bluuebunny/crossref_metadata_2025 huggingface dataset:
Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning
Authors: Greenwald Noah F. , Miller Geneva , Moen Erick , Kong Alex , Kagel Adam , Fullaway Christine Camacho , McIntosh Brianna J. , Leow Ke , Schwartz Morgan Sarah , Dougherty Thomas , Pavelchek Cole , Cui Sunny , Camplisson Isabella , Bar-Tal Omer , Singh Jaiveer , Fong Mara , Chaudhry Gautam , Abraham Zion , Moseley Jackson , Warshawsky Shiri , Soon Erin , Greenbaum Shirley , Risom Tyler , Hollmann Travis , Keren Leeat , Graf Will , Angelo Michael , Van Valen David
Published: March 2021

Understanding the spatial organization of tissues is of critical importance for both basic and translational research. While recent advances in tissue imaging are opening an exciting new window into the biology of human tissues, interpreting the data that they create is a significant computational challenge. Cell segmentation, the task of uniquely identifying each cell in an image, remains a substantial barrier for tissue imaging, as existing approaches are inaccurate or require a substantial amount of manual curation to yield useful results. Here, we addressed the problem of cell segmentation in tissue imaging data through large-scale data annotation and deep learning. We constructed TissueNet, an image dataset containing >1 million paired whole-cell and nuclear annotations for tissue images from nine organs and six imaging platforms. We created Mesmer, a deep learning-enabled segmentation algorithm trained on TissueNet that performs nuclear and whole-cell segmentation in tissue imaging data. We demonstrated that Mesmer has better speed and accuracy than previous methods, generalizes to the full diversity of tissue types and imaging platforms in TissueNet, and achieves human-level performance for whole-cell segmentation. Mesmer enabled the automated extraction of key cellular features, such as subcellular localization of protein signal, which was challenging with previous approaches. We further showed that Mesmer could be adapted to harness cell lineage information present in highly multiplexed datasets. We used this enhanced version to quantify cell morphology changes during human gestation. All underlying code and models are released with permissive licenses as a community resource.
A drastic shift in the energetic landscape of toothed whale sperm cells
Authors: Alves L. Q. , Ruivo R. , Valente R. , Fonseca M. M. , Machado A. M. , Plön S. , Monteiro N. , García-Parraga D. , Ruiz-Díaz S. , Sánchez-Calabuig M.L. , Gutiérrez-Adán A. , Castro L. Filipe C.
Published: March 2021

Mammalia spermatozoa are a notable example of energetic compartmentalization. While mitochondrial oxidative phosphorylation is restricted to the midpiece, sperm-specific glycolysis operates in the flagellum. Consequently, these highly specialized cells exhibit a clear adaptability to fuel substrates. This plasticity is essential to ensure sperm motility, and is known to vary among species. Here we describe an extreme example of spermatozoa-energetics adaptation. We show that toothed whales exhibit impaired sperm glycolysis, due to gene and exon erosion, and demonstrate that dolphin spermatozoa motility depends uniquely on endogenous fatty acidβ-oxidation, but not carbohydrates. Our findings substantiate the observation of large mitochondria in spermatozoa, possibly boosting ATP production from endogenous fatty acids. This unique energetic rewiring emphasizes the physiological body reorganisation imposed by the carbohydrate-depleted marine environment.
Employing connectome-based models to predict working memory in multiple sclerosis
Authors: Manglani Heena R. , Fountain-Zaragoza Stephanie , Shankar Anita , Nicholas Jacqueline A. , Prakash Ruchika Shaurya
Published: March 2021

Background

Individuals with multiple sclerosis (MS) are vulnerable to deficits in working memory, and the search for neural correlates of working memory in circumscribed areas has yielded inconclusive findings. Given the widespread neural alterations observed in MS, predictive modeling approaches that capitalize on whole-brain connectivity may better capture individual-level working memory in this population.

Methods

Here, we applied connectome-based predictive modeling to functional MRI data from working memory tasks in two independent samples with relapsing-remitting MS. In the internal validation sample (ninternal= 36), functional connectivity data were used to train a model through cross-validation to predict accuracy on the Paced Visual Serial Addition Test, a gold-standard measure of working memory in MS. We then tested its ability to predict performance on the N-back working memory task in the external validation sample (nexternal= 36).

Results

The resulting model successfully predicted working memory in the internal validation sample but did not extend to the external sample. We also tested the generalizability of an existing model of working memory derived in healthy young adults to people with MS. It showed successful prediction in both MS samples, demonstrating its translational potential. We qualitatively explored differences between the healthy and MS models in intra- and inter-network connectivity amongst canonical networks.

Discussion

These findings suggest that connectome-based predictive models derived in people with MS may have limited generalizability. Instead, models identified in healthy individuals may offer superior generalizability to clinical samples, such as MS, and may serve as more useful targets for intervention.

Impact Statement

Working memory deficits in people with multiple sclerosis have important consequence for employment, leisure, and daily living activities. Identifying a functional connectivity-based marker that accurately captures individual differences in working memory may offer a useful target for cognitive rehabilitation. Manglani et al. demonstrate machine learning can be applied to whole-brain functional connectivity data to identify networks that predict individual-level working memory in people with multiple sclerosis. However, existing network-based models of working memory derived in healthy adults outperform those identified in multiple sclerosis, suggesting translational potential of brain networks derived in large, healthy samples for predicting cognition in multiple sclerosis.
GMSECT: Genome-Wide Massive Sequence Exhaustive Comparison Tool for structural and copy number variations
Authors: Singh Abhishek Narain
Published: March 2021

GMSECT is a parallel robust ‘Application Interface’ that efficiently handles the large genomic sequences for rapid and efficient processing. It is a ‘message passing interface’ based parallel computing ‘Tool’ that can be operated on a cluster for ‘Massive Sequences Exhaustive Comparison’, to identify matches such as the structural variants. The GMSECT algorithm can be implemented using other parallel application programming interfaces as well such as Posix-Threads or can even be implemented in a serial submission fashion. There is complete flexibility to the choice of comparison tool that can be deployed and with the optional parameters as of the choice of comparison tools to suit the speed, sensitivity and specificity of pair wise alignment. The algorithm is simple and robust, and can be applied to compare multiple genomes, chromosomes or large sequences, of different individuals for personalized genome comparison and works good for homologous as well as distant species. The tool can even be applied to smaller genomes like the microbial genome such as theEscherichia colior algae such asChlamydomonas reihardttior yeastSaccharomyces cerevisiaeto quickly conduct comparisons, and thus finds its application to the pharmaceuticals and microbial product based firms for research and development. The application Interface can efficiently and rapidly compare massive sequences to detect for the presence of numerous types of DNA variation existing in the genome ranging from single nucleotide polymorphism (SNPs) to larger structural alterations, such as copy-number variants (CNVs) and inversions. The new algorithm has been tested for comparing the chromosome 21 of Celera’s R27c compilation with all the 48 chromosomes of Celera’s R27c compilation and with all the 48 chromosomes of the human Build 35 reference sequence, which took just 2 Hours and 10 minutes using the pair wise blast algorithm choice and with 110 processors each with 2.2 GHz capacity and 2 GB memory. GMSECT facilitates rapid scanning and interpretation in personalized sequencing project. The application interface with the above resources and alignment choice is estimated to do exhaustive comparison of the human genome with itself in just 2.35 days. An exhaustive comparison of an individual’s genome with a reference genome would comprise of a two ‘self genome’ comparison and a ‘non-self genome’ comparison which is estimated to take about 9.4 days with the above resources. With the advent of personalized genome sequencing project, it would be desirable to compare 100s of individual’s genome with a reference genome. This would involve a ‘non-self genome’ and a ‘self genome’ comparison for each genome, and would take around 7 days for each individual’s genome using GMSECT and the above mentioned resources.
DNMT family induced down-regulation of NDRG1 via DNA methylation and clinicopathological significance in gastric cancer
Authors: Chang Xiaojing , MA Jinguo , Xue Xiaoying , Wang Guohui , Su Linlin , Han Xuetao , Zhou Huandi , Hou Liubing
Published: March 2021

Background

Aberrant DNA methylation of tumor suppressor genes is a common event in the development and progression of gastric cancer(GC). Our previous study showed NDRG1, which could suppress cell invasion and migration, was frequently down-regulated by DNA methylation of its promoter in GC.

Purpose and Methods

To analyze the relationship between the expression and DNA methylation of NDRG1 and DNA methyltransferase (DNMT) family. We performed a comprehensive comparison analysis using 407 patients including sequencing analysis data of GC from TCGA.

Results

NDRG1 was negatively correlative to DNMT1 (p=0.03), DNMT3A(p=0.01), DNMT3B(p=0.88), respectively. Whereas, the DNA methylation of NDRG1 was positively correlative to DNMT family(DNMT1 p<0.01, DNMT3A p<0.001, DNMT3B p=0.57, respectively). NDRG1 expression was significantly inverse correlated with invasion depth (p=0.023), and DNMT1 was significantly positive correlated with the degree of tumor cell differentiation (p=0.049). DNMT3B was significantly correlated with tumor cell differentiation (p=0.030). However, there was no association between the expression of DNMT3A and clinicopathological features. The univariate analysis showed that NDRG1and DNMTs had no association with prognosis of GC patients. But, multivariate analysis showed DNMT1 was significantly correlated with prognosis of GC patients.

Conclusion

These data suggest that down-regulation of NDRG1 in gastric cancer is due to DNA methylation of NDRG1 gene promoter via DNMT family. The demethylating agent maybe a potential target drug for GC patients.
Self-Assembling Peptide Hydrogels - PeptiGels®as a Platform for Hepatic Organoid Culture
Authors: Olayanju Adedamola , Miller Aline F , Ansari Tahera , Goldring Christopher E.
Published: March 2021

A major challenge in advancing preclinical studies is the lack of robust in vitro culture systems that fully recapitulate thein vivoscenario together with limited clinical translational to humans. Organoids, as 3-dimensional (3D) self-replicating structures are increasingly being shown as powerful models forex vivoexperimentation in the field of regenerative medicine and drug discovery. Organoid formation requires the use of extracellular matrix (ECM) components to provide a 3D platform. However, the most commonly used ECM, essential for maintaining organoid growth is Matrigel and is derived from a tumorigenic source which limits its translational ability. PeptiGels®which are self-assembling peptide hydrogels present as alternatives to traditional ECM for use in 3D culture systems. Synthetic PeptiGels®are non-toxic, biocompatible, biodegradable and can be tuneable to simulate different tissue microenvironments. In this study, we validated the use of different types of PeptiGels®for porcine hepatic organoid growth. Hepatic organoids were assessed morphologically and using molecular techniques to determine the optimum PeptiGel®formulation. The outcome clearly demonstrated the ability of PeptiGel®to support organoid growth and offer themselves as a technological platform for 3D cultured physiologically and clinically relevant data.
A role for the immune system-released activating agent (ISRAA) in the ontogenetic development of brain astrocytes
Authors: Al-Awadi Aminah M. I. , AlJawder Abdulaziz Isa , Mousa Alyaa , Taha Safa , Bakhiet Moiz
Published: March 2021

The Immune System-Released Activating Agent (ISRAA) was discovered as a novel molecule that functions as a mediator between the nervous and immune systems in response to a nervous stimulus following an immune challenge. This research investigated the role of ISRAA) in promoting the ontogeny of the mouse brain astrocytes. Astrocyte cultures were prepared from two-month-old BALB/c mice. Recombinant ISRAA protein was used to stimulate astrocyte cultures. Immunohistochemistry and ELISA were utilized to measure ISRAA and IFN-γ levels, IFN-γR expression and STAT1 nuclear translocation. MTT-assay was used to evaluate cellular survival and proliferation. To assess astrocyte cell lysates and tyrosine-phosphorylated proteins, SDS-PAGE and western blot were used. ISRAA was highly expressed in mouse embryonic astrocytes, depending on cell age. Astrocytes aged seven days (E7) showed increased proliferation and diminished differentiation, while 21-day-old (E21) astrocytes depicted reversed effects. ISRAA stimulated the tyrosine phosphorylation of numerous cellular proteins and the nuclear translocation of STAT1. IFN-γ was involved in the ISRAA action as ISRAA induced IFN-γin both age groups, but only E21 astrocytes expressed IFN-γR. The results suggest that ISRAA is involved in mouse brain development through the cytokine network involving IFN-γ.
Derivation and Characterization of an inositol phosphate-independent HIV-1
Authors: Poston Daniel , Zang Trinity , Bieniasz Paul
Published: March 2021

A critical step in the HIV-1 replication cycle is the assembly of Gag proteins to form virions at the plasma membrane. Virion assembly and maturation is facilitated by the cellular polyanion inositol hexaphosphate (IP6), which is proposed to stabilize both the immature Gag lattice and the mature capsid lattice by binding to rings of primary amines at the center of Gag or capsid protein (CA) hexamers. The amino acids comprising these rings are critical for proper virion formation and their substitution results in assembly deficits or impaired infectiousness. To better understand the nature of the deficits that accompany IP6-deficiency, we passaged HIV-1 mutants that had substitutions in IP6-coordinating residues to select for compensatory mutations. We found a mutation, a threonine to isoleucine substitution at position 371 (T371I) in Gag, that restored replication competence to an IP6-binding-deficient HIV-1 mutant. Notably, unlike wild-type HIV-1, the assembly and infectiousness of resulting virus was not impaired when IP6 biosynthetic enzymes were genetically ablated. Surprisingly, we also found that the maturation inhibitor Bevirimat (BVM) could restore the assembly and replication of an IP6-binding deficient mutant. Moreover, using BVM-dependent mutants we were able to image the BVM-inducible assembly of individual HIV-1 particles assembly in living cells. Overall these results suggest that IP6-Gag and Gag-Gag contacts are finely tuned to generate a Gag lattice of optimal stability, and that under certain conditions BVM can functionally replace IP6.

Author Summary

A key step in HIV-1 replication is the assembly of virions that are released from the infected cell. Previous work has suggested that a small molecule called IP6is critical role in this process, promoting both HIV-1 assembly and the stability of mature fully infectious virions. Since IP6is required for multiple steps in HIV-1 assembly and maturation, it is a candidate for the development of anti-retroviral therapies. Here, we identify an HIV-1 mutant that replicates independently of IP6, and show that a different small molecule can functionally substitute for IP6under certain conditions. These findings suggest that IP6regulates the stability of protein interactions during virion assembly and that the precise degree stability of these interactions is finely tuned and important for generating infectious virions. Finally, our work identifies an inducible virion assembly system that can be utilized to visualize HIV-1 assembly events using live cell microscopy.
Identify phage hosts from metaviromic short reads based on deep learning and Markov chain model
Authors: Tan Jie , Fang Zhencheng , Wu Shufang , Guo Qian , Jiang Xiaoqing , Zhu Huaiqiu
Published: March 2021

Phages - viruses that infect bacteria and archaea - are dominant in the virosphere and play an important role in the microbial community. It is very important to identify the host of a given phage fragment from metavriome data for understanding the ecological impact of phage in a microbial community. State-of-the-art tools for host identification only present reliable results on long sequences within a narrow candidate host range, while there are a large number of short fragments in real metagenomic data and the taxonomic composition of a microbial community is often complicated. Here, we present a method, named HoPhage, to identify the host of a given phage fragment from metavirome data at the genus level. HoPhage integrates two modules using the deep learning algorithms and the Markov chain model, respectively. By testing on both the artificial benchmark dataset of phage contigs and the real virome data, HoPhage demonstrates a satisfactory performance on short fragments within a wide candidate host range at every taxonomic level. HoPhage is freely available athttp://cqb.pku.edu.cn/ZhuLab/HoPhage/.
Parvalbumin interneuron inhibition onto anterior insula neurons projecting to the basolateral amygdala orchestrates aversive taste memory retrieval
Authors: Yiannakas Adonis , Chandran Sailendrakumar Kolatt , Kayyal Haneen , Gould Nathaniel , Khamaisy Mohammad , Rosenblum Kobi
Published: March 2021

Memory retrieval refers to the fundamental ability of organisms to make use of acquired, sometimes inconsistent, information about the world. While memory acquisition has been studied extensively, the neurobiological mechanisms underlying memory retrieval remain largely unknown. The anterior insula (aIC) is indispensable in the ability of mammals to retrieve associative information regarding tastants that have been previously linked with gastric malaise. Here, we show that aversive taste memory retrieval promotes cell-type-specific activation in the aIC. Aversive, but not appetitive taste memory retrieval, relies on specific changes in activity and connectivity at parvalbumin (PV) inhibitory synapses onto aIC pyramidal neurons projecting to the basolateral amygdala. PV aIC interneurons, coordinate aversive taste memory retrieval, and are necessary for its dominance when conflicting internal representations are encountered. This newly described interaction of PV and a subset of excitatory neurons can explain the coherency of aversive memory retrieval, an evolutionary pre-requisite for animal survival.

Graphical Abstract

Retrieval of Conditioned Taste Aversion (CTA) memories at the anterior insular cortex activates Parvalbumin (PV) interneurons and increases synaptic inhibition onto activated pyramidal neurons projecting to the basolateral amygdala (aIC-BLA).

Unlike innately appetitive taste memory retrieval, CTA retrieval increases the amplitude and frequency of synaptic inhibition onto aIC-BLA projecting neurons, that is dependent on activity in aIC PV interneurons.

Activation of aIC PV interneurons is necessary for the expression of learned taste avoidance, in both sexes, regardless of stimulus identity.

Extinction of aversive taste memories suppresses the frequency, but not the amplitude of synaptic inhibition on aIC-BLA projecting neurons.

The reinstatement of aversive taste memories following extinction is dependent upon activation of aIC PV interneurons and increases in the frequency of inhibition on aIC-BLA projecting neurons.
PRDM9 directs recombination hotspots to prevent competition with meiotic transcription
Authors: Schwarzkopf Enrique J. , Cornejo Omar E.
Published: March 2021

PRDM9 drives recombination hotspots in some mammals, including mice and apes. Non-functional orthologs of PRDM9 are present in a wide variety of vertebrates, but why it is functionally maintained in some lineages is not clear. One possible explanation is that PRDM9 plays a role in ensuring that meiosis is successful. During meiosis, available DNA may be a limiting resource given the tight packaging of chromosomes and could lead to competition between two key processes: meiotic transcription and recombination. Here we explore this potential competition and the role that PRDM9 might play in their interaction. Leveraging existing mouse genomic data, we use resampling schemes that simulate shuffled features along the genome and models that account for the rarity of features in the genome, to test if PRDM9 influences interactions between recombination hotspots and meiotic transcription in a whole genome framework. We also explored possible DNA sequence motifs associated to clusters of hotspots not tied to transcription or PRDM9. We find evidence of competition between meiotic transcription and recombination, with PRDM9 appearing to relocate recombination to avoid said conflict. We also find that retrotransposons may be playing a role in directing hotspots in the absence of other factors.
Approximate Hidden Semi-Markov Models for Dynamic Connectivity Analysis in Resting-State fMRI
Authors: Fiecas Mark B. , Coffman Christian , Xu Meng , Hendrickson Timothy J. , Mueller Bryon A. , Klimes-Dougan Bonnie , Cullen Kathryn R.
Published: March 2021

Motivated by a study on adolescent mental health, we conduct a dynamic connectivity analysis using resting-state functional magnetic resonance imaging (fMRI) data. A dynamic connectivity analysis investigates how the interactions between different regions of the brain, represented by the different dimensions of a multivariate time series, change over time. Hidden Markov models (HMMs) and hidden semi-Markov models (HSMMs) are common analytic approaches for conducting dynamic connectivity analyses. However, existing approaches for HSMMs are limited in their ability to incorporate covariate information. In this work, we approximate an HSMM using an HMM for modeling multivariate time series data. The approximate HSMM model allows one to explicitly model dwell-time distributions that are available to HSMMs, while maintaining the theoretical and methodological advances that are available to HMMs. We conducted a simulation study to show the performance of the approximate HSMM relative to other approaches. Finally, we used the approximate HSMM to conduct a dynamic connectivity analysis, where we showed how dwell-time distributions vary across the severity of non-suicidal self-injury (NSSI) in female adolescents, and how those with moderate or severe NSSI have greater state-switching frequency.
An evolutionary genomic approach reveals both conserved and species-specific genetic elements related to human disease in closely relatedAspergillusfungi
Authors: Mead Matthew E. , Steenwyk Jacob L. , Silva Lilian P. , de Castro Patrícia A. , Saeed Nauman , Hillmann Falk , Goldman Gustavo H. , Rokas Antonis
Published: March 2021

Aspergillosis is an important opportunistic human disease caused by filamentous fungi in the genusAspergillus. Roughly 70% of infections are caused byAspergillus fumigatus, with the rest stemming from approximately a dozen otherAspergillusspecies. Several of these pathogens are closely related toA. fumigatusand belong in the same taxonomic section, sectionFumigati. Pathogenic species are frequently most closely related to non-pathogenic ones, suggestingAspergilluspathogenicity evolved multiple times independently. To understand the repeated evolution ofAspergilluspathogenicity, we performed comparative genomic analyses on 18 strains from 13 species, including 8 species in sectionFumigati, which aimed to identify genes, both ones previously connected to virulence as well as ones never before implicated, whose evolution differs between pathogens and non-pathogens. We found that most genes were present in all species, including approximately half of those previously connected to virulence, but a few genes were section- or species-specific. Evolutionary rate analyses identified hundreds of genes in pathogens that were faster-evolving than their orthologs in non-pathogens. For example, over 25% of all single-copy genes examined inA. fumigatuswere faster-evolving. Functional testing of deletion mutants of 17 transcription factor-encoding genes whose evolution differed between pathogens and non-pathogens identified eight genes that affect either fungal survival in a model of phagocytic killing, host survival in an animal model of fungal disease, or both. These results suggest that the evolution of pathogenicity inAspergillusinvolved both conserved and species-specific genetic elements, illustrating how an evolutionary genomic approach informs the study of fungal disease.
Analysis of Classic Tomato Mutants Reveals Influence of Leaf Vein Density on Fruit BRIX
Authors: Cheng Zizhang , Rowland S.D. , Czarnecki Karo , Zumstein Kristina , Nakayama Hokuto , Sinha Neelima R.
Published: March 2021

Tomatobipinnate(bip) is a classic leaf mutant, with highly increased leaf complexity resulting from the loss of function of aBEL-LIKE HOMEODAMAIN(BELL) gene. Here, we analyzed severalbipmutants and their isogenic wildtype backgrounds for a suite of leaf morphology traits, ranging from leaf complexity, leaflet shape and size, to leaf vascular density to investigate how changes in leaf morphology influence fruit traits. Our analyses showed an unexpected relationship between leaf vein density and fruit sugar levels, where leaf vein density was negatively correlated with fruit BRIX. RNA-Seq analysis suggested variation inGlucose-6-phosphate translocator2(GPT2) gene expression caused correlated changes in leaf vein density and BRIX whenbipmutant and wildtype were compared, suggesting that the correlation between leaf vein density and fruit sugar may result from the genes regulating leaf vein development that are also involved in regulating leaf sugar biosynthesis. Our results provide a resource for further exploration of the genetic basis for the complex relationship between fruit quality and leaf traits in natural populations.
Two Types of Cinnamoyl-CoA Reductase Function Divergently in Tissue Lignification, Phenylpropanoids Flux Control, and Inter-pathway Cross-talk with Glucosinolates as Revealed inBrassica napus
Authors: Yin Nengwen , Li Bo , Liu Xue , Liang Ying , Lian Jianping , Xue Yufei , Qu Cunmin , Lu Kun , Wei Lijuan , Wang Rui , Li Jiana , Chai Yourong
Published: March 2021

Cinnamoyl-CoA reductase (CCR) is the entry point of lignin pathway and a crucial locus in dissection and manipulation of associated traits, but its functional dissection in Brassicaceae plants is largely lagged behind thoughArabidopsis thaliana CCR1has been characterized to certain extent. Here, 16CCRgenes are identified fromBrassica napusand its parental speciesB. rapaandB. oleracea. BrassicaceaeCCRgenes are divided intoCCR1subfamily andCCR2subfamily with divergent organ-specificity, yellow-seed trait participation and stresses responsiveness.CCR1is preferential in G- and H-lignins biosynthesis and vascular development, whileCCR2has a deviation to S-lignin biosynthesis and interfascicular fiber development.CCR1has stronger effects on lignification-related development, lodging resistance, phenylpropanoid flux control and seed coat pigmentation, whereasCCR2controls sinapates levels.CCR1upregulation could delay bolting and flowering time, whileCCR2upregulation weakens vascular system in leaf due to suppressed G lignin accumulation. Besides,CCR1andCCR2are deeply but almost oppositely linked with glucosinolates metabolism through inter-pathway crosstalk. Strangely, upregulation of bothCCR1andCCR2could not enhance resistance to UV-B andS. sclerotiorumthoughCCR2is sharply induced by them. These results provide systemic dissection onBrassica CCRs andCCR1-CCR2divergence in Brassicaceae.

Highlight

Brassicaceae contains two types of Cinnamoyl-CoA reductase. As revealed inBrassica napus, they are divergently involved in lignin monomer biosynthesis, tissue lignification, phenylpropanoid flux control, and inter-pathway crosstalk with glucosinolates.
Conformational changes in twitchin kinasein vivorevealed by FRET imaging of freely movingC. elegans
Authors: Porto Daniel , Matsunaga Yohei , Franke Barbara , Williams Rhys M. , Qadota Hiroshi , Mayans Olga , Benian Guy M. , Lu Hang
Published: March 2021

The force-induced unfolding and refolding of proteins is speculated to be a key mechanism in the sensing and transduction of mechanical signals in the living cell. Yet, little evidence has been gathered for its existencein vivo. Prominently, stretch-induced unfolding is postulated to be the activation mechanism of the twitchin/titin family of autoinhibited sarcomeric kinases linked to the mechanical stress response of muscle. To test the occurrence of mechanical kinase activation in living working muscle, we generated transgenicC. elegansexpressing twitchin containing FRET moieties flanking the kinase domain and developed a quantitative technique for extracting FRET signals in freely movingC. elegans, using tracking and simultaneous imaging of animals in three channels (donor fluorescence, acceptor fluorescence, and transmitted light). Computer vision algorithms were used to extract fluorescence signals and muscle contraction states in each frame, in order to obtain fluorescence and body curvature measurements with spatial and temporal precisionin vivo. The data revealed statistically significant periodic changes in FRET signals during muscle activity, consistent with a periodic change in the conformation of twitchin kinase. We conclude that stretch-unfolding of twitchin kinase occurs in the active muscle, whereby mechanical activity titrates the signalling pathway of this cytoskeletal kinase. We anticipate that the methods we have developed here could be applied to obtainingin vivoevidence for force-induced conformational changes or elastic behavior of other proteins not only inC. elegansbut in other animals in which there is optical transparency (e.g zebrafish).
A ciliopathy complex builds distal appendages to initiate ciliogenesis
Authors: Kumar Dhivya , Rains Addison , Herranz-Pérez Vicente , Lu Quanlong , Shi Xiaoyu , Swaney Danielle L. , Stevenson Erica , Krogan Nevan J. , Huang Bo , Westlake Christopher , Garcia-Verdugo Jose Manuel , Yoder Bradley , Reiter Jeremy F.
Published: March 2021

Cells inherit two centrioles, the older of which is uniquely capable of generating a cilium. Using proteomics and super-resolved imaging, we identified a module which we term DISCO (DIStal centriole COmplex). DISCO components CEP90, MNR and OFD1 underlie human ciliopathies. This complex localized to both distal centrioles and centriolar satellites, proteinaceous granules surrounding centrioles. Cells and mice lacking CEP90 or MNR did not generate cilia, failed to assemble distal appendages, and did not transduce Hedgehog signals. Disrupting the satellite pools did not affect distal appendage assembly, indicating that it is the centriolar populations of MNR and CEP90 that are critical for ciliogenesis. CEP90 recruited the most proximal known distal appendage component, CEP83, to root distal appendages formation, an early step in ciliogenesis. In addition, MNR, but not CEP90, restricted centriolar length by recruiting OFD1. We conclude that DISCO acts at the distal centriole to support ciliogenesis by restraining centriole length and assembling distal appendages, defects in which cause human ciliopathies.

eTOC summary

Kumar et al. identifies a multi-protein complex called DISCO (DIStal centriole COmplex) required to nucleate distal appendages and restrain centriole elongation, essential for the initiation of cilium assembly. Without DISCO, cells fail to ciliate and transduce Hedgehog signals, critical for mammalian development.
Circular RNA repertoires are associated with evolutionarily young transposable elements
Authors: Gruhl Franziska , Janich Peggy , Kaessmann Henrik , Gatfield David
Published: March 2021

Abstract

Circular RNAs (circRNAs) are found across eukaryotes and can function in post-transcriptional gene regulation. Their biogenesis through a circle-forming backsplicing reaction is facilitated by reverse-complementary repetitive sequences promoting pre-mRNA folding. Orthologous genes from which circRNAs arise, overall contain more strongly conserved splice sites and exons than other genes, yet it remains unclear to what extent this conservation reflects purifying selection acting on the circRNAs themselves. Our analyses of circRNA repertoires from five species representing three mammalian lineages (marsupials, eutherians: rodents, primates) reveal that surprisingly few circRNAs arise from orthologous exonic loci across all species. Even the circRNAs from orthologous loci are associated with young, recently active and species-specific transposable elements, rather than with common, ancient transposon integration events. These observations suggest that many circRNAs emerged convergently during evolution – as a byproduct of splicing in orthologs prone to transposon insertion. Overall, our findings argue against widespread functional circRNA conservation.
The Fkh1 Forkhead Associated Domain Promotes ORC Binding to a Subset of DNA Replication Origins in Budding Yeast
Authors: Hoggard Timothy , Hollatz Allison J. , Cherney Rachel , Fox Catherine A.
Published: March 2021

The pioneer event in eukaryotic DNA replication is binding of chromosomal DNA by the origin recognition complex (ORC), which directs the formation of origins, the specific chromosomal regions where DNA will be unwound for the initiation of DNA synthesis. In all eukaryotes, incompletely understood features of chromatin promote ORC-DNA binding. Here, we uncover a role for the Fkh1 (forkhead homolog) protein, and, in particular, its forkhead associated (FHA) domain in promoting ORC-origin binding and origin activity at a subset of origins inSaccharomyces cerevisiae.The majority of the FHA-dependent origins within the experimental subset examined contain a distinct Fkh1 binding site located 5’ of and proximal to their ORC sites (5’-FKH-T site). Epistasis experiments using selected FHA-dependent origins provided evidence that the FHA domain promoted origin activity through Fkh1 binding directly to this 5’ FKH-T site. Nucleotide substitutions within two of these origins that enhanced the affinity of their ORC sites for ORC bypassed these origins’ requirement for their 5’ FKH-T sites and for the FHA domain. Significantly, direct assessment of ORC-origin binding by ChIPSeq provided evidence that this mechanism affected ~25% of yeast origins. Thus, this study reveals a new mechanism to enhance ORC-origin binding in budding yeast that requires the FHA domain of the conserved cell-cycle transcription factor Fkh1.
Taxon-specific phytoplankton growth, nutrient utilization, and light limitation in the oligotrophic Gulf of Mexico
Authors: Yingling Natalia , Kelly Thomas B. , Shropshire Taylor A. , Landry Michael R. , Selph Karen E. , Knapp Angela N. , Kranz Sven A. , Stukel Michael R.
Published: March 2021

The highly stratified, oligotrophic regions of the oceans are predominantly nitrogen limited in the surface ocean and light limited at the deep chlorophyll maximum (DCM). Hence, determining light and nitrogen co-limitation patterns for diverse phytoplankton taxa is crucial to understanding marine primary production throughout the euphotic zone. During two cruises in the deep-water Gulf of Mexico, we measured primary productivity (H13CO3−), nitrate uptake (15NO3−), and ammonium uptake (15NH4+) throughout the water column. Primary productivity declined with depth from the mixed-layer to the DCM, averaging 27.1 mmol C m−2d−1. The fraction of growth supported by NO3−was consistently low, with upper euphotic zone values ranging from 0.01 to 0.14 and lower euphotic zone values ranging from 0.03 to 0.44. Nitrate uptake showed strong diel patterns (maximum during the day), while ammonium uptake exhibited no diel variability. To parameterize taxon-specific phytoplankton nutrient and light utilization, we used a data assimilation approach (Bayesian Markov Chain Monte Carlo) including primary productivity, nutrient uptake, and taxon-specific growth rate measurements. Parameters derived from this analysis define distinct niches for five phytoplankton taxa (Prochlorococcus, Synechococcus, diatoms, dinoflagellates, and prymnesiophytes) and may be useful for constraining biogeochemical models of oligotrophic open-ocean systems.
A Comparison of Performance for Different SARS-Cov-2 Sequencing Protocols
Authors: Bermúdez Juanjo
Published: March 2021

SARS-Cov-2 genome sequencing has been identified as a fundamental tool for fighting the COVID-19 pandemic. It is used, for example, for identifying new variants of the virus and for elaborating phylogenetic trees that help to trace the spread of the virus. In the present study we provide a comprehensive comparison between the quality of the assemblies obtained from different sequencing protocols. We demonstrate how some protocols actively promoted by different high-level administrations are inefficient and how less-used alternative protocols show a significant increased performance. This increase of performance could lead to cheaper sequencing protocols and therefore to a more convenient escalation of the sequencing efforts around the world.
Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell
Authors: Puray-Chavez Maritza , LaPak Kyle M. , Schrank Travis P. , Elliott Jennifer L. , Bhatt Dhaval P. , Agajanian Megan J. , Jasuja Ria , Lawson Dana Q. , Davis Keanu , Rothlauf Paul W. , Jo Heejoon , Lee Nakyung , Tenneti Kasyap , Eschbach Jenna E. , Mugisha Christian Shema , Vuong Hung R. , Bailey Adam L. , Hayes D. Neil , Whelan Sean P.J. , Horani Amjad , Brody Steven L. , Goldfarb Dennis , Major M. Ben , Kutluay Sebla B.
Published: March 2021

Establishedin vitromodels for SARS-CoV-2 infection are limited and include cell lines of non-human origin and those engineered to overexpress ACE2, the cognate host cell receptor. We identified human H522 lung adenocarcinoma cells as naturally permissive to SARS-CoV-2 infection despite complete absence of ACE2. Infection of H522 cells required the SARS-CoV-2 spike protein, though in contrast to ACE2-dependent models, spike alone was not sufficient for H522 infection. Temporally resolved transcriptomic and proteomic profiling revealed alterations in cell cycle and the antiviral host cell response, including MDA5-dependent activation of type-I interferon signaling. Focused chemical screens point to important roles for clathrin-mediated endocytosis and endosomal cathepsins in SARS-CoV-2 infection of H522 cells. These findings imply the utilization of an alternative SARS-CoV-2 host cell receptor which may impact tropism of SARS-CoV-2 and consequently human disease pathogenesis.
Expression levels of long noncoding natural antisense transcripts overlapping theUGT73C6gene affect rosette size ofArabidopsis thaliana
Authors: Meena Shiv Kumar , Heidecker Michel , Engelmann Susanne , Jaber Ammar , de Vries Tebbe , Baumann-Kaschig Katja , Abel Steffen , Behrens Sven-Erik , Gago-Zachert Selma
Published: March 2021

Natural antisense long noncoding RNAs (lncNATs) are involved in the regulation of gene expression in plants, modulating different relevant developmental processes and responses to various stimuli. We identified and characterized two lncNATs (NAT1UGT73C6andNAT2UGT73C6, collectivelyNATsUGT73C6) inArabidopsis thalianathat are transcribed from a gene overlappingUGT73C6, a member of theUGT73Csubfamily of genes encoding UDP-glycosyltransferases (UGTs). Expression of bothNATsUGT73C6is developmentally controlled and occurs independently of the transcription ofUGT73C6incis. Downregulation ofNATsUGT73C6levels through artificial microRNAs results in a reduction of the rosette area, while constitutive overexpression ofNAT1UGT73C6orNAT2UGT73C6leads to the opposite phenotype, an increase in rosette size. This activity ofNATsUGT73C6relies on its RNA sequence, and, although modulation ofUGT73C6inciscannot be excluded, the observed phenotypes are not a consequence of the regulation ofUGT73C6intrans. TheNATsUGT73C6levels were shown to affect cell proliferation and thus individual leaf size. Consistent with this concept, our data suggest that theNATsUGT73C6modulate the expression levels of key transcription factors involved in regulating leaf growth by modulating cell proliferation. These findings thus reveal an additional regulatory layer on the process of leaf growth.
Brain expression quantitative trait locus and network analysis reveals downstream effects and putative drivers for brain-related diseases
Authors: de Klein Niek , Tsai Ellen A. , Vochteloo Martijn , Baird Denis , Huang Yunfeng , Chen Chia-Yen , van Dam Sipko , Deelen Patrick , Bakker Olivier B. , Garwany Omar El , Ouyang Zhengyu , Marshall Eric E. , Zavodszky Maria I. , van Rheenen Wouter , Bakker Mark K. , Veldink Jan , Gaunt Tom R. , Runz Heiko , Franke Lude , Westra Harm-Jan
Published: March 2021

Gaining insight into the downstream consequences of non-coding variants is an essential step towards the identification of therapeutic targets from genome-wide association study (GWAS) findings. Here we have harmonized and integrated 8,727 RNA-seq samples with accompanying genotype data from multiple brain-regions from 14 datasets. This sample size enabled us to perform bothcis- andtrans-expression quantitative locus (eQTL) mapping. Upon comparing the brain cortexcis-eQTLs (for 12,307 unique genes at FDR<0.05) with a large bloodcis-eQTL analysis (n=31,684 samples), we observed that brain eQTLs are more tissue specific than previously assumed.

We inferred the brain cell type for 1,515cis-eQTLs by using cell type proportion information. We conducted Mendelian Randomization on 31 brain-related traits usingcis-eQTLs as instruments and found 159 significant findings that also passed colocalization. Furthermore, two multiple sclerosis (MS) findings had cell type specific signals, a neuron-specificcis-eQTL forCYP24A1and a macrophage specificcis-eQTL forCLECL1.

To further interpret GWAS hits, we performedtrans-eQTL analysis. We identified 2,589trans-eQTLs (at FDR<0.05) for 373 unique SNPs, affecting 1,263 unique genes, and 21 replicated significantly using single-nucleus RNA-seq data from excitatory neurons.

We also generated a brain-specific gene-coregulation network that we used to predict which genes have brain-specific functions, and to perform a novel network analysis of Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), multiple sclerosis (MS) and Parkinson’s disease (PD) GWAS data. This resulted in the identification of distinct sets of genes that show significantly enriched co-regulation with genes inside the associated GWAS loci, and which might reflect drivers of these diseases.
Top-down control of hippocampal signal-to-noise by prefrontal long-range inhibition
Authors: Malik Ruchi , Li Yi , Schamiloglu Selin , Sohal Vikaas S.
Published: March 2021

The prefrontal cortex (PFC) is postulated to exert ‘top-down control’ by modulating information processing throughout the brain to promote specific actions based on current goals. However, the pathways mediating top-down control remain poorly understood. In particular, knowledge about direct prefrontal connections that might facilitate top-down prefrontal control of information processing in the hippocampus remains sparse. Here we describe novel monosynaptic long-range GABAergic projections from PFC to hippocampus. These preferentially inhibit vasoactive intestinal polypeptide expressing interneurons, which are known to disinhibit hippocampal microcircuits. Indeed, stimulating prefrontal–hippocampal GABAergic projections increases hippocampal feedforward inhibition and reduces hippocampal activityin vivo. The net effect of these actions is to specifically enhance the signal-to-noise ratio for hippocampal representations of objects. Correspondingly, stimulation of PFC-to-hippocampus GABAergic projections promotes object exploration. Together, these results elucidate a novel top-down pathway in which long-range GABAergic projections target disinhibitory microcircuits, thereby enhancing signals and network dynamics underlying exploratory behavior.
The SWI/SNF chromatin remodeling assemblies BAF and PBAF differentially regulate cell cycle exit and cellular invasionin vivo
Authors: Smith Jayson J. , Xiao Yutong , Parsan Nithin , Medwig-Kinney Taylor N. , Martinez Michael A. Q. , Moore Frances E. Q. , Palmisano Nicholas J. , Kohrman Abraham Q. , Reyes Mana Chandhok Delos , Adikes Rebecca C. , Liu Simeiyun , Bracht Sydney A. , Zhang Wan , Wen Kailong , Kratsios Paschalis , Matus David Q.
Published: March 2021

Chromatin remodelers such as the SWI/SNF complex coordinate metazoan development through broad regulation of chromatin accessibility and transcription, ensuring normal cell cycle control and cellular differentiation in a lineage-specific and temporally restricted manner. Mutations in genes encoding the structural subunits of chromatin, such as histone subunits, and chromatin regulating factors (CRFs) are associated with a variety of disease mechanisms including cancer metastasis, in which cancer co-opts cellular invasion programs functioning in healthy cells during development. Here we utilizeCaenorhabditis elegansanchor cell (AC) invasion as anin vivomodel to identify the suite of chromatin agents and CRFs that promote cellular invasiveness. We demonstrate that the SWI/SNF ATP-dependent chromatin remodeling complex is a critical regulator of AC invasion, with pleiotropic effects on both G0cell cycle arrest and activation of invasive machinery. Using targeted protein degradation and enhanced RNA interference (RNAi) vectors, we show that SWI/SNF contributes to AC invasion in a dose-dependent fashion, with lower levels of activity in the AC corresponding to aberrant cell cycle entry and increased loss of invasion. Our data specifically implicate the SWI/SNF BAF assembly in the regulation of the G0cell cycle arrest in the AC, whereas the SWI/SNF PBAF assembly promotes AC invasion via cell cycle-independent mechanisms, including attachment to the basement membrane (BM) and activation of the pro-invasivefos-1/FOS gene. Together these findings demonstrate that the SWI/SNF complex is necessary for two essential components of AC invasion: arresting cell cycle progression and remodeling the BM. The work here provides valuable single-cell mechanistic insight into how the SWI/SNF assemblies differentially contribute to cellular invasion and how SWI/SNF subunit-specific disruptions may contribute to tumorigeneses and cancer metastasis.

SUMMARY STATEMENT

Cellular invasion through the basement membrane by theC. elegansanchor cell requires both BAF and PBAF SWI/SNF assemblies to arrest the cell cycle and promote the expression of pro-invasive genes.