signaling regulations between interacting cells, which can advance the mechanistic and functional understanding of spatial CCCs.
Biofilms with a dash of color: A hands-on activity for school students to build a biofilm model, and use it to understand antibiotic tolerance in biofilms
Authors: Kadam Snehal , Methwani Kashish , Kaushik Karishma S
Published: June 2022

It is increasingly recognized that microbes, such as bacteria, exist in communities or biofilms, both in the environment and human body. However, school biology curriculum continues to focus on the free-floating form of bacterial life, with minimal descriptions of biofilms. Consequently, there is a need to introduce biofilms to school students, to not only to develop a fundamental understanding of microbial life, but to also highlight the challenges posed by biofilm infections to antibiotic treatment. We have developed a hands-on activity in which students build a biofilm model, and use it to understand the role of the extracellular matrix in the antibiotic tolerance of biofilms. The activity uses simple, easy to obtain supplies, and can be conducted in an in-person or virtual format, with students participating from school or home. We conducted the activity in virtual mode for a group of 59 school students across India, and present feedback and learnings that could be used to execute and adapt this accessible and engaging science experience.
Deep Learning Explains the Biology of Branched Glycans from Single-Cell Sequencing Data
Authors: Qin Rui , Mahal Lara K. , Bojar Daniel
Published: June 2022

Glycosylation is ubiquitous and often dysregulated in disease. However, the regulation and functional significance of various types of glycosylation at cellular levels is hard to unravel experimentally. Multi-omics, single-cell measurements such as SUGAR-seq, which quantifies transcriptomes and cell surface glycans, facilitate addressing this issue. Using SUGAR-seq data, we pioneered a deep learning model to predict the glycan phenotypes of cells (mouse T lymphocytes) from transcripts, with the example of predicting β1,6GlcNAc-branching across T cell subtypes (test set F1 score: 0.9351). Model interpretation via SHAP (SHapley Additive exPlanations) identified highly predictive genes, in part known to impact (i) branched glycan levels and (ii) the biology of branched glycans. These genes included physiologically relevant low-abundance genes that were not captured by conventional differential expression analysis. Our work shows that interpretable deep learning models are promising for uncovering novel functions and regulatory mechanisms of glycans from integrated transcriptomic and glycomic datasets.
Morphological integrity of insulin amyloid-like aggregates depends on preparation methods and post-production treatments
Authors: Thorlaksen Camilla , Stanciu Adriana-Maria , Neergaard Martin Busch , Hatzakis Nikos , Foderà Vito , Groenning Minna
Published: June 2022

Protein aggregates are often varying extensively in their morphological characteristics, which may lead to various biological outcomes related to e.g., immunogenicity risk. However, isolation of aggregates with a specific morphology within an ensemble is often challenging. To gain vital knowledge on the effects of aggregate characteristics, samples containing a single morphology must be produced by direct control of the aggregation process. Moreover, the formed aggregates need to be in a solvent suitable for biological assays, while keeping their morphology intact. Here we evaluated the dependence of morphology and integrity of amyloid-like fibrils and spherulites on preparation conditions and post-treatment methods. Samples containing either amyloid-like fibrils or spherulites produced from human insulin in acetic acid solutions are dependent on the presence of salt (NaCl). Moreover, mechanical shaking (600 rpm) inhibits spherulite formation, while only affecting the length of the formed fibrils compared to quiescent conditions. Besides shaking, the initial protein concentration in the formulation was found to control fibril length. Surprisingly, exchanging the solvent used for aggregate formation to a physiologically relevant buffer, had a striking effect on the morphological integrity of the fibril and spherulite samples. Especially the secondary structure of one of our spherulite samples presented dramatic changes of the aggregated β-sheet content after solvent exchange, emphasizing the importance of the aggregate stability. These results and considerations have profound implications on the data interpretation and should be implemented in the workflow for both fundamental characterization of aggregates as well as assays for evaluation of their corresponding biological effects.
Massive accumulation of strontium and barium in diplonemid protists
Authors: Pilátová Jana , Tashyreva Daria , Týč Jiří , Vancová Marie , Hussain Bokhari Syed Nadeem , Skoupý Radim , Klementová Mariana , Küpper Hendrik , Mojzeš Peter , Lukeš Julius
Published: June 2022

Barium (Ba) and strontium (Sr) are often used as proxies for the reconstruction of past marine productivity and global climate. The ability to accumulate Ba2+ and Sr2+ in the form of crystals is rare among eukaryotes. Here we report that unicellular heterotrophs called diplonemids (Euglenozoa), one of the most abundant groups of marine planktonic protists, accumulate conspicuous amounts of these trace elements in the form of intracellular barite (BaSO4) and celestite (SrSO4) crystals, in concentrations greater than in other known Ba/Sr-accumulating organisms. Moreover, these flagellates can uptake Sr2+ exclusively or together with Ba2+ and form (Ba,Sr)SO4. One species, Namystinia karyoxenos, is naturally capable of intracellular accumulation of Ba2+ and Sr2+ 42,000 and 10,000 times relative to the surrounding medium. Altering the amounts of both elements in the medium resulted in corresponding changes in the quantity and composition of crystals. Planktonic copepods fed with diplonemids produce celestite-rich fecal pellets, which facilitate deposition of these minerals on the seafloor. We propose that diplonemids, which emerged during the Neoproterozoic era, qualify as impactful players of Ba2+/Sr2+ cycling in the ocean that possibly contributed to sedimentary rock formation over long geological periods.
Assessing the pathogenic potential of less common Salmonella enterica serotypes circulating in the Thai pork production chain
Authors: Eiamsam-ang Thanaporn , Tadee Pakpoom , Pascoe Ben , Patchanee Prapas
Published: June 2022

Salmonella is a frequent zoonotic foodborne pathogen, with swine and pork meats the most common source of human infection. In Chiang Mai and Lamphun Province in northern Thailand, there has been a high prevalence of salmonellosis for over a decade. Infection is usually with several dominant S. enterica serotypes, including serotypes Rissen and Monophasic Typhimurium. However, several less common serotypes also contribute to disease. Whole genome sequencing of 43 of these less common S. enterica serotypes isolated from the pork production chain through 2011-2014 were used to evaluate their genetic diversity and virulence potential. Salmonella contamination at local retail markets represented cross-contamination from multiple sources, including decontaminated foodstuff. Previous studies have highlighted the importance of host cell adhesion, invasion and intracellular survival for the development of clinical salmonellosis. We screened our dataset for known virulence genes and antimicrobial resistance genes, identifying at least 10 antimicrobial resistance genes in all isolates. These results indicate that these less common S. enterica serotypes also pose a significant public health risk. Our findings support the need for appropriate surveillance of food products going to market to reduce public exposure to highly pathogenic, multi-drug resistant Salmonella. Surveillance throughout the pork production chain would motivate stakeholders to reinforce sanitation standards and help reduce the risk of salmonellosis in humans.
Emerging Evidence for Poxvirus-Mediated Unfolded Protein Response: Lumpy Skin Disease Virus Maintains Self-replication by Activating PERK and IRE1
Authors: Tan Jinlong , Liu Yinju , Yang Fan , Chen Guohua , Fang Yongxiang , He Xiaobing , Lou Zhongzi , Jia Huaijie , Jing Zhizhong , Li Weike
Published: June 2022

The cytoplasmic replication of poxviruses requires extensive protein synthesis, challenging the capacity of the endoplasmic reticulum (ER). However, the role of the ER in the life cycle of poxviruses is unclear. In this study, we demonstrate that infection with the lumpy skin disease virus (LSDV), a poxvirus, causes ER stressin vivoandin vitro, further facilitating the activation of the unfolded protein response (UPR). Although UPR activation aids in the restoration of the cellular environment, its significance in the LSDV life cycle remains unclear. Furthermore, the role of ER imbalance for viral replication is also unknown. We show that LSDV replication is hampered by an unbalanced ER environment. In addition, we verify that the LSDV replication depends on the activation of PERK-eIF2α and IRE1-XBP1 signaling cascades rather than ATF6, implying that global translation and XBP1 cleavage are deleterious to LSDV replication. Our findings suggest that LSDV engages all UPR signaling sensors, and that activation of PERK and IRE1 sensors is indispensable to maintaining its own replication.

IMPORTANCE

Although numerous viruses cause ER stress and employ endogenous UPR components to control viral growth, there is no such evidence for poxviruses. Recent real-world epidemics of poxviruses such as monkeypox and LSDV indicated a lack of available coping strategies. Our findings show that LSDV encoding up to 156 open reading frames (ORFs) causes pressure to the stabilization of ER, triggers ER stress, and further promotes the activation of all three UPR signaling pathways. However, inhibiting PERK-eIF2α and IRE1-XBP1 was not conducive for LSDV replication. Since LSDV efficiently utilizes UPR components to assist its own replication, signal-blocking agents of PERK and IRE1 may be useful in the treatment of LSDV. More evidence for the efficacy of such therapy for LSDV, even monkeypox, could come from a clearer characterization of the ER stress-mediated viral replication process.
Avian Influenza A Virus polymerase can utilise human ANP32 proteins to support cRNA but not vRNA synthesis
Authors: Swann Olivia C. , Rasmussen Amalie B. , Peacock Thomas P. , Sheppard Carol M. , Barclay Wendy S.
Published: June 2022

Host restriction limits the emergence of novel pandemic strains from the Influenza A Virus avian reservoir. For efficient replication in mammalian cells, the avian influenza RNA-dependent RNA polymerase must adapt to use human orthologues of the host factor ANP32, which lack a 33 amino acid insertion relative to avian ANP32A. Here we find that influenza polymerase requires ANP32 proteins to support both steps of replication: cRNA and vRNA synthesis. Nevertheless, avian strains are only restricted in vRNA synthesis in human cells. Therefore, avian polymerase can use human ANP32 orthologues to support cRNA synthesis, without acquiring mammalian adaptations. This implies a fundamental difference in the mechanism by which ANP32 proteins support cRNA vs vRNA synthesis.

Importance

In order to infect humans and cause a pandemic, avian influenza must first learn how to use human versions of the proteins the virus hijacks for replication – instead of the avian versions found in bird cells. One such protein is ANP32. Understanding the details of how host proteins such as ANP32 support viral activity may allow the design of new antiviral treatments that disrupt these interactions. In this work, we use cells that lack ANP32 to unambiguously demonstrate ANP32 is needed for both steps of influenza genome replication. Surprisingly however, we find that avian influenza can use human ANP32 proteins for the first step of replication without any adaptation, but only avian ANP32 for the second step of replication. This suggests ANP32 may have an additional role in supporting the second step of replication, and it is this activity that is specifically blocked when avian influenza infects human cells.
Human gut metagenomes encode diverse GH156 sialidases
Authors: Mann Evan , Shekarriz Shahrokh , Surette Michael G.
Published: June 2022

The intestinal lining is protected by a mucous barrier composed predominantly of complex carbohydrates. Gut microbes employ an array of glycoside hydrolases (GHs) to liberate mucosal sugars as a nutrient source to facilitate host colonization. Intensive catabolism of mucosal glycans, however, may contribute to barrier erosion, pathogen encroachment and inflammation.

Sialic acid is an acidic sugar featured at terminal positions of host glycans. Characterized sialidases from the microbiome belong to the GH33 family, according to CAZy (Carbohydrate Active enZyme) database classification. A 2018 functional metagenomics screen using thermal spring DNA uncovered the founding member of the GH156 sialidase family, which lacks homology to GH33 sialidases and could not be taxonomically assigned. Subsequent structural analysis revealed critical active site residues. We sought to determine if GH156 sialidases are present in the human gut microbiome where they might contribute to mucous erosion.

A subset of GH156 sequences from the CAZy database containing key sialidase residues was used to build a Hidden Markov Model. HMMsearch against public databases revealed ∼10X more putative GH156 sialidases than currently recognized by CAZy. Represented phyla include Bacteroidota, Verrucomicrobiota and Firmicutes_A from human microbiomes, all of which play notable roles in carbohydrate fermentation. Genomic analyses suggested that taxa containing GH156-encoding genes may utilize host-glycans. Analyses of metagenomic datasets revealed that GH156s are frequently encoded in metagenomes, with a greater variety and abundance of GH156 genes observed in traditional hunter-gatherer or agriculturalist societies than in industrialized societies, particularly relative to individuals with IBD. A GH156 gene frequently detected in traditional populations was cloned from stool sample DNA and the recombinant protein exhibited sialidase activity with a fluorogenic substrate.

Importance

Sialic acids occupy terminal positions of human glycans where they act as receptors for microbes, toxins and immune signaling molecules. Microbial enzymes that remove sialic acids, sialidases, are abundant in the human microbiome where they may contribute to shaping the microbiota community structure or contribute to pathology. Furthermore, sialidases have proven to hold therapeutic potential for cancer therapy. Here we examined the sequence space of a sialidase family of enzymes, GH156, previously unknown to the human gut environment. Our analyses suggest that human populations with disparate dietary practices harbour distinct varieties and abundances of GH156-encoding genes. Furthermore, we demonstrate the sialidase activity of a gut derived GH156. These results expand the diversity of sialidases that may contribute to host glycan degradation and these sequences may have biotechnological or clinical utility.
NFATc1 negatively determines chondrocyte differentiation in articular cartilage progenitors
Authors: Zhang Fan , Zhao Ying , Wang Manqi , Zhou Bin , Zhou Bin , Ge Xianpeng
Published: June 2022

The origin and differentiation mechanism of articular chondrocytes remain poorly understood. Broadly, the difference in developmental mechanisms of articular and growth-plate cartilage is still less elucidated. Here, we identified that the nuclear factor of activated T-cells cytoplasmic 1 (NFATc1) is a crucial regulator of articular, but not growth-plate, chondrocyte differentiation during development. At the early stage of mouse knee development (embryonic day 13.5), NFATc1-expressing cells were mainly located in the flanking region of the joint interzone. With development, NFATc1-expressing cells generated almost all articular chondrocytes, but not chondrocytes in limb growth-plate primordium. NFATc1-expressing cells displayed prominent capacities for colony formation and multipotent differentiation. Transcriptome analyses revealed a set of characteristic genes in NFATc1-enriched articular cartilage progenitors. Strikingly, the expression of NFATc1 was diminished with articular chondrocyte differentiation, and suppressing NFATc1 expression in articular cartilage progenitors was sufficient to induce spontaneous chondrogenesis while overexpressing NFATc1 suppresses chondrogenesis. Mechanistically, NFATc1 negatively regulated the transcriptional activity of the Col2a1 gene. Thus, our results reveal that NFATc1 characterizes articular, but not growth-plate, cartilage progenitors and negatively determines articular chondrocyte differentiation at least partly through regulating COL2A1 gene transcription.
A Chemical-mechanical Coupled Model Predicts Roles of Spatial Distribution of Morphogen in Maintaining Tissue Growth
Authors: Ramezani Alireza , Britton Samuel , Zandi Roya , Alber Mark , Netmatbakhsh Ali , Chen Weitao
Published: June 2022

The exact mechanism controlling cell growth remains a grand challenge in developmental biology and regenerative medicine. The Drosophila wing disc tissue serves as an ideal biological model to study growth regulation due to similar features observed in other developmental systems. The mechanism of growth regulation in the wing disc remains a subject of intense debate. Most existing models to study tissue growth focus on either chemical signals or mechanical forces only. Here we developed a multiscale chemical-mechanical coupled model to test a growth regulation mechanism depending on the spatial range of the morphogen gradient. By comparing the spatial distribution of cell division and the overall shape of tissue obtained in the coupled model with experimental data, our results show that the distribution of the Dpp morphogen can be critical in resulting tissue size and shape. A larger tissue size with a faster growth rate and more symmetric shape can be achieved if the Dpp gradient spreads in a larger domain. Together with the absorbing boundary conditions, the feedback regulation that downregulates Dpp receptors on the cell membrane allows the further spread of the morphogen away from its source region, resulting in prolonged tissue growth at a more spatially homogeneous growth rate.

Summary Statement

A multiscale chemical-mechanical model was developed by coupling submodels representing dynamics of a morphogen gradient at the tissue level, intracellular chemical signals, and mechanical properties at the subcellular level. By applying this model to study the Drosophila wing disc, it was found that the spatial range of the morphogen gradient affected tissue growth in terms of the growth rate and the overall shape.