bluuebunny/crossref_metadata_2025 huggingface dataset:
Resolving single-cell copy number profiling for large datasets
Authors: Wang Ruohan , Zhang Yuwei , Wang Mengbo , Feng Xikang , Wang Jianping , Li Shuai Cheng
Published: February 2022

The advances of single-cell DNA sequencing (scDNA-seq) enable us to characterize the genetic heterogeneity of cancer cells. However, the high noise and low coverage of scDNA-seq impede the estimation of copy number variations (CNVs). In addition, existing tools suffer from intensive execution time and often fail on large datasets. Here, we propose SeCNV, a novel method that leverages structural entropy, to profile the copy numbers. SeCNV adopts a local Gaussian kernel to construct a matrix, depth congruent map, capturing the similarities between any two bins along the genome. Then SeCNV partitions the genome into segments by minimizing the structural entropy from the depth congruent map. With the partition, SeCNV estimates the copy numbers within each segment for cells. We simulate nine datasets with various breakpoint distributions and amplitudes of noise to benchmark SeCNV. SeCNV achieves a robust performance, i.e., the F1-scores are higher than 0.95 for breakpoint detections, significantly outperforming state-of-the-art methods. SeCNV successfully processes large datasets (>50,000 cells) within four minutes while other tools failed to finish within the time limit, i.e., 120 hours. We apply SeCNV to single-nucleus sequencing (SNS) datasets from two breast cancer patients and acoustic cell tagmentation (ACT) sequencing datasets from eight breast cancer patients. SeCNV successfully reproduces the distinct subclones and infers tumor heterogeneity. SeCNV is available at https://github.com/deepomicslab/SeCNV.
Rheological transition driven by matrix makes cancer spheroids resilient under confinement
Authors: Dutt Tavishi , Langthasa Jimpi , Monica U , Mishra Satyarthi , Bothra Siddharth , Vadaparty Annapurna , Sen Prosenjit , Bhat Ramray
Published: February 2022

Cancer metastasis through a confining peritoneal fluid microenvironment is mediated by spheroids: clusters of disseminated transformed cells. Ovarian cancer spheroids are frequently cavitated and their ‘blastuloid’ morphology is correlated with an extracellular matrix (ECM) coat. Here, we investigate the effects of such morphology on the mechanical integrity of confined cancer spheroids. Atomic force microscopy showed higher elastic modulus for blastuloid spheroids relative to their prefiguring non-lumen ‘moruloid’ counterparts. Subsequently, spheroids were flowed through microfluidic conditions mimicking peritoneal confinement. Traversing moruloids exhibited asymmetric cell flows during entry, often deformed and disintegrated through travel, and showed an incomplete- and slow shape recovery upon exit. In contrast, blastuloids traveled faster, exhibited rapid and efficient shape recovery upon exit, symmetric vector flows, and lesser disintegration. A multiscale computational model predicted higher intercellular adhesion and a dynamical lumen make blastuloids resilient. Although, E-cadherin overexpression in moruloids did not affect their resilience, blastuloid ECM-debridement decreased E-cadherin membrane localization, obliterated the lumen, and reversed the rheological properties of blastuloids to those typifying moruloids. The ECM-induced lumen therefore drives spheroidal transition from a labile viscoplastic to a resilient elastic state allowing them to survive spatially-constrained peritoneal flows.
Seasonal dynamics of the wild rodent faecal virome
Authors: Raghwani Jayna , Faust Christina L. , François Sarah , Nguyen Dung , Marsh Kirsty , Raulo Aura , Hill Sarah C. , Parag Kris V. , Simmonds Peter , Knowles Sarah C. L. , Pybus Oliver G.
Published: February 2022

Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Leveraging non-invasive faecal samples from a long-term wild rodent study, we characterised viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis, andM. glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most abundant virus families, Picornaviruses, show pronounced temporal changes in viral richness and diversity, which were associated with concurrent and up to ∼3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.
Pathogen prevalence modulates medication behavior in ant Formica fusca
Authors: Rissanen Jason , Helanterä Heikki , Freitak Dalial
Published: February 2022

Ants face unique challenges regarding pathogens, as the sociality which has allowed them to form large and complex colonies also raises the potential for transmission of disease within these colonies. To cope with the threat of pathogens, ants have developed a variety of behavioral and physiological strategies. One of these strategies is self-medication, in which animals use biologically active compounds to combat pathogens in a way which would be harmful in the absence of them. Formica fusca ants are to date the only species of ants proven to successfully self-medicate against an active infection caused by a fungal pathogen by supplementing their diet with food containing hydrogen peroxide. Here, we build on that research by investigating how the prevalence of disease in colonies of F. fusca affects the strength of the self-medication response. We exposed either half of the workers of each colony or all of them to a fungal pathogen and offered them different combinations of diets. We see that workers of F. fusca engage in self-medication behavior even if exposed to a low lethal dose of a pathogen, and that the strength of that response is affected by the prevalence of the disease in the colonies. We also saw that the infection status of the individual foragers did not significantly affect their decision to forage on either control food or medicinal food as uninfected workers were also foraging on hydrogen peroxide food, which opens up the possibility of kin medication in partially infected colonies. Our results further affirm the ability of ants to self-medicate against fungal pathogens, shed new light on plasticity of self-medication and raise new questions to be investigated on the role self-medication has in social immunity.
Shoulder muscle recruitment of small amplitude motor units during the delay period encodes a reach movement plan which is sensitive to task context
Authors: Rungta Satya , Murthy Aditya
Published: February 2022

Understanding how motor plans are transformed into appropriate patterns of muscle activity is a central question in motor control. While muscle activity during the delay period has not been reported using conventional EMG approaches, we isolated motor unit activity using a high-density surface EMG signal from the anterior deltoid muscle to test whether heterogeneity in motor units could reveal early preparatory activity. Consistent with our previous work (Rungta et al., 2021), we observed early selective recruitment of small-amplitude size motor units during the delay period for hand movements like early recruitment of small-amplitude motor units in neck muscles of non-human primates performing delayed saccade tasks. This early activity was spatially specific and increased with time and resembled an accumulation to threshold model that correlated with movement onset time. Such early recruitment of ramping motor units was also observed at the single trial level as well. In contrast, no such recruitment of large amplitude size motor units, called non-rampers, was observed during the delay period. Instead, non-rampers became spatially specific and predicted movement onset time after the delay period. Interestingly, spatially specific delay period activity was only observed for hand movements but was absent for isometric force-driven cursor movements. Nonetheless, muscle activity was correlated with the time it took to initiate movements in both task conditions for non-rampers. Overall, our results reveal a novel heterogeneity in the EMG activity which allows the expression of early motor preparation via small amplitude size motor units which are differentially activated during initiation of movements.

Significance statement

We studied the spatial and temporal aspects of response preparation in the anterior deltoid muscle using high-density surface EMG. Our results show that early spatially specific ramping activity that predicted reaction times could be accessed from muscle activity but was absent during isometric force-driven cursor movements. Such ramping activity could be quantified using an accumulator framework across trials, as well as within single trials but was not observed in isometric reach tasks involving cursor movements.
A single dose of the catecholamine precursor Tyrosine reduces physiological arousal and decreases decision thresholds in reinforcement learning and temporal discounting
Authors: Mathar David , Abdoust Mani Erfanian , Tuszus Deniz , Marrenbach Tobias , Peters Jan
Published: February 2022

Supplementation with the catecholamine precursor L-Tyrosine might enhance cognitive performance, but overall findings are mixed. Here, we investigate the effect of a single dose of tyrosine (2g) vs. placebo on two key aspects of catecholamine-dependent decision-making: model-based reinforcement learning (2-step task) and temporal discounting, using a double-blind, placebo-controlled, within-subject design (n=28 healthy male participants). We leveraged drift diffusion models in a hierarchical Bayesian framework to jointly model participants’ choices and response times in both tasks. Furthermore, comprehensive autonomic monitoring (heart rate, heart rate variability, pupillometry, spontaneous eye-blink rate) was performed both pre- and post-supplementation, to explore potential physiological effects of supplementation. Across tasks, tyrosine consistently reduced participants’ RTs without deteriorating task-performance. Diffusion modeling linked this effect to attenuated decision-thresholds in both tasks and further revealed increased model-based control (2-step task) and (if anything) attenuated temporal discounting. On the physiological level, participants’ pupil dilation was predictive of the individual degree of temporal discounting. Tyrosine supplementation reduced physiological arousal as revealed by increases in pupil dilation variability and reductions in hear rate. Supplementation-related changes in physiological arousal predicted individual changes in temporal discounting. Our findings provide first evidence that tyrosine supplementation might impact psychophysiological parameters, and suggest that modeling approaches based on sequential sampling models can yield novel insights into latent cognitive processes modulated by amino-acid supplementation.
Sen1 is a key regulator of transcription-driven conflicts
Authors: Aiello Umberto , Challal Drice , Wentzinger Griselda , Lengronne Armelle , Appanah Rowin , Pasero Philippe , Palancade Benoit , Libri Domenico
Published: February 2022

Cellular homeostasis requires the coordination of several machineries concurrently engaged on the DNA. Wide-spread transcription can interfere with other processes and transcription-replication conflicts (TRCs) threaten genome stability. The conserved Sen1 helicase terminates non-coding transcription, but also interacts with the replisome and reportedly resolves genotoxic R-loops. Sen1 prevents genomic instability but how this relates to its molecular functions remains unclear. We generated high-resolution, genome-wide maps of transcription-dependent conflicts and R-loops using a Sen1 mutant that has lost interaction with the replisome but is termination proficient. We show that Sen1 removes RNA polymerase II at TRCs within genes and the rDNA, but also at sites of transcription-transcription conflicts under physiological conditions, thus qualifying as a “key regulator of conflicts”. We demonstrate that genomic stability is only affected by Sen1 mutation when, in addition to its role at the replisome, termination of non-coding transcription or R-loop removal are additionally compromised.
An evaluation of RNA-seq differential analysis methods
Authors: Li Dongmei , Zand Martin , Dye Timothy , Goniewicz Maciej , Rahman Irfan , Xie Zidian
Published: February 2022

RNA-seq is a high-throughput sequencing technology widely used for gene transcript discovery and quantification under different biological or biomedical conditions. A fundamental research question in most RNA-seq experiments is the identification of differentially expressed genes among experimental conditions or sample groups. Numerous statistical methods for RNA-seq differential analysis have been proposed since the emergence of the RNA-seq assay.

To evaluate popular differential analysis methods used in the open source R and Bioconductor packages, we conducted multiple simulation studies to compare the performance of eight RNA-seq differential analysis methods used in RNA-seq data analysis (edgeR, DESeq, DESeq2, baySeq, EBSeq, NOISeq, SAMSeq, Voom). The comparisons were across different scenarios with either equal or unequal library sizes, different distribution assumptions and sample sizes. We measured performance using false discovery rate (FDR) control, power, and stability. No significant differences were observed for FDR control, power, or stability across methods, whether with equal or unequal library sizes. For RNA-seq count data with negative binomial distribution, when sample size is 3 in each group, EBSeq performed better than the other methods as indicated by FDR control, power, and stability. When sample sizes increase to 6 or 12 in each group, DESeq2 performed slightly better than other methods. All methods have improved performance when sample size increases to 12 in each group except DESeq. For RNA-seq count data with log-normal distribution, both DESeq and DESeq2 methods performed better than other methods in terms of FDR control, power, and stability across all sample sizes. Real RNA-seq experimental data were also used to compare the total number of discoveries and stability of discoveries for each method.

For RNA-seq data analysis, the EBSeq method is recommended for studies with sample size as small as 3 in each group, and the DESeq2 method is recommended for sample size of 6 or higher in each group when the data follow the negative binomial distribution. Both DESeq and DESeq2 methods are recommended when the data follow the log-normal distribution.
The LINC complex inhibits excessive chromatin repression
Authors: Amiad Pavlov Daria , Unnikannan CP , Lorber Dana , Bajpai Gaurav , Olender Tsviya , Stoops Elizabeth , Reuveny Adriana , Safran Samuel , Volk Talila
Published: February 2022

We show here that the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex is needed to minimize chromatin repression. The genomic binding profile of Polycomb, Heterochromatin Protein1 (HP1a) repressors, and of RNA-Pol II were studied inDrosophilalarval muscles lacking functional LINC complex. A significant increase in the binding of Polycomb, and parallel reduction of RNA-Pol-II binding to a set of muscle genes was observed. Consistently, enhanced tri-methylated H3K9 and H3K27 repressive modifications, and reduced chromatin activation by H3K9 acetylation were found. Furthermore, larger tri-methylated H3K27me3 repressive clusters, and chromatin redistribution from the nuclear periphery towards nuclear center, were detected in live LINC mutant larval muscles. Computer simulation indicated that the observed dissociation of the chromatin from the nuclear envelope promotes growth of tri-methylated H3K27 repressive clusters. Thus, we suggest that by promoting chromatin-nuclear envelope binding, the LINC complex restricts the size of repressive H3K27 tri-methylated clusters, thereby limiting the binding of Polycomb transcription repressor, directing robust transcription in muscle fibers.
Spatially Resolved Transcriptomics for Evaluation of Intracranial Vessels in a Rabbit Model: Proof of Concept
Authors: Zabriskie Matthew S. , Cooke Daniel L. , Wang Chuanzhuo , Alexander Matthew D.
Published: February 2022

Background

Better understanding of vessel biology and vascular pathophysiology is needed to improve understanding of cerebrovascular disorders. Tissue from diseased vessels can offer the best data. Rabbit models can be effective for studying intracranial vessels, filling gaps resulting from difficulties acquiring human tissue. Spatially-resolved transcriptomics (SRT) in particular hold promise for studying such models as they build on RNA sequencing methods, augmenting such data with histopathology.

Methods

Rabbit brains with intact arteries were flash frozen, cryosectioned, and stained with H&E to confirm adequate inclusion of intracranial vessels before proceeding with tissue optimization and gene expression analysis using the Visium SRT platform. SRT results were analyzed with k-means clustering analysis, and differential gene expression was examined, comparing arteries to veins.

Results

Cryosections were successfully mounted on Visium proprietary slides. Quality control thresholds were met. Optimum permeabilization was determined to be 24 minutes for the tissue optimization step. In analysis of SRT data, k-means clustering distinguished vascular tissue from parenchyma. When comparing gene expression traits, the most differentially expressed genes were those found in smooth muscle cells. These genes were more commonly expressed in arteries compared to veins.

Conclusions

Intracranial vessels from model rabbits can be processed and analyzed with the Visium SRT platform. Face validity is found in the ability of SRT data to distinguish vessels from parenchymal tissue and differential expression analysis accurately distinguishing arteries from veins. SRT should be considered for future animal model investigations into cerebrovascular diseases.
Selective integration of diverse taste inputs within a single taste modality
Authors: Deere Julia U. , Sarkissian Arvin A. , Yang Meifeng (Maia) , Uttley Hannah A. , Santana Nicole Martinez , Nguyen Lam , Ravi Kaushiki , Devineni Anita V.
Published: February 2022

A fundamental question in sensory processing is how different channels of sensory input are processed to regulate behavior. Different input channels may converge onto common downstream pathways to drive the same behaviors, or they may activate separate pathways to regulate distinct behaviors. We investigated this question in theDrosophilabitter taste system, which contains diverse bitter-sensing cells residing in different taste organs. First, we optogenetically activated subsets of bitter neurons within each organ. These subsets elicited broad and highly overlapping behavioral effects, suggesting that they converge onto common downstream pathways, but we also observed behavioral differences that argue for biased convergence. Consistent with these results, transsynaptic tracing revealed that bitter neurons in different organs connect to overlapping downstream pathways with biased connectivity. We investigated taste processing in one type of second-order bitter neuron that projects to the higher brain. These neurons integrate input from multiple organs and regulate specific taste-related behaviors. We then traced downstream circuits, providing the first glimpse into taste processing in the higher brain. Together, these results reveal that different bitter inputs are selectively integrated early in the circuit, enabling the pooling of information, while the circuit then diverges into multiple pathways that may have different roles.
Identification of Catechins Binding Pockets in Monomeric Aβ42Through Ensemble Docking and MD Simulations
Authors: Firouzi Rohoullah , Sowlati-Hashjin Shahin , Chávez-García Cecilia , Ashouri Mitra , Karimi-Jafari Mohammad Hossein , Karttunen Mikko
Published: February 2022

The assembly of the Amyloid-βpeptide (Aβ) into toxic oligomers and fibrils is associated with Alzheimer’s disease and dementia. Therefore, disrupting amyloid assembly by direct targeting of the Aβmonomeric form with small molecules or antibodies is a promising therapeutic strategy. However, given the dynamic nature of Aβ, standard computational tools cannot be easily applied for high-throughput structure-based virtual screening in drug discovery projects. In the current study, we propose a computational pipeline – in the framework of the ensemble docking strategy – to identify catechins’ binding pockets in monomeric Aβ42. It is shown that both hydrophobic aromatic interactions and hydrogen bonding are crucial for the binding of catechins to Aβ42. Also, it has been found that all the studied ligands, especially theEGCG, can act as potent inhibitors against amyloid aggregation by blocking the central hydrophobic region of the Aβ. Our findings are evaluated and confirmed with multi-microsecond MD simulations. Finally, it is suggested that our proposed pipeline, with low computational cost in comparison with MD simulations, is a suitable approach for the virtual screening of ligand libraries against Aβ.
The interplay between developmental stage and environment underlies the adaptive effect of a natural transposable element insertion
Authors: Merenciano Miriam , González Josefa
Published: February 2022

Establishing causal links between adaptive mutations and their ecologically relevant phenotypes is key to understanding the process of adaptation, a central goal in evolutionary biology that is also relevant for conservation biology, medicine and agriculture. Although progress has been made, the number of causal adaptive mutations identified so far is still limited as gene by gene, and gene by environment interactions, among others, complicates linking genetic variation with its fitness–related effects. Transposable elements, often ignored in the quest for the genetic basis of adaptive evolution, are known to be a genome-wide source of regulatory elements across organisms that at times can lead to adaptive phenotypes. In this work, we combine gene expression, in vivo reporter assays, CRISPR/Cas9 genome editing, and survival experiments to characterize in detail the molecular and phenotypic consequences of a natural Drosophila melanogaster transposable element insertion: the roo solo-LTR FBti0019985. This transposable element provides an alternative promoter to the transcription factor Lime, involved in cold- and immune-stress responses. We found that the effect of FBti0019985 on Lime expression depends on the interplay between the developmental stage and the environmental conditions. We further establish a causal link between the presence of FBti0019985 and increased survival to cold- and immune-stress. Our results exemplify how several developmental stages and environmental conditions need to be considered to characterize the molecular and functional effects of a genetic variant, and add to the growing body of evidence that transposable elements can induce complex mutations with ecologically relevant effects.
CELLoGeNe - an Energy Landscape Framework for Logical Networks Controlling Cell Decisions
Authors: Andersson Emil , Sjö Mattias , Kaji Keisuke , Olariu Victor
Published: February 2022

Experimental and computational efforts are constantly made to elucidate mechanisms controlling cell fate decisions during development and cell reprogramming. One powerful method is to consider cell commitment and reprogramming as movements in an energy landscape. Here, we develop CELLoGeNe (Computation of Energy Landscapes of Logical Gene Networks), which maps Boolean implementation of gene regulatory networks (GRNs) into energy landscapes. CELLoGeNe removes inadvertent symmetries in the energy landscapes normally arising from standard Boolean operators. Furthermore, CELLoGeNe provides a tool for visualising multi-dimensional energy landscapes and a platform to stochastically probe and analyse the shapes of the computed landscapes corresponding to the epigenetic landscapes for development and reprogramming. We demonstrate CELLoGeNe on a GRN governing maintenance and self-renewal of pluripotency, identifying attractors experimentally validated. We also apply CELLoGeNe on a network controlling reprogramming from mouse embryonic fibroblast (MEF) to induced pluripotent stem cells (iPSCs) where we identify potential roadblocks as attractors. CELLoGeNe is a general framework that can be applied to various biological systems offering a broad picture of intracellular dynamics otherwise inaccessible with existing methods.
Isocitrate dehydrogenase 3b is required for spermiogenesis but dispensable for retinal degeneration
Authors: Zhu Siyan , Huang Jiancheng , Xu Rong , Wang Yekai , Wan Yiming , McNeel Rachel , Parker Edward , Kolson Douglas , Yam Michelle , Webb Bradley , Zhao Chen , Du Jianhai
Published: February 2022

Isocitrate dehydrogenase 3 (IDH3), a key enzyme in mitochondrial tricarboxylic acid (TCA) cycle, catalyzes the decarboxylation of isocitrate into α-ketoglutarate (αKG), converting NAD+ into NADH. We have found that IDH3 β subunit (IDH3B) is essential for IDH3 activity in multiple tissues. Loss of Idh3b in mice causes substantial accumulation of the isocitrate and its precursors in the TCA cycle, particularly in the testes, whereas the levels of the downstream metabolites remain unchanged or slightly increased. The Idh3b-knockout (KO) mice have normal visual function without retinal degeneration. However, the male KO mice are infertile. Loss of Idh3b causes energetic deficit and disrupts the biogenesis of acrosome and flagellum, resulting in spermiogenesis arrestment in sperm cells. Together, we demonstrate IDH3B controls its substrate levels in the TCA cycle and it is required for sperm mitochondrial metabolism and spermiogenesis, highlighting the importance of the tissue-specific function of the ubiquitous TCA cycle.
Dissecting aggregation and seeding dynamics of α-Syn polymorphs using the phasor approach to FLIM
Authors: Tittelmeier Jessica , Druffel-Augustin Silke , Alik Ania , Melki Ronald , Nussbaum-Krammer Carmen
Published: February 2022

Synucleinopathies are a heterogenous group of neurodegenerative diseases characterized by the progressive accumulation of pathological α-synuclein (α-Syn). The importance of structural polymorphism of α-Syn assemblies for distinct synucleinopathies and their progression is increasingly recognized. However, the underlying mechanisms are poorly understood. Here we use fluorescence lifetime imaging microscopy (FLIM) to investigate seeded aggregation of α-Syn in a biosensor cell line. We show that conformationally distinct α-Syn polymorphs exhibit characteristic fluorescence lifetimes. FLIM further revealed that α-Syn polymorphs were differentially processed by cellular clearance pathways, yielding fibrillar species with increased seeding capacity. Thus, FLIM is not only a powerful tool to distinguish different amyloid structures, but also to monitor the dynamic process of amyloid remodeling by the cellular environment. Our data suggest that the accumulation of highly seeding competent degradation products for particular polymorphs may account for accelerated disease progression in some patients.
The GTPase Activity of the Double FYVE Domain Containing Protein 1 (DFCP1) Regulates Lipid Droplet Metabolism
Authors: Ismail V.A. , Naismith T. , Kast D.J.
Published: February 2022

Lipid droplets (LDs) are transient lipid storage organelles that can be readily tapped to resupply cells with energy or lipid building blocks, and therefore play a central role in cellular metabolism. However, the molecular factors and underlying mechanisms that regulate the growth and degradation of LDs are poorly understood. It has emerged that LD metabolism is sensitive to the autophagy- and LD-associated protein Double FYVE Domain Containing Protein 1 (DFCP1), however, little is known about DFCP1’s roles in autophagy and LD metabolism. Here, we show that DFCP1 contains a novel GTPase domain that regulates LD size by controlling the assembly of DFCP1 onto LDs in response to changes in nutrient availability. Specifically, we show that DFCP1 accumulation on LDs is independent of PI3P-binding, but requires a combination of the ER-binding domain and a unique GTPase domain. This novel GTPase domain possesses a low basal GTP turnover rate and has the ability to dimerize. Furthermore, mutations in the DFCP1 that either impact GTP hydrolysis or dimerization, result in changes in the accumulation of DFCP1 on LDs, as well as in changes in LD density and size. Importantly, the magnitude of these changes depends on the nutritional status of the cell. Collectively, our findings indicate that DFCP1 is a GTP-dependent metabolic sensor capable of modulating cellular storage of free fatty acids.
Ethylene Insensitive 3-Like 2 (EIL2) is a Brassicaceae-specific transcriptional regulator involved in fine-tuning ethylene-dependent hypocotyl elongation, lateral root formation and flowering time in Arabidopsis thaliana
Authors: Houben Maarten , Vaughan-Hirsch John , Mou Wangshu , Van de Poel Bram
Published: February 2022

Ethylene signaling directs a pleiotropy of developmental processes in plants. In Arabidopsis, ethylene signaling converges at the master transcription factor Ethylene Insensitive 3 (EIN3), which has five homologs, EIN3-like 1-5 (EIL1-5). EIL1 is most characterized and operates similar as EIN3, while EIL3-5 are not involved in ethylene signaling. EIL2 remains less investigated. Our phylogenetic analysis revealed that EIL2 homologs are only retrieved in the Brassicaceae family, suggesting EIL2 diverged to have specific functions in the mustard family. By characterizing eil2 mutants, we found that EIL2 is involved in regulating ethylene-specific developmental processes in Arabidopsis thaliana, albeit in a more subtle way compared to EIN3/EIL1. EIL2 steers ethylene-triggered hypocotyl elongation in light-grown seedlings and it is involved in lateral root formation. Furthermore, EIL2 takes part in regulating flowering time as eil2 mutants flower on average one day earlier and have fewer leaves. A pEIL2:EIL2:GFP translational reporter line revealed that EIL2 protein abundance is restricted to the stele of young developing roots. EIL2 expression, and not EIL2 protein stability, is regulated by ethylene in an EIN3/EIL1-dependent way. Despite EIL2 taking part in several developmental processes, the precise upstream and downstream regulation of this ethylene- and Brassicaceae-specific transcription factor remains to be elucidated.

Highlight

EIL2 is an ethylene-dependent transcription factor that evolved exclusively in the mustard family and operates downstream from EIN3/EIL1. EIL2 is involved in fine-tuning hypocotyl elongation, lateral root formation and flowering time in Arabidopsis thaliana.
A systems biology approach to elucidate the post-translational regulome of coronary artery disease
Authors: Sharma Ankit , Ghatge Madankumar , Deshpande Vrushali , Vangala Rajani Kanth
Published: February 2022

Coronary Artery Disease is a major killer in India and world at large but the molecular regulators which modulate clinically relevant pathways are not completely understood. This study was aimed at identifying essential post-translational modifications (PTM) regulome network and its master regulator modulating the CAD associated pathways. 995 CAD associated genes were taken from InCardiome database (www.tri-incardiome.org) were analyzed for all possible PTMs. Two important interdependent molecular processes which define the function of a protein are protein-protein interactions and PTMs of which PTMs play regulatory role. Using PTMCode2 we evaluated the co-evolving amino acid residues for important PTMs and found that serine-serine phosphorylation is highly represented combinatorial regulator in these set of proteins. Furthermore, in the CAD associated pathways we again found that serine phosphorylation was dominant player in all the processes of atherosclerosis. In order to identify the master regulator kinase, we further assessed the kinome network associated with CAD and identified 5 most important kinases namely GSK3B, PRKCA, PRKCD, SRC and PRKACA which might modulate clinically important pathways. GSK3B with the highest network parameters (node degree and betweenness centrality) was identified as master regulator and 1 U/l increase of phsophoGSK3B (on a log scale) increased the odds ratio (OR) by 4.07 fold (AUC 0.620) and 6.27 fold (AUC 0.752) upon addition of conventional risk factors (CRFs).
Rtt109 promotes nucleosome replacement ahead of the replicating fork
Authors: Jonas Felix , Yaakov Gilad , Barkai Naama
Published: February 2022

DNA replication perturbs chromatin by triggering the eviction, replacement and incorporation of nucleosomes. How this dynamic is orchestrated in time and space is poorly understood. Here, we apply a recently established sensor for histone exchange to follow the time-resolved histone H3 exchange profile in budding yeast cells undergoing synchronous replication. We find that new histones are incorporated not only behind, but also ahead of the replication fork. We provide evidence that Rtt109, the S phase-specific acetyltransferase, stabilizes nucleosomes behind the fork, but promotes H3 replacement ahead of the fork. Unexpectedly, increased replacement ahead of the fork is independent of the primary Rtt109 acetylation target H3K56, and rather results from Rtt109 activity towards the H3 N-terminus. Our results suggest that selective incorporation of differentially modified H3s behind and ahead of the replication fork results in opposing effects on histone exchange, which may contribute to genome stability by overcoming replication-associated challenges.
Validation of a colorimetric LAMP to detect Loxosceles experimental envenomation
Authors: Fernandes Luana Paula , Rocha Marcele Neves , Duarte Clara Guerra , Minozzo João Carlos , do Monte-Neto Rubens L. , Felicori Liza F.
Published: February 2022

Diagnostic tests for brown spider accidents are unavailable and impact treatment decisions, increasing costs and patient risks. In this work, we used for the first time a fast, simple, and visual method based on the loop-mediated isothermal amplification assay (LAMP) to detect Loxosceles envenomation. Using the DNA from L. similis legs, we observed a high sensitivity using this test since as low as 0.32 pg of DNA could be detected. This pH-dependent colorimetric assay was 64 times more sensitive than PCR to detect spider DNA. The test was specific for Loxosceles once no cross-reaction was observed when testing DNA from different agents that cause similar dermonecrotic injuries. The test allowed the detection of Loxosceles intermedia DNA from hair, serum, and swab samples obtained from experimentally-envenomed rabbit within 72 h. The method sensitivity varied according to the sample and the collection time, reaching 100% sensitivity in serum and hair, respectively, 1 h and 24 h after the experimental envenomation. Due to its ease of execution, speed, sensitivity, and specificity, LAMP presents an excellent potential for identifying Loxosceles spp. envenomation. This can reduce the burden on the Health System and the morbidity for the patient by implementing the appropriate therapy immediately.In addition, this work opens up the perspective to other venomous animal accident identification using LAMP.

Highlights

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Using 28S primers it was possible to identify L. similis’ DNA with high sensitivity;

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LAMP was 62-fold more sensitive than PCR and detected as low as 0.32 pg of DNA;

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LAMP detected L. intermedia DNA from hair, serum, and exudate from experimentally-envenomed rabbits;

*

LAMP presents an excellent potential for identifying Loxosceles spp. envenomation.
Screening for functional regulatory variants in open chromatin using GenIE-ATAC
Authors: Cooper Sarah , Schwartzentruber Jeremy , Coomber Eve L , Wu Qianxin , Bassett Andrew
Published: February 2022

Understanding the effects of genetic variation in gene regulatory elements is crucial to interpreting genome function. This is particularly pertinent for the hundreds of thousands of disease-associated variants identified by GWAS, which frequently sit within gene regulatory elements but whose functional effects are often unknown. Current methods are limited in their scalability and ability to assay regulatory variants in their endogenous context, independently of other tightly linked variants. Here we present a new medium-throughput screening system: genome engineering based interrogation of enhancers assay for transposase accessible chromatin (GenIE-ATAC), that measures the effect of individual variants on chromatin accessibility in their endogenous genomic and chromatin context. We employ this assay to screen for the effects of regulatory variants in human induced pluripotent stem cells, validating a subset of causal variants, and extend our software package (rgenie) to analyse these new data. We demonstrate that this methodology can be used to understand the impact of defined deletions and point mutations within transcription factor binding sites. We thus establish GenIE-ATAC as a method to screen for the effect of gene regulatory element variation, allowing identification and prioritisation of causal variants from GWAS for functional follow-up and understanding the mechanisms of regulatory element function.
Linear DNA amplicons as a novel cancer vaccine strategy
Authors: Conforti Antonella , Salvatori Erika , Lione Lucia , Compagnone Mirco , Pinto Eleonora , Shorrock Clay , Hayward James A. , Sun Yuhua , Liang Ben Minghwa , Palombo Fabio , Viscount Brian , Aurisicchio Luigi
Published: February 2022

DNA-based vaccines represent a simple, safe and promising strategy for harnessing the immune system to fight infectious diseases as well as various forms of cancer and thus are considered an important tool in the cancer immunotherapy toolbox. Nonetheless, the manufacture of plasmid DNA vaccines has several drawbacks, including long lead times and the need to remove impurities from bacterial cultures. Here we report the development of polymerase chain reaction (PCR)-produced amplicon expression vectors as DNA vaccines and their in vivo application to elicit antigen-specific immune responses in animal cancer models. Amplicons encoding tumor-associated-antigens, such as telomerase reverse transcriptase or neoantigens expressed by murine tumor cell lines were able to elicit antigen-specific immune responses and proved to significantly impact tumor growth when administered in combination with immune-checkpoint inhibitors (ICIs). These results strongly support the further exploration of the use of PCR-based amplicons as an innovative immunotherapeutic approach to cancer treatment.
Functional Characterization oflncRNA152as an Angiogenesis-Inhibiting Tumor Suppressor in Triple-Negative Breast Cancers
Authors: Kim Dae-Seok , Gadad Shrikanth S. , Setlem Rohit , Kim Kangsan , Malladi Srinivas , Hou Tim Y. , Nandu Tulip , Camacho Cristel V. , Kraus W. Lee
Published: February 2022

Abstract

Long non-coding RNAs have been implicated in many of the hallmarks of cancer. Herein, we found that the expression oflncRNA152(lnc152; a.k.a.DRAIC), which we annotated previously, is highly upregulated in luminal breast cancer (LBC) and downregulated in triple-negative breast cancer (TNBC). Knockdown oflnc152promotes cell migration and invasion in LBC cell lines. In contrast, ectopic expression oflnc152inhibits growth, migration, invasion, and angiogenesis in TNBC cell lines. In mice,lnc152inhibited the growth of TNBC cell xenografts, as well as metastasis of TNBC cells in an intracardiac injection model. Transcriptome analysis of the xenografts indicated thatlnc152downregulates genes controlling angiogenesis. Using pull down assays coupled with LC-MS/MS, we identified RBM47, a known tumor suppressor in breast cancer, as alnc152-interacting protein. The effects oflnc152in TNBC cells are mediated, in part, by regulating the expression of RBM47. Collectively, our results demonstrate thatlnc152is an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC.

Statement ofSignificance

This study identifieslncRNA152as an angiogenesis-inhibiting tumor suppressor that attenuates the aggressive cancer-related phenotypes found in TNBC by upregulating the expression of the tumor suppressor RBM47. As such,lncRNA152may serve as a biomarker to track aggressiveness of breast cancer, as well as therapeutic target for treating TNBC.
Plants cope with fluctuating light by frequency-dependent non-photochemical quenching and cyclic electron transport
Authors: Niu Yuxi , Lazár Dušan , Holzwarth Alfred R. , Kramer David M. , Matsubara Shizue , Fiorani Fabio , Poorter Hendrik , Schrey Silvia D. , Nedbal Ladislav
Published: February 2022

In natural environments, plants are exposed to rapidly changing light. Maintaining photosynthetic efficiency while avoiding photodamage requires equally rapid regulation of photoprotective mechanisms. We asked what the operation frequency range of regulation is in which plants can efficiently respond to varying light.

Chlorophyll fluorescence, P700, plastocyanin, and ferredoxin responses of wild-typeArabidopsis thalianawere measured in oscillating light of various frequencies. We also investigated thenpq1mutant lacking violaxanthin de-epoxidase, thenpq4mutant lacking PsbS-protein, and the mutantscrr2-2, andpgrl1abimpaired in different pathways of the cyclic electron transport.

The fastest was the PsbS-regulation responding to oscillation periods longer than 10s. Processes involving violaxanthin de-epoxidase dampened changes of chlorophyll fluorescence in oscillation periods of 2min or longer. Knocking out the PGRL1-PGR5 pathway strongly reduced variations of all monitored parameters, probably due to congestion in the electron transport. Incapacitating the NDH-like pathway only slightly changed the photosynthetic dynamics.

Our observations are consistent with the assumption that non-photochemical quenching in slow light oscillations involves violaxanthin de-epoxidase to produce, presumably, a stationary, non-oscillating level of zeaxanthin. We interpret the observed dynamics of Photosystem I components as being formed in slow light oscillations partially by thylakoid remodeling that modulates the redox rates.
A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding
Authors: Xu Gen , Lyu Jing , Obata Toshihiro , Liu Sanzhen , Ge Yufeng , Schnable James C. , Yang Jinliang
Published: February 2022

Understanding the patterns of selection during plant evolution and recent crop improvement processes is the central topic in plant breeding and genetics. As an essential macronutrient for plant growth and development, nitrogen (N) is a key factor in affecting plant adaptation and crop improvement. The widespread adoption of less expensive industrial N fixation has dramatically reshaped plant morphology by favoring compact maize plants to tolerant crowding stress. The associated genetic changes, however, have not been systematically studied. Here, we investigated maize inbred lines developed before and after the 1960s — the time point when inorganic N fertilizer started to be widely used for maize production. We identified a strong selective sweep exhibiting pronounced genomic differentiation between Old-Era (pre-1960s) and New-Era (post-1960s) inbred lines. Further study revealed population genetics statistics in the sweep exhibited patterns consistent with historical balancing selection. This balanced genomic interval is associated with a number of morphological, physiological, and metabolite traits related to vegetative N responses. A cluster of three glutamate receptor-like (GLR) genes is located within the region targeted by selection. Functional characterizations suggested differences in transcriptional activity of the GLR genes between the haplotypes carried by Old-Era and New-Era inbred lines likely play an essential role in mediating distinct N responses. The identification of both targets of selection and changes in the regulation of N responsive genes between maize lines developed in different eras sheds light on the N sensing and regulation pathways and paves the way to developing N resilient crops.
Targeting fatty acid beta-oxidation impairs monocyte differentiation and prolongs heart allograft survival
Authors: Zhu Yuehui , Dun Hao , Ye Li , Terada Yuriko , Shriver Leah P. , Patti Gary J. , Kreisel Daniel , Gelman Andrew E. , Wong Brian W.
Published: February 2022

Abstract

Monocytes play an important role in the regulation of alloimmune responses after heart transplantation (HTx). Recent studies have highlighted the importance of immunometabolism in the differentiation and function of myeloid cells. While the importance of glucose metabolism in monocyte differentiation and function has been reported, a role for fatty acid β-oxidation (FAO) has not been explored. Heterotopic HTx was performed using hearts from Balb/c donor mice implanted into C57Bl/6 recipient mice and treated with etomoxir (eto), an irreversible inhibitor of carnitine palmitoyltransferase 1 (Cpt1), a rate-limiting step of FAO, or vehicle control. FAO inhibition prolonged HTx survival, reduced early T cell infiltration/ activation and reduced dendritic cell (DC) and macrophage infiltration to heart allografts of eto-treated HTx recipients. ELISPOT demonstrated eto-treated HTx were less reactive to activated donor antigen presenting cells. FAO inhibition reduced monocyte-to-DC and monocyte-to-macrophage differentiation in vitro and in vivo. Further, FAO inhibition did not alter the survival of heart allografts when transplanted into Ccr2-deficient recipients, suggesting the effects of FAO inhibition on reduced immune cell infiltration and increased heart allograft survival were dependent on monocyte mobilization. Finally, we confirmed the importance of FAO on monocyte differentiation in vivo using conditional deletion of Cpt1a. Our findings demonstrate that targeting FAO attenuates alloimmunity after HTx, in part through impairing monocyte differentiation.
MraZ is a transcriptional inhibitor of cell division in Bacillus subtilis
Authors: White Maria L. , Hough-Neidig Abigail , Khan Sebastian J. , Eswara Prahathees J.
Published: February 2022

The bacterial division and cell wall (dcw) cluster is a highly conserved region of the genome which encodes several essential cell division factors including the central divisome protein FtsZ. Understanding the regulation of this region is key to our overall understanding of the division process. mraZ is found at the 5’ end of the dcw cluster and previous studies have described MraZ as a sequence-specific DNA binding protein. In this article, we investigate MraZ to elucidate its role in Bacillus subtilis. Through our investigation, we demonstrate that increased levels of MraZ result in lethal filamentation due to repression of its own operon (mraZ-mraW-ftsL-pbpB). We observe rescue of filamentation upon decoupling ftsL expression, but not other genes in the operon, from MraZ control. Furthermore, through timelapse microscopy we were able to identify that overexpression of mraZ, results in de-condensation of the FtsZ ring (Z-ring). This is likely due to depletion of FtsL, and thus, we believe the precise role of FtsL is likely in Z-ring maturation and promotion of subsequent treadmilling. Our data suggests that regulation of the mra operon may be an alternative way for cells to quickly arrest cytokinesis potentially during entry into stationary phase and in the event of DNA replication arrest.