bluuebunny/crossref_metadata_2025 huggingface dataset:
StrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data
Authors: Hu Han , Tan Yuxiang , Li Chenhao , Chen Junyu , Kou Yan , Xu Zhenjiang Zech , Liu Yang-Yu , Tan Yan , Dai Lei
Published: February 2022

Background

Microbial strains of variable functional capacities co-exist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data.

Methods

Here we present StrainPanDA (Strain-level Pangenome Decomposition Analysis), a novel method that uses the pangenome coverage profile of multiple metagenomic samples to simultaneously reconstruct the composition and gene content variation of co-existing strains in microbial communities.

Results

We systematically validate the accuracy and robustness of StrainPanDA using synthetic datasets. To demonstrate the power of gene-centric strain profiling, we then apply StrainPanDA to analyze the gut microbiome samples of infants, as well as patients treated with fecal microbiota transplantation. We show that the linked reconstruction of strain composition and gene content profiles is critical for understanding the relationship between microbial adaptation and strain-specific functions (e.g., nutrient utilization, pathogenicity).

Conclusions

StrainPanDA can be applied to metagenomic datasets to detect association between molecular functions and microbial/host phenotypes to formulate testable hypotheses and gain novel biological insights at the strain or subspecies level.
Genetic and epigenetic driven variation in regulatory regions activity contribute to adaptation and evolution under endocrine treatment
Authors: Slaven Neil , Lopes Rui , Canale Eleonora , Ivanoiu Diana , Pacini Claudia , Monteiro Barbosa Ines Amorim , Bleu Melusine , Bravaccini Sara , Ravaioli Sara , Dieci Maria Vittoria , Pruneri Giancarlo , Galli Giorgio G. , Barozzi Iros , Magnani Luca
Published: February 2022

Comprehensive profiling of hormone-dependent breast cancer (HDBC) has identified hundreds of protein-coding alterations contributing to cancer initiation1, 2, but only a handful have been linked to endocrine therapy resistance, potentially contributing to 40% of relapses1, 3–9. If other mechanisms underlie the evolution of HDBC under adjuvant therapy is currently unknown. In this work, we employ integrative functional genomics to dissect the contribution of cis-regulatory elements (CREs) to cancer evolution by focusing on 12 megabases of non-coding DNA, including clonal enhancers10, gene promoters, and boundaries of topologically associating domains11. Massive parallel perturbation in vitro reveals context-dependent roles for many of these CREs, with a specific impact on dormancy entrance12, 13 and endocrine therapy resistance9. Profiling of CRE somatic alterations in a unique, longitudinal cohort of patients treated with endocrine therapies identifies non-coding changes involved in therapy resistance. Overall, our data uncover actionable transient transcriptional programs critical for dormant persister cells and unveil new regulatory nodes driving evolutionary trajectories towards disease progression.
Emergent regulation of ant foraging frequency through a computationally inexpensive forager movement rule
Authors: Baltiansky Lior , Frankel Guy , Feinerman Ofer
Published: February 2022

1

Ant colonies regulate foraging in response to their collective hunger, yet the mechanism behind this distributed regulation remains unclear. Previously, by imaging food flow within ant colonies we showed that the frequency of foraging events declines linearly with colony satiation ([1]). Our analysis implied that as a forager distributes food in the nest, two factors affect her decision to exit for another foraging trip: her current food load and its rate of change. Sensing these variables can be attributed to the forager’s individual cognitive ability. Here, new analyses of the foragers’ trajectories within the nest imply a different way to achieve the observed regulation. Instead of an explicit decision to exit, foragers merely tend toward the depth of the nest when their food load is high and toward the nest exit when it is low. Thus, the colony shapes the forager’s trajectory by controlling her unloading rate, while she senses only her current food load. Using an agent-based model and mathematical analysis, we show that this simple mechanism robustly yields emergent regulation of foraging frequency. These findings demonstrate how the embedding of individuals in physical space can reduce their cognitive demands without compromising their computational role in the group.
Uniformity of spheroid-on-chip by surface treatment of PDMS microfluidic platforms
Authors: Azizipour Neda , Avazpour Rahi , Sawan Mohamad , Rosenzweig Derek H. , Ajji Abdellah
Published: February 2022

Spheroids have emerged as a more reliable model for drug screening when compared with 2D culture models. Microfluidic based biochips have many advantages over other 3D cell culture models for drug testing on spheroids, including precise control of the cellular microenvironment. The control of the cell adhesion to the surface is one of the most important challenges affecting the size and the geometry of the spheroids which could be controlled by appropriate surface engineering methods. We have studied the modification of the PDMS surface properties treated by applying different concentrations of the two anti-fouling coatings (BSA and Pluronic F-68). The desired treatment of PDMS surface effectively inhibits cell adhesion to the surface and promotes cells self-aggregations to form more uniform and healthy spheroids for a longer period of time. The microscopic observations with qualitative and quantitate data revealed that surface properties drastically affect the number of the spheroids formed on-chip and their geometry. We used human breast cancer cell line (MDA-MB-231-GFP) while the concentration of the chemical coatings and incubation time were adjusted. Proper repellent PDMS surfaces were provided with minimum cell attachment and facilitated spheroid formation when compared with non-treated PDMS. The results demonstrate fundamental and helpful patterns for microfluidic based cell culture applications to improve the quantity and quality of spheroid formation on-chip which are strongly manipulated by surface properties (i.e., morphology, roughness, wettability and etc.)
An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data
Authors: Zhou Boyan , Wang Chan , Putzel Gregory , Hu Jiyuan , Liu Menghan , Wu Fen , Chen Yu , Pironti Alejandro , Li Huilin
Published: February 2022

The development of sequencing technology and analytic tools have advanced our insights into the complexity of microbiome. Since different strains within species may display great phenotypic variability, studying within-species variations enhances the understanding of microbial biological processes. However, most existing methods for strain-level analysis do not allow for the simultaneous interrogation of strain proportions and genome-wide variants in longitudinal metagenomic samples. In this study, we introduce LongStrain, an integrated pipeline for the analysis of metagenomic data from individuals with longitudinal or repeated samples. Our algorithm improves the efficiency and accuracy of strain identification by jointly modeling the strain proportion and genomic variants in combined multiple samples within individuals. With simulation studies of a microbial community and single species, we show that LongStrain is superior to three extensively used methods in variant calling and proportion estimation. Furthermore, we illustrate the potential applications of LongStrain in the real data analysis of The Environmental Determinants of Diabetes in the Young (TEDDY) study and a gastric intestinal metaplasia microbiome study. We investigate the association between the dynamic change of strain proportions and early life events, such as birth delivery mode, antibiotic treatment, and weaning. By joint analysis of phylogeny and strain transition, we also identify a subspecies clade of Bifidobacterium longum which is significantly correlated with breastfeeding.
DeepVelo: Single-cell Transcriptomic Deep Velocity Field Learning with Neural Ordinary Differential Equations
Authors: Chen Zhanlin , King William C. , Hwang Aheyon , Gerstein Mark , Zhang Jing
Published: February 2022

Recent advances in single-cell RNA sequencing technology have provided unprecedented opportunities to simultaneously measure the gene expression profile and transcriptional velocity of individual cells, enabling us to sample gene regulatory network dynamics along developmental trajectories. However, traditional methods have faced challenges in modeling gene expression dynamics within individual cells due to sparse, non-linear (e.g., obligate heterodimer transcription factors), and high-dimensional measurements. Here, we present DeepVelo, a neural-network-based ordinary differential equation model that can learn non-linear, high-dimensional single-cell transcriptome dynamics and describe continuous gene expression changes within individual cells across time. We applied DeepVelo to multiple published datasets from different technical platforms and demonstrated its utility to 1) formulate transcriptome dynamics on different timescales, 2) measure the instability of cell states, and 3) identify developmental driver genes upstream of a signaling cascade. Benchmarking against state-of-the-art methods shows that DeepVelo can improve velocity field representation accuracy by at least 50% in out-of-sample cells. Further, perturbation studies revealed that single-cell dynamical systems may exhibit properties similar to those of chaotic systems. In summary, DeepVelo allows for the data-driven discovery of differential equations that delineate single-cell transcriptome dynamics.

Teaser

Embedding neural networks into ordinary differential equations to model gene expression changes within single cells across time.
Hamiltonian Monte Carlo with strict convergence criteria reduces run-to-run variability in forensic DNA mixture deconvolution
Authors: Susik Mateusz , Schönborn Holger , Sbalzarini Ivo F.
Published: February 2022

Motivation

Analysing mixed DNA profiles is a common task in forensic genetics. Due to the complexity of the data, such analysis is often performed using Markov Chain Monte Carlo (MCMC)-based genotyping algorithms. These trade off precision against execution time. When the default settings are used, as large as a 10-fold changes in inferred likelihood ratios (LR) are observed when the software is run twice on the same case. So far, this uncertainty has been attributed to the stochasticity of MCMC algorithms. Since LRs translate directly to strength of the evidence in a criminal trial, forensic laboratories desire LR with small run-to-run variability.

Results

We present a Hamiltonian Monte Carlo (HMC) algorithm that reduces run-to-run variability in forensic DNA mixture deconvolution by around an order of magnitude without increased runtime. We achieve this by enforcing strict convergence criteria. We show that the choice of convergence metric strongly influences precision. We validate our method by reproducing previously published results for benchmark DNA mixtures (MIX05, MIX13, and ProvedIt). We also present a complete software implementation of our algorithm that is able to leverage GPU acceleration, accelerating the inference process. In the benchmark mixtures, on consumer-grade hardware, the runtime is less than 7 minutes for 3 contributors, less than 35 minutes for 4 contributors, and less than an hour for 5 contributors with one known contributor.
Secondary sexual dimorphism traits under abiotic stress in dioecious species: The case of Amaranthus palmeri
Authors: Korres Nicholas E. , Norsworthy Jason K. , FitzSimons Toby , Roberts Trenton L. , Oosterhuis Derrick M. , Govindjee Govindjee
Published: February 2022

The evolution of secondary sex-specific traits of dioecious species under abiotic stress conditions has received limited research, especially in the case of Amaranthus palmeri, a fast adapting and highly competing plant. Here, we have examined the interactive effects of abiotic stress on mineral accumulation, chlorophyll a and b content, and the operating capacity of Photosystem II (PSII) in both male and female A. palmeri plants grown under three different intensities (150, 450 and 1300 μmol photons m−2 s−1) of white light, and under N, K or P deficiency. Mineral profiling of the leaves and stems (with inflorescence) highlighted intra- and intersexual differences in their accumulation pattern and mineral associations. Chlorophyll a and b content was different between the male and the female plants, being lower in the latter, at high light intensity, especially as the flowering progressed, or when they were under K or P deficient condition. Further, the chlorophyll a/b ratio was lower at the higher light intensity in the female, over that in the male, plants. Chlorophyll fluorescence parameters, i.e., steady state (F’S) and maximum (F’M) fluorescence increased under high light intensity, whereas the PSII operating efficiency (ΦPSII) decreased in the female plants, indicating reduced PSII capacity. Sex-specific differences in A. palmeri showed a differential response to stressful conditions because of differences in their ontogeny and physiology, and possibly due to the cost of reproduction. We suggest that the breeding system of dioecious species has weaknesses that can be used for the ecological management of dioecious weed species.
Blood Concentrations of Per- and Polyfluoroalkyl Substances are Associated with Autoimmunity-like Effects in the American Alligator
Authors: Guillette T. C. , Jackson Thomas W. , Guillette Matthew P. , McCord James P. , Belcher Scott M.
Published: February 2022

Surface and ground water of the Cape Fear River basin in central and coastal North Carolina is contaminated with high levels of per- and polyfluoroalkyl substances (PFAS). Elevated levels of PFAS have also been found in blood of fish and wildlife living in and around the Cape Fear River, and in the blood of human populations reliant on contaminated well or surface water from the Cape Fear River basin as a sources of drinking water. While the public and environmental health impacts of long-term PFAS exposures are poorly understood, elevated blood concentrations of some PFAS are linked with immunotoxicity and increased incidence of some chronic autoimmune diseases in human populations. The goal of this study was to evaluate PFAS exposure and biomarkers related to immune health in populations of American alligators (Alligator mississippiensis), a protected and predictive sentinel species of adverse effects caused by persistent toxic pollutants. We found that serum PFAS concentrations in a representative population of alligators from the Cape Fear River were increased compared to a reference population of alligators from the adjoining Lumber River basin. The elevated serum PFAS concentrations in the Cape Fear River alligators were associated with increased innate immune activities, and autoimmune-like phenotypes were observed in this population. In addition to evidence of significantly higher double stranded-DNA binding autoantibodies in adult Cape Fear River alligators, our qRT-PCR analysis found remarkably high induction of Interferon-α αsignature genes implicated in the pathology of human autoimmune disease. We interpret the association of increased PFAS exposure with disrupted immune functions to indicate that PFAS broadly alters immune activities resulting in autoimmune-like pathology in American alligators. This work substantiates and extends evidence from experimental models and human epidemiology studies showing that some PFAS are immune toxicants.

Highlights

Serum PFAS concentration were elevated in alligator populations from the Cape Fear River

Higher PFAS concentrations were associated with disrupted innate immune functions

Infa-responsive autoimmunity signature genes were induced in Cape Fear River alligators

Elevated PFAS levels were associated with autoimmune-like activity in alligators 26
Neocentromere formation through Robertsonian fusion and centromere repositioning during the evolution of zebras
Authors: Cappelletti Eleonora , Piras Francesca M. , Sola Lorenzo , Santagostino Marco , Abdelgadir Wasma A. , Raimondi Elena , Nergadze Solomon G. , Giulotto Elena
Published: February 2022

Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated to highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres inEquus caballusandE. asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebrasE. burchelli(15 of 22) andE. grevyi(13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine neocenstromeres are shared between the two species in agreement with their recent separation. Wede novoassembled all neocentromeric regions and improved the reference genome ofE. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a neocentromere was seeded on an inversion breakpoint. At eleven chromosomes, whose primary constrictions seemed to be associated to satellite repeats by cytogenetic analysis, neocentromeres were instead located near the ancestral inactivated satellite-based centromeres, therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position.
Nuclear Receptor 5A2 Regulation of Agrp underlies Olanzapine-induced Hyperphagia
Authors: Zapata Rizaldy C. , Zhang Dinghong , Libster Avraham , Porcu Alessandra , Montilla-Perez Patricia , Zhang Zhi , Correa Stephanie M , Telese Francesca , Osborn Olivia
Published: February 2022

Summary/Abstract

Antipsychotic (AP) drugs are highly efficacious treatments for psychiatric disorders, but a serious side effect of their use is excessive weight gain and subsequent development of metabolic disease. Increased food intake is the underlying driver of AP-induced weight gain, although the underlying mechanisms remain unknown. In previous studies, we identified hypothalamic genes whose expression level was altered following APs-induced hyperphagia. Among these genes, the orexigenic peptide Agrp and the transcription factor nuclear receptor subfamily 5 group A member 2 (Nr5a2) were two of the most significantly upregulated genes by APs. NR5a2 is broadly expressed throughout the body, but little is known about its role in the brain. In this study, we investigated the role of hypothalamic NR5a2 in AP-induced hyperphagia and weight gain. In hypothalamic cell lines, OLZ treatment resulted in a dose-dependent increase in gene expression of NR5a2 and Agrp. In mice, administration of a specific Nr5a2 inhibitor decreased olanzapine-induced hyperphagia and weight gain, while knockdown of Nr5a2 in the arcuate nucleus (ARC) partially reversed olanzapine-induced hyperphagia. Chromatin-immunoprecipitation-PCR studies showed for the first time that NR5a2 directly binds to the Agrp promoter region. In addition, in situ hybridization studies confirm that NR5a2 and Agrp are co-localized in a subset of cells in the arcuate nucleus. In summary, we identify Nr5a2 as a key mechanistic driver of AP-induced food intake and these findings can be used to inform future clinical development of APs that do not activate hyperphagia and weight gain.
Seeing light from a different angle: the effects of diffuse light on the function, structure, and growth of tomato plants
Authors: Ellertson Kendra B. L. , Goldsmith Gregory R. , Berry Z. Carter
Published: February 2022

While considerable attention has been paid to how plants respond to changes in the spectral distribution and quantity of light, less attention has been paid to how plants respond to changes in the angular qualities of light. Evidence from both leaf- and ecosystem-scale measurements indicate that plants vary in their response to diffuse compared to direct light growing environments. Because of the significant implications for agricultural production, we quantified how changes in light quality affect the structure, function, and growth of Roma tomatoes in an open-air greenhouse experiment with direct and diffuse light treatments. Diffuse light conditions (ca. 50-60% diffuse) were created with a glass coating to diffuse light without significantly reducing the quantity of light. We measured leaf physiology and structure, as well as whole plant physiology, morphology, and growth. Light-saturated photosynthetic rates were set by the growing light environment and were unchanged by short-term exposure to the opposite light environment. Thus, after two months, plants in the diffuse light treatment demonstrated lower photosynthesis and had thinner leaves with higher chlorophyll concentration. However, relative growth rates did not differ between treatments and plants grown in diffuse light had significantly higher biomass at the conclusion of the experiment. While there was no difference in leaf or whole-plant water-use efficiency, plants in the diffuse light treatment demonstrated significantly lower leaf temperatures, highlighting the potential for diffuse light coatings and/or materials to reduce greenhouse energy use. Our results highlight the need to advance our understanding of the effects of diffuse light conditions on agricultural crops growing on a changing planet.
Measuring drift by mean deviation: unequal breeding sex ratio revisited
Authors: Qin Ben
Published: February 2022

When it comes to estimating the magnitude of genetic drift, there is hardly any indexes other than the effective population size. Starting from the binomial sampling distribution, this research proposed using mean deviation of allele frequency change as a direct measurement of drift, then tested it in a classical example concerning unequal breeding sex ratio. This study found that: (1) mean deviation offers a new dimension in measuring the magnitude of drift; (2) the measurement displays a “half-half” pattern; (3) allele frequency determines the efficacy of hitchhiking effect of rare alleles, and in what way that “half-half” pattern should be divided.
RAID: Regression Analysis based Inductive DNA microarray for Precise Read-Across
Authors: Amano Yuto , Yamane Masayuki , Honda Hiroshi
Published: February 2022

Chemical structure-based read-across represents a promising method for chemical toxicity evaluation without the need for animal testing; however, a chemical structure is not necessarily related to toxicity. Therefore, in vitro studies were often used for read-across reliability refinement; however, their external validity has been hindered by the gap between in vitro and in vivo conditions. Thus, we developed a virtual DNA microarray, Regression Analysis based Inductive DNA microarray (RAID), which quantitatively predicts in vivo gene expression profiles based on the chemical structure and/or in vitro transcriptome data. For each gene, elastic-net models were constructed using chemical descriptors and in vitro transcriptome data to predict in vivo data from in vitro data (in vitro to in vivo extrapolation; IVIVE). In feature selection, useful genes for assessing the quantitative structure activity relationship (QSAR) and IVIVE were identified. Predicted transcriptome data derived from the RAID system reflected the in vivo gene expression profiles of characteristic hepatotoxic substances. Moreover, gene ontology and pathway analyses indicated that xenobiotic response and metabolic activation via nuclear receptors are related to those gene expressions. The identified IVIVE-related genes were associated with fatty acid-, xenobiotic-, and drug metabolism, indicating that in vitro studies were effective in evaluating these key events. Furthermore, validation studies revealed that chemical substances associated with these key events could be detected as hepatotoxic biosimilar substances. These results indicate that the RAID system could represent an alternative screening test for repeated-dose toxicity test and toxicogenomic analyses. Our technology provides a critical solution to IVIVE-based read-across by considering the mode of action and chemical structures.
Niche differentiation following whole-genome duplication? The importance of considering the intricate evolutionary history of polyploids when assessing climatic niche evolution
Authors: Padilla-García Nélida , Šrámková Gabriela , Záveská Eliška , Šlenker Marek , Clo Josselin , Zeisek Vojtěch , Lučanová Magdalena , Rurane Ieva , Kolář Filip , Marhold Karol
Published: February 2022

Aim

Although whole genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, the role of genome doubling per se vs. later divergence on polyploid’s niche evolution remains obscure. One reason for this might be that the intraspecific genetic structure of polyploid complexes and interploidy gene flow is often neglected in ecological studies. Here, we aim to investigate to which extent these evolutionary processes impact our inference on niche differentiation of autopolyploids.

Location

Europe

Taxon

Arabidopsis arenosa (Brassicaceae)

Methods

Leveraging a total of 352 cytotyped populations of diploid-autotetraploid A. arenosa, we examined differences among climatic niches of diploid and tetraploid lineages both globally, and independently for each tetraploid lineage with respect to the niche of its evolutionary closest relative. Then, we tested if there was an effect of additional interploidy introgression from other sympatric but more ancestral diploid lineages of A. arenosa on climatic niches of tetraploids.

Results

Ecological niche shift of tetraploids is only detected when the assignment of populations to intraspecific genetic lineages is considered. We found different patterns of climatic niche evolution (i.e. niche conservatism, contraction or expansion) in each tetraploid lineage when compared to its evolutionary closest relatives. We observed an effect of interploidy gene flow in patterns of climatic niche evolution of tetraploid ruderal plants of A. arenosa.

Main conclusions

The niche shift of tetraploids in A. arenosa is not driven by WGD per se but rather reflects dynamic post-WGD evolution in the species, involving tetraploid migration out of their ancestral area and interploidy introgression with other diploid lineages. Our study supports that evolutionary processes following WGD - which usually remain undetected by studies neglecting evolutionary history of polyploids - may play a key role in the adaptation of polyploids to challenging environments.
The GDF15-GFRAL pathway is dispensable for the effects of metformin on energy balance
Authors: Klein Anders B. , Nicolaisen Trine S. , Johann Kornelia , Fritzen Andreas M. , Mathiesen Cecilie V. , Gil Cláudia , Pilmark Nanna S. , Karstoft Kristian , Blond Martin B. , Quist Jonas S. , Seeley Randy J. , Færch Kristine , Lund Jens , Kleinert Maximilian , Clemmensen Christoffer
Published: February 2022

Metformin is a blood glucose lowering medication with physiological effects that extend beyond its anti-diabetic indication. Recently, it was reported that metformin lowers body weight via induction of growth differentiation factor 15 (GDF15), which suppresses food intake by binding to the GDNF family receptor α-like (GFRAL) in the hindbrain. At the same time, we demonstrated that recombinant GDF15 suppresses voluntary exercise in a GFRAL-dependent fashion. Here, we corroborate that metformin increases circulating GDF15 in mice and humans, but that it does not reduce voluntary running activity in mice. Unexpectedly, we fail to confirm previous reports that the GDF15-GFRAL pathway is necessary for the weight-lowering effects of metformin. Instead, our studies in wild-type, GDF15 knockout and GFRAL knockout mice suggest that the GDF15-GFRAL pathway is dispensable for the effects of metformin on energy balance. The data presented here question whether metformin is a sufficiently strong stimulator of GDF15 to drive anorexia and weight loss and emphasize that additional work is needed to untangle the relationship among metformin, GDF15 and energy balance.
Engineering of an electrically charged hydrogel implanted into a traumatic brain injury model for stepwise neuronal tissue reconstruction
Authors: Tanikawa Satoshi , Ebisu Yuki , Sedlačík Tomáš , Semba Shingo , Nonoyama Takayuki , Hirota Akira , Takahashi Taiga , Yamaguchi Kazushi , Imajo Masamichi , Kato Hinako , Nishimura Takuya , Tanei Zen-ichi , Tsuda Masumi , Nemoto Tomomi , Gong Jian Ping , Tanaka Shinya
Published: February 2022

Neural regeneration is extremely difficult to achieve. In traumatic brain injuries, the loss of brain parenchyma volume hinders neural regeneration. In this study, neuronal tissue engineering was performed by using electrically charged hydrogels composed of cationic and anionic monomers in a 1:1 ratio (C1A1 hydrogel), which served as an effective scaffold for the attachment of neural stem cells (NSCs). In the 3D environment of porous C1A1 hydrogels engineered by the cryogelation technique, NSCs differentiated into neuroglial cells. The C1A1 porous hydrogel was implanted into brain defects in a mouse traumatic damage model. The VEGF-immersed C1A1 porous hydrogel promoted host-derived vascular network formation together with the infiltration of macrophages/microglia and astrocytes into the gel. Furthermore, the stepwise transplantation of GFP-labeled NSCs supported differentiation to glial and neuronal cells. Therefore, this two-step method for neural regeneration may become a new approach for therapeutic brain tissue reconstruction after brain damage in the future.

One Sentence Summary

Brain tissue reconstruction using charged hydrogel and stepwise NCS injection
AAV2/9-mediated gene transfer into murine lacrimal gland leads to a long-term targeted tear film modification
Authors: Gautier Benoit , Meneux Lena , Feret Nadège , Audrain Christine , Hudecek Laetitia , Kuony Alison , Bourdon Audrey , Guiner Caroline Le , Blouin Véronique , Delettre Cécile , Michon Frédéric
Published: February 2022

Corneal blindness is the fourth leading cause of blindness worldwide. Since the corneal epithelium is constantly renewed, non-integrative gene transfer cannot be used to treat corneal diseases. In numerous of these diseases, the tear film has been reported to be defective. Tears are a complex biological fluid secreted by the lacrimal apparatus. Their composition is modulated according to the context. For instance, after a corneal wound, the lacrimal gland secretes reflex tears, which contain specific growth factors supporting the wound healing process. In specific pathological contexts, such as dry eye diseases, the tear composition can support neither corneal homeostasis, nor wound healing. Here, we propose to use the lacrimal gland as bioreactor to produce and secrete specific factors to support corneal physiology. In this study, we used an AAV2/9-mediated gene transfer to supplement the tear film. First, we demonstrate that a single injection of AAV2/9 is sufficient to transduce all epithelial cell types of the lacrimal gland efficiently and widely. Then, we show that lacrimal gland physiology and corneal integrity are maintained after the injection of an AAV2/9-mediated nerve growth factor expression in the lacrimal gland. Remarkably, this injection induces an important and long-lasting secretion of this growth factor in the tear film. Altogether, our findings provide a new clinically applicable approach to tackle corneal blindness.
Salt Induced Transitions in the Conformational Ensembles of Intrinsically Disordered Proteins
Authors: Maity Hiranmay , Baidya Lipika , Reddy Govardhan
Published: February 2022

Salts modulate the behavior of intrinsically disordered proteins (IDPs). In low ionic strength solutions, IDP conformations are primarily perturbed by the screening of electrostatic interactions, independent of the identity of the salt. In this regime, insight into the IDP behavior can be obtained using the theory for salt-induced transitions in charged polymers. However, in high ionic strength solutions, salt-specific interactions with the charged and uncharged residues, known as the Hofmeister effect, influence IDP behavior. There is a lack of reliable theoretical models in high salt concentration regimes to predict the salt effect on IDPs. Using a coarse-grained simulation model for the IDPs and experimentally measured water to salt solution transfer free-energies of various chemical groups, we studied the salt-specific transitions induced in the IDPs conformational ensemble. We probed the effect of three different salts, ranging from protective osmolyte to denaturant, on five IDPs belonging to various polymer classes classified based on charge content. The transitions observed in the IDP conformational ensembles are dependent on the salt used and the IDP polymer class. An important implication of these results is that a suitable salt can be identified to induce condensation of an IDP through liquid–liquid phase separation.
Benchmarking methods for detecting differential states between conditions from multi-subject single-cell RNA-seq data
Authors: Junttila Sini , Smolander Johannes , Elo Laura L
Published: February 2022

Single-cell RNA-sequencing (scRNA-seq) enables researchers to quantify transcriptomes of thousands of cells simultaneously and study transcriptomic changes between cells. scRNA-seq datasets increasingly include multi-subject, multi-condition experiments to investigate cell-type-specific differential states (DS) between conditions. This can be performed by first identifying the cell types in all the subjects and then by performing a DS analysis between the conditions within each cell type. Naïve single-cell DS analysis methods that treat cells statistically independent are subject to false positives in the presence of variation between biological replicates, an issue known as the pseudo-replicate bias. While several methods have already been introduced to carry out the statistical testing in multi-subject scRNA-seq analysis, comparisons that include all these methods are currently lacking. Here, we performed a comprehensive comparison of 18 methods for the identification of DS changes between conditions from multi-subject scRNA-seq data. Our results suggest that the pseudo-bulk methods performed generally best. Both pseudo-bulks and mixed models that model the subjects as a random effect were superior compared with the naive single-cell methods that do not model the subjects in any way. While the naive models achieved higher sensitivity than the pseudo-bulk methods and the mixed models, they were subject to a high number of false positives. In addition, accounting for subjects through latent variable modeling did not improve the performance of the naive methods.
Inhibition of Glycogen Metabolism Induces Reactive Oxygen Species-Dependent Apoptosis in Anaplastic Thyroid Cancer
Authors: Davidson Cole D. , Tomczak Jennifer A. , Amiel Eyal , Carr Frances E.
Published: February 2022

Anaplastic thyroid cancer (ATC) is one of the most lethal solid tumors, yet there are no effective, long-lasting treatments for ATC patients. Most tumors, including tumors of the endocrine system, exhibit an increased consumption of glucose to fuel cancer progression, and some cancers meet this high glucose requirement by metabolizing glycogen. Our goal was to determine if ATC cells metabolize glycogen and if this could be exploited for treatment. We detected glycogen synthase and glycogen phosphorylase (PYG) isoforms in normal thyroid and thyroid cancer cell lines and patient-derived biopsy samples. Inhibition of PYG using CP-91,149 induced apoptosis in ATC cells but not normal thyroid cells. CP-91,149 decreased NADPH levels and induced reactive oxygen species accumulation. CP-91,149 severely blunted ATC tumor growth in vivo. Our work establishes glycogen metabolism as a novel metabolic process in thyroid cells that presents a unique, oncogenic target that could offer an improved clinical outcome.

Significance

Glycogen metabolism plays an important role in combating reactive oxygen species and apoptosis in anaplastic thyroid cancer. Glycogen phosphorylase was inhibited with small molecule inhibitors that limited cell proliferation in vitro and blunted tumor growth in a nude mouse xenograft. This study demonstrates that glycogen metabolism is a viable target in one of the most lethal solid tumors.
Hypoxia modulates cellular endocytic pathways and organelles with enhanced cell migration and 3D cell invasion
Authors: Naveena A Hema , Bhatia Dhiraj
Published: February 2022

Hypoxia, a decrease in cellular or tissue level oxygen content, is characteristic of most tumours and shown to drive cancer progression by altering multiple subcellular processes. We hypothesized that the cancer cells in a hypoxic environment might have slower proliferation rates and increased invasion and migration rate with altered endocytosis when compared to the cancer cells in the periphery of the tumour mass that experiences normoxic condition. Using chemically induced hypoxia, a short hypoxic exposure increased the uptake of clathrin independent endocytic marker Galectin-3, but a prolonged hypoxic exposure decreased clathrin-independent endocytic uptake, while clathrin mediated endocytosis remained unaffected. Subcellular organelles such as mitochondria showed enhanced intensity to withstand the hypoxic stress, while other organelles such as ER were significantly decreased. The proliferation rates decreased, and the migration and invasion rate increased in cancer cells in hypoxic condition compared to normoxic cancer cells.These data suggest that hypoxia modulates cellular endocytic pathways with decreased proliferation and enhanced cell migration and invasion.

Abstract Figure
Transglutaminase 2 associated with PI3K and PTEN in a putative membrane-bound signalosome platform blunts cell death
Authors: Jambrovics Károly , Botó Pál , Pap Attila , Sarang Zsolt , Kolostyák Zsuzsanna , Czimmerer Zsolt , Szatmari Istvan , Fésüs László , Uray Iván P. , Balajthy Zoltán
Published: February 2022

Atypically expressed transglutaminase 2 (TG2) has been identified as a poor prognostic factor in a variety of cancers. In this study, we evaluated the contribution of TG2 to the prolonged cell survival of differentiated acute promyelocytic leukaemia (APL) cells in response to the standard treatment with combined retinoic acid (ATRA) and arsenic trioxide (ATO). We report that one advantage of ATRA + ATO treatment compared to ATRA alone diminishes the amount of activated and non-activated CD11b/CD18 and CD11c/CD18 cell surface integrin receptors. These changes suppress ATRA-induced TG2 docking on the cytosolic part of CD18 β2-integrin subunits and reduce cell survival. In addition, TG2 overexpresses and hyperactivates the phosphatidylinositol-3-kinase (PI3K), phospho-AKT S473, and phospho-mTOR S2481 signalling axis. mTORC2 acts as a functional switch between cell survival and death by promoting the full activation of AKT. We show that TG2 presumably triggers the formation of a signalosome platform, hyperactivates downstream mTORC2-AKT signalling, which in turn phosphorylates and inhibits the activity of FOXO3, a key pro-apoptotic transcription factor. In contrast, the absence of TG2 restores basic phospho-mTOR S2481, phospho-AKT S473, PI3K, and PTEN expression and activity, thereby sensitising APL cells to ATO-induced cell death. We conclude, that atypically expressed TG2 may serve as a hub, facilitating signal transduction via signalosome formation by the CD18 subunit with both PI3K hyperactivation and PTEN inactivation through the PI3K PTEN cycle in ATRA-treated APL cells.
Detecting clonemates in multicellular clonal species based on “Shared Heterozygosity (SH)” and technical replicates
Authors: Yu Lei , Stachowicz John J. , DuBois Katie , Reusch Thorsten B. H.
Published: February 2022

Clonal reproduction, the formation of new individuals that are genetically nearly identical to the parent via mitosis in the absence of genetic recombination, is a very common reproductive mode across plants, fungi, and animals. Current genetic marker based methods fail to detect clonal structure when all collected samples belong to one single clone, which seems to be more common than previously thought. Here we propose a new similarity index, “Shared Heterozygosity (SH)” based on the number of genetic markers (typically SNPs, single-nucleotide polymorphisms) that are identically heterozygous among two or more genomes (i.e., NSH). Ideally NSH should be on the order of approximately >=3,000, which can be easily achieved nowadays via Restriction-site Associated DNA (RAD) sequencing or whole-genome resequencing. One should be careful when NSH is small (roughly <1,000). We analyze two large seagrass clones (Posidonia australis, Zostera marina) along with two Z. marina clones of known age (17-yrs), and show that SH can potentially extend the detection of clonemates to any pair of samples with the aid of technical replicates. Another potential application of SH is to detect possible parent-descendant pairs under selfing, because the heterozygous loci in the selfing-produced descendants represent a subset of those in the parent. Our proposed workflow takes advantage of the availability of the larger number of genetic markers in the genomic era, and fills a gap in detecting clonemates in the growing number of cases where many or all samples at a location belong to one single clone.
Changing flows balance nutrient absorption and bacterial growth along the gut
Authors: Codutti Agnese , Cremer Jonas , Alim Karen
Published: February 2022

Small intestine motility and its ensuing flow of luminal content impact both nutrient absorption and bacterial growth. To explore this interdependence we introduce a biophysical description of intestinal flow and absorption. Rooted in observations of mice we identify the average flow velocity as the key control of absorption efficiency and bacterial growth, independently of the exact contraction pattern. We uncover self-regulation of contraction and flow in response to nutrients and bacterial levels to promote efficient absorption while restraining detrimental bacterial overgrowth.
First record of anti-predator behavior in the gall-forming aphidMordwilkoja vagabunda
Authors: Legan Andrew Wesley
Published: February 2022

The gall-forming aphidMordwilkoja vagabundahas been an outgroup in molecular studies of the evolution of social behavior in thePemphigusgenus, butMordwilkojaaphids have not previously been assayed for social behavior, such as altruistic defense. This study reports experiments carried out in July in Ithaca, NY, USA, in which nymphs (immature aphids) ofM. vagabundawere video recorded under a stereo microscope while they encountered pyralid moth larvae in a plastic arena.M. vagabundanymphs of all instars used their legs to claw moth larvae while pressing their rostrums against the larvae, possibly to pierce the cuticle. Many of the attacking aphids were alatoid nymphs, rather than the specialized first instar soldiers typically observed inPemphigusspecies.M. vagabundanymphs moved in bursts that sometimes became synchronized among several aphids in the same vicinity. These synchronized, rhythmic movements may be anti-predator defense strategies comparable to the collective twitching and kicking response observed in colonies ofAphis neriiand other aphid species. Defensive behaviors byM. vagabundanymphs may be altruistic fortress defense strategies which maximize inclusive fitness of the clone.

Open Research statement

Video data are shared publicly on a repository, Zenodo, at this DOI:https://doi.org/10.5281/zenodo.5636845
The infiltration pattern of microenvironmental cells and different immune escape mechanisms in colorectal cancer
Authors: Mao Yihao , Feng Qingyang , Chang Wenju , Lv Yang , Xu Yuqiu , Chang Jiang , Zheng Peng , Yu Shanchao , Zhang Zhiyuan , Li Zhiqiang , Lin Qi , Tang Wentao , Zhu Dexiang , Ji Meiling , Ren Li , Wei Ye , He Guodong , Xu Jianmin
Published: February 2022

Background

The tumour microenvironment (TME) plays a crucial role in tumour progression and metastasis. However, the infiltration pattern of TME cells in CRC samples and the immune escape mechanism underneath have not been studied sufficiently.

Methods

Transcriptomic data from public datasets were retrieved online. In total, 1802 samples from the microarray dataset and 619 samples from the TCGA dataset were enrolled. The ssGSEA algorithm and unsupervised clustering were used for TME cells infiltration speculation and infiltration pattern recognition.

Results

CRC samples can be classified into three distinct TME cell subtypes. Subtype 1, the immune-active subtype, was characterised by high infiltration of activated adaptive immune cells. Subtype 2, the immune-desert subtype, featured high tumour purity and low infiltration of immune and stromal cells. And subtype 3, stroma-rich subtype, had high infiltration of stromal cells. The stroma-rich subtype conferred a significantly worse prognosis. Three subtypes had different immune escape mechanisms. The immune-active subtype has the highest immune checkpoint expression level. In comparison, the immune-desert subtype had the lowest immunogenicity and the defective antigen presentation. And the stroma-rich subtype lacked activated immune cells.

Conclusions

Distinct TME cell subtypes and immune escape mechanisms may provide inspiration and direction for further researches on CRC immunotherapy.
pycoMeth: A toolbox for differential methylation testing from Nanopore methylation calls
Authors: Snajder Rene , Leger Adrien , Stegle Oliver , Bonder Marc Jan
Published: February 2022

Abstract

Advances in base and methylation calling of Oxford Nanopore Technologies (ONT) sequencing data have opened up the possibility for joint profiling of genomic and epigenetic variation on the same long reads. Existing data storage and analysis frameworks that were developed for CpG-methylation arrays or short-read bisulfite sequencing data have severe shortcomings for handling of ONT data, failing to fully exploit methylation profiles obtained from long read technologies. To address these issues, we present pycoMeth, a toolbox to store, manage and analyse DNA methylation data obtained from long-read ONT sequencing data. Our toolbox centers around a new storage format called MetH5, which allows simultaneously for efficient storage of and rapid data access for read-level and reference-anchored methylation call data. Building on this storage format, we propose efficient algorithms for the segmentation and differential methylation testing of methylation calls from ONT data. Our methods draw from read-group and read-level information, as well as methylation call uncertainties, and allow for de novo discovery of methylation patterns and differentially methylated regions in a haplotyped multi-sample setting. We show that MetH5 is more efficient than existing solutions for storing ONT methylation calls, and carry out benchmarking for segmentation and differential methylation analysis, demonstrating increased performance and sensitivity of pycoMeth compared to existing solutions.