bluuebunny/crossref_metadata_2025 huggingface dataset:
Unconventional secretion of α-synuclein mediated by palmitoylated DNAJC5 oligomers
Authors: Wu Shenjie , Hernandez Villegas Nancy C. , Sirkis Daniel W. , Thomas-Wright Iona , Wade-Martins Richard , Schekman Randy
Published: January 2022

Alpha-synuclein (α-syn), a major component of Lewy bodies found in Parkinson’s disease (PD) patients, has been found exported outside of cells and may mediate its toxicity via cell-to-cell transmission. Here, we reconstituted soluble, monomeric α-syn secretion by the expression of DnaJ homolog subfamily C member 5 (DNAJC5) in HEK293T cells. DNAJC5 undergoes palmitoylation and anchors on the membrane. Palmitoylation is essential for DNAJC5-induced α-syn secretion, and the secretion is not limited by substrate size or unfolding. Cytosolic α-syn is actively translocated and sequestered in an endosomal membrane compartment in a DNAJC5-dependent manner. Reduction of α-syn secretion caused by a palmitoylation-deficient mutation in DNAJC5 can be reversed by a membrane-targeting peptide fusion-induced oligomerization of DNAJC5. The secretion of endogenous α-syn mediated by DNAJC5 is also found in a human neuroblastoma cell line, SH-SY5Y, differentiated into neurons in the presence of retinoic acid, and in human induced pluripotent stem cell-derived midbrain dopamine neurons. We propose that DNAJC5 forms a palmitoylated oligomer to accommodate and export α-syn.
Age and experience affect the biosynthesis and emission of a Drosophila pheromone
Authors: Cortot Jérôme , Farine Jean-Pierre , Cobb Matthew , Everaerts Claude , Ferveur Jean-François
Published: January 2022

The most studied pheromone in Drosophila melanogaster, cis-Vaccenyl Acetate (cVA), is synthesized in the male ejaculatory bulb and transferred to the female during copulation. Combined with other chemicals cVA can modulate fly aggregation, courtship, mating and fighting. It is not detected on the cuticle of isolated males and is only released by males involved in social or sexual interaction. We explored the mechanisms underlying both cVA biosynthesis and emission in males of two wild types and a pheromonal mutant line. The effects of ageing, adult social interaction, and maternally-transmitted cVa and microbes — both associated with the egg chorion— on cVA biosynthesis and emission were measured. While ageing and genotype changed both biosynthesis and emission in similar ways, early developmental exposure to maternally-transmitted cVA and microbes strongly decreased cVA emission but not the biosynthesis of this molecule. This indicates that the release — but not the biosynthesis — of this sex pheromone strongly depends on early developmental context. The mechanism by which the preimaginal effects occur is unknown, but reinforces the significance of development in determining adult physiology and behaviour.

Summary statement

We show how the biosynthesis and release of a key Drosophila pheromone is affected by ageing, by early exposure to this pheromone and to microbes, and by social context.
Validation of SNP markers for marker-assisted selection of genotypes with increased carotenoid and dry matter contents in cassava
Authors: Ige Adenike D. , Olasanmi Bunmi , Bauchet Guillaume J. , Kayondo Ismail S. , Mbanjo Edwige Gaby Nkouaya , Uwugiaren Ruth , Motomura-Wages Sharon , Norton Joanna , Egesi Chiedozie , Parkes Elizabeth Y. , Kulakow Peter , Ceballos Hernan , Rabbi Ismail Y.
Published: January 2022

Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness in developing countries. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. SNP markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for marker-assisted selection (MAS). Assessment of marker performance in diverse genetic backgrounds is an important step towards their deployment for routine MAS. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific PCR assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r < 0.40) due to the more quantitative nature of the trait. This work confirmed marker effectiveness in multiple backgrounds, therefore, further strengthening its value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker development, thus leading to more routine use of markers in MAS in cassava improvement programs.
Sporadic Diurnal Fluctuations of Cyanobacterial Populations in Oligotrophic Temperate Systems Can Prevent Accurate Characterization of Change and Risk in Aquatic Systems
Authors: Cameron Ellen S. , Krishna Anjali , Emelko Monica B. , Müller Kirsten M.
Published: January 2022

Continental-scale increases in aquatic system eutrophication are linked with increased cyanobacteria threats to recreational water use and drinking water resources globally. Increasing evidence suggests that diurnal vertical migration of cyanobacteria are key factors that must be considered in cyanobacterial bloom risk management. While this has been discussed in marine and eutrophic freshwater contexts, reports of diurnal vertical migration of cyanobacteria in oligotrophic freshwater lakes are scant. Typical monitoring protocols do not reflect these dynamics and frequently focus only on surface water sampling approaches, and either ignore sampling time or recommend large midday timeframes (e.g., 10AM-3PM), thereby preventing accurate characterization of cyanobacterial community dynamics. To evaluate the impact of diurnal migrations and water column stratification on cyanobacterial abundance and composition, communities were characterized in a shallow well-mixed lake interconnected to a thermally stratified lake in the Turkey Lakes Watershed (Ontario, Canada) using amplicon sequencing of the 16S rRNA gene across a multi-time point sampling series in 2018 and 2022. This work showed that cyanobacteria are present in oligotrophic lakes and their community structure varies (i) diurnally, (ii) across the depth of the water column, (iii) interannually within the same lake and (iv) between different lakes that are closely interconnected within the same watershed. It underscored the need for integrating multi-timepoint, multi-depth discrete sampling guidance into lake and reservoir monitoring programs to describe cyanobacteria community dynamics and signal change to inform risk management associated with the potential for cyanotoxin production. Ignoring variability in cyanobacterial community dynamics (such as that reported herein) and reducing sample numbers can lead to a false sense of security and missed opportunities to identify and mitigate changes in trophic status and associated risks such as toxin or taste and odor production, especially in sensitive, oligotrophic systems.

Graphical Abstract

Highlights

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Cyanobacterial populations fluctuate sporadically across diurnal cycles

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Cyanobacterial communities can vary significantly between interconnected lakes

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Significant annual shifts in communities signal higher risk and need for monitoring

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Cyanobacteria monitoring for risk management should incorporate time and depth
Allatotropin in the Corpora Allata and Ovaries of Rhodnius prolixus: Probable in situ regulatory mechanisms
Authors: Villalobos Sambucaro María José , Ronderos Jorge Rafael
Published: January 2022

Originally described by Sir V. Wigglesworth in the Chagas disease vector Rhodnius prolixus, Juvenile Hormones (JHs) play critical roles during growth and reproduction. The JH described by Wigglesworth is the JH III skipped bisepoxide (JHSB3), and its titer in hemolymph varies along the 4th larval instar molting cycle. Allatotropin (AT), was originally characterized based on its ability to induce the synthesis of the JHs by the corpora allata (CA) in Lepidoptera. Beyond this function, AT has proved to be a myoregulator. Indeed, AT modulates muscle contractions in the gut, dorsal vessel and reproductive tissues. The presence of AT in the CA of 4th instar larvae of R. prolixus and the related species Triatoma infestans was previously shown, suggesting that AT might be involved in the regulation of JH synthesis in triatominae. Furthermore, the existence of allatotropic cells in this gland in T. infestans was also shown. This neuron-like cells show cytoplasmic processes projecting deeply between the cells engaged with JH synthesis. By using RT-qPCR we studied now the expression of both, AT and its receptor in the CA/CC complex along the 4th instar molting cycle, and in the ovaries of adult females. The expression of AT in the CA is highest between days 3 to 5 after meal, correlating with Mev-K and PPMev-D, two enzymes involved in the mevalonate pathway, as well as with the peak of JHSB3 on day 6. The results show that AT transcript is also present in the ovary suggesting a myoregulatory paracrine mechanism of regulation. Finally, our data suggest the existence of in situ mechanisms in the CA and ovaries of R. prolixus involving AT in both JHs synthesis and muscle contraction.
Circadian desynchronization attenuates information throughput of prefrontal cortex pyramidal neurons in mice
Authors: Roberts Brandon L. , Karatsoreos Ilia N.
Published: January 2022

The prefrontal cortex (PFC) is heavily involved in cognitive and emotional processes, including working memory, cognition, stress responses, and fear associated behaviors. Many PFC-associated behaviors are time-of-day dependent, and disruption of daily rhythms negatively impacts these behavioral outputs, yet how the disruption of daily rhythms impacts the fundamental function of PFC neurons, and the mechanism(s) by which this occurs, remains unknown. Using a mouse model, we demonstrate that the activity and action potential dynamics of prelimbic PFC neurons are regulated by time-of-day in a sex specific manner. Further, we show that postsynaptic K+channels play a central role in mediating these rhythms, suggesting an intrinsic gating mechanism mediating information throughput. Finally, we demonstrate that environmental circadian desynchronization alters the intrinsic functioning of these neurons in part by increasing sensitivity GIRK channel activation. These key discoveries demonstrate daily rhythms contribute to the mechanisms underlying the essential physiology of PFC circuits, and provide potential mechanisms by which circadian disruption may impact the fundamental properties of neurons.

Significance Statement

Disruption of circadian rhythms, such as shift work and jet lag, are associated with negative physiological and behavioral outcomes, including changes in affective state, cognitive function, learning and memory. The prefrontal cortex (PFC) plays a critical role in these functions, yet how daily rhythms and desynchronization of these rhythms impact the physiology of neurons in the PFC is unknown. Here we demonstrate that daily rhythms impact the physiological function of PFC neurons in a sex-dependent manner, and that environmental circadian desynchronization alters PFC function irrespective of time-of-day. These findings provide not only a physiological context to the neural and behavioral changes associated with circadian desynchronization, but also highlight the importance of considering the temporal dimension in studies of neural circuits.
Inter-animal variability in activity phase is constrained by synaptic dynamics in an oscillatory network
Authors: Anwar Haroon , Martinez Diana , Bucher Dirk , Nadim Farzan
Published: January 2022

The levels of voltage-gated and synaptic currents in the same neuron type can vary substantially across individuals. Yet, the phase relationships between neurons in oscillatory circuits are often maintained, even in the face of varying oscillation frequencies. We examined whether synaptic and intrinsic currents are matched to maintain constant activity phases across preparations, using the lateral pyloric (LP) neuron of the stomatogastric ganglion of the crab, Cancer borealis. LP produces stable oscillatory bursts upon release from inhibition, with an onset phase that is independent of oscillation frequency. We quantified the parameters that define the shape of the synaptic current inputs across preparations and found no linear correlations with voltage-gated currents. However, several synaptic parameters were correlated with oscillation period and burst onset phase, suggesting they may play a role in phase maintenance. We used the dynamic clamp to apply artificial synaptic inputs and found that those synaptic parameters correlated with phase and period were ineffective in influencing burst onset. Instead, parameters that showed the least variability across preparations had the greatest influence. Thus, parameters that influence circuit phasing are constrained across individuals, while those that have little effect simply co-vary with phase and frequency.
An organoid CRISPRi screen revealed that SOX9 primes human fetal lung tip progenitors to receive WNT and RTK signals
Authors: Sun Dawei , Batlle Oriol Llora , van den Ameele Jelle , Thomas John C. , He Peng , Lim Kyungtae , Tang Walfred , Xu Chufan , Meyer Kerstin B. , Teichmann Sarah A. , Marioni John C. , Jackson Stephen P. , Brand Andrea H. , Rawlins Emma L.
Published: January 2022

The balance between self-renewal and differentiation in human fetal lung epithelial progenitors controls the size and function of the adult organ. Moreover, progenitor cell gene regulation networks are employed by both regenerating and malignant lung cells, where modulators of their effects could potentially be of therapeutic value. Details of the molecular networks controlling human lung progenitor self-renewal remain unknown. We performed the first CRISPRi screen in primary human lung organoids to identify transcription factors controlling progenitor self-renewal. We show that SOX9 promotes proliferation of lung progenitors and inhibits precocious airway differentiation. Moreover, by identifying direct transcriptional targets using Targeted DamID we place SOX9 at the centre of a transcriptional network which amplifies WNT and RTK signalling to stabilise the progenitor cell state. In addition, the proof-of-principle CRISPRi screen and Targeted DamID tools establish a new approach for using primary human organoids to elucidate detailed functional mechanisms underlying normal development and disease.

Highlights

A pooled CRISPRi screen in human fetal lung organoids identified transcription factors controlling progenitor cell self-renewal.

SOX9 promotes tip progenitor cell proliferation and supresses precocious airway differentiation.

Targeted DamID (TaDa) identified SOX9 direct binding targets, revealing that SOX9 lies at the intersection of WNT and RTK signalling.

SOX9 and ETVs co-regulate the human fetal lung progenitor self-renewal programme.
ArabidopsisCONSERVED BINDING OF EIF4E1 negatively regulates the NADPH oxidase RESPIRATORY BURST OXIDASE HOMOLOG D
Authors: George Jeoffrey , Stegmann Martin , Monaghan Jacqueline , Zipfel Cyril
Published: January 2022

Cell-surface pattern recognition receptors sense invading pathogens by binding microbial or endogenous elicitors to activate plant immunity. These responses are under tight control to avoid excessive or untimely activation of cellular responses, which may otherwise be detrimental to host cells. How this fine-tuning is accomplished is an area of active study. We previously described a suppressor screen that identifiedArabidopsis thalianamutants with regained immune signaling in the immunodeficient genetic backgroundbak1-5, which we namedmodifier of bak1-5(mob)mutants. Here, we report thatbak1-5 mob7restores elicitor-induced signaling. Using a combination of map-based cloning and whole-genome resequencing, we identifiedMOB7asCONSERVED BINDING OF EIF4E1(CBE1), a plant-specific protein that interacts with highly-conserved eukaryotic translation initiation factor eIF4E1. Our data demonstrate that CBE1 regulate the accumulation of RESPIRATORY BURST OXIDASE HOMOLOG D (RBOHD), the NADPH oxidase responsible for elicitor-induced apoplast reactive oxygen species (ROS) production. Furthermore, several mRNA decapping and translation initiation factors co-localize with CBE1 and similarly regulate immune signaling. This study thus identifies a novel regulator of immune signaling and provides new insights into ROS regulation, and more generally translational control during plant stress responses.
Knockout of OsSWEET15 impaired rice embryo formation and seed-setting
Authors: Tang Zhenjia , Yang Jing , Bao Shuhui , Hu Zhi , Xia Huihuang , Ma Lai , Zheng Qingsong , Yang Fang , Zhang Dechun , Wang Tai , Sun Shubin , Hu Yibing
Published: January 2022

we show that the knockout of a sugar transporter gene OsSWEET15 led to a significant drop in rice fertility because near half of the knockout mutant spikelets bore blighted or empty grains. The rest spikelets bore fertile grains with slightly reduced weight. Notably, the ovaries in the blighted grains of the ossweet15 mutants expanded after flowering but terminated development before the endosperm cellularization stage and aborted subsequently. GUS and GFP representing OsSWEET15 expression showed that the protein was strongly expressed in the embryo surrounding region (ESR) which was supposed to supply nutrients for the embryo development. These results joined with the protein’s sucrose transport capacity and plasma membrane localization suggest that OsSWEET15 plays a prominent role during the caryopsis formation stage probably by releasing sucrose from the ESR to support the embryo development. By contrast, the empty grains were probably caused by the reduced pollen viability of the ossweet15 mutants. Investigation of the makeup of ossweet11 mutant grains revealed similar phenotypes that were observed in the ossweet15 mutants. These results indicate that both OsSWETT15 and OsSWEET11 play important and similar roles during rice pollen development, caryopsis formation, and seed-setting in addition to their function in seed-filling that was demonstrated previously.
Discovering highly potent antimicrobial peptides with deep generative model HydrAMP
Authors: Szymczak Paulina , Możejko Marcin , Grzegorzek Tomasz , Jurczak Radosław , Bauer Marta , Neubauer Damian , Sikora Karol , Michalski Michał , Sroka Jacek , Setny Piotr , Kamysz Wojciech , Szczurek Ewa
Published: January 2022

Antimicrobial peptides emerge as compounds that can alleviate the global health hazard of antimicrobial resistance, prompting a need for novel computational approaches to peptide generation. Here, we propose HydrAMP, a conditional variational autoencoder that learns lower-dimensional, continuous representation of peptides and captures their antimicrobial properties. The model disentangles the learnt representation of a peptide from its antimicrobial conditions and leverages parameter-controlled creativity. HydrAMP is the first model that is directly optimized for diverse tasks, including unconstrained and analogue generation and outperforms other approaches in these tasks. An additional preselection procedure based on ranking of generated peptides and molecular dynamics simulations increases experimental validation rate. Wet-lab experiments on five bacterial strains confirm high activity of nine peptides generated as analogues of clinically relevant prototypes, as well as six analogues of an inactive peptide. HydrAMP enables generation of diverse and potent peptides, making a step towards resolving the antimicrobial resistance crisis.
Multiscale Entropy Analysis of Retinal Signals Reveals Reduced Complexity in a Mouse Model of Alzheimer’s Disease
Authors: Araya-Arriagada Joaquín , Garay Sebastián , Rojas Cristóbal , Duran-Aniotz Claudia , Palacios Adrián G. , Chacón Max , Medina Leonel E.
Published: January 2022

Alzheimer’s disease (AD) is one of the most significant health challenges of our time, affecting a growing number of the elderly population. In recent years, the retina has received increased attention as a candidate for AD biomarkers since it appears to manifest the pathological signatures of the disease. Therefore, its electrical activity may hint at AD-related physiological changes. However, it is unclear how AD affects retinal electrophysiology and what tools are more appropriate to detect these possible changes. In this study, we used entropy tools to estimate the complexity of the dynamics of healthy and diseased retinas at different ages. We recorded microelectroretinogram responses to visual stimuli of different nature from retinas of young and adult, wild-type and 5xFAD –an animal model of AD– mice. To estimate the complexity of signals, we used the multiscale entropy approach, which calculates the entropy at several time scales using a coarse graining procedure. We found that young retinas had more complex responses to different visual stimuli. Further, the responses of young, wild-type retinas to natural-like stimuli exhibited significantly higher complexity than young, 5xFAD retinas. Our findings support a theory of complexity-loss with aging and disease and can have significant implications for early AD diagnosis.
DNA uptake by cell wall-deficient bacteria reveals a putative ancient macromolecule uptake mechanism
Authors: Kapteijn Renée , Shitut Shraddha , Aschmann Dennis , Zhang Le , de Beer Marit , Daviran Deniz , Roverts Rona , Akiva Anat , van Wezel Gilles P. , Kros Alexander , Claessen Dennis
Published: January 2022

Horizontal gene transfer in bacteria is widely believed to occur via three main mechanisms: conjugation, transduction and transformation. These mechanisms facilitate the passage of DNA across the protective cell wall using sophisticated machinery. We present here a new mechanism of DNA uptake that is independent of canonical DNA uptake machineries and is used by bacteria that live without a cell wall. We show that the cell wall-deficient bacteria engulf extracellular material, whereby intracellular vesicles are formed, and DNA is internalized. This mechanism is not specific to DNA, and allows uptake of other macromolecules and even 125 nm lipid nanoparticles (LNPs). Uptake was prevented by molecules known to inhibit eukaryotic endocytosis, suggesting this to be an energy-dependent process. Given that cell wall-deficient bacteria are considered a model for early life forms, our work provides a possible mechanism for primordial cells to acquire new genetic material or food before invention of the bacterial cell wall.
Innate immune cell response to host-parasite interaction in a human intestinal tissue microphysiological system
Authors: Humayun Mouhita , Ayuso Jose M , Park Keon Young , Di Genova Bruno Martorelli , Skala Melissa , Kerr Sheena C , Knoll Laura J. , Beebe David J.
Published: January 2022

Protozoan parasites that infect humans are widespread, and lead to varied clinical manifestations, including life-threatening illnesses in immunocompromised individuals. Animal models have provided insight into innate immunity against parasitic infections, however, species-specific differences and complexity of innate immune responses make translation to humans challenging. Thus, there is a need for novelin vitrosystems that can elucidate mechanisms of immune control and parasite dissemination. We have developed a human microphysiological system of intestinal tissue to evaluate parasite-immune-specific interactions during infection, which integrates primary intestinal epithelial cells and immune cells to investigate the role of innate immune cells during epithelial infection by the protozoan parasite, Toxoplasma gondii, which affects billions of people worldwide. Our data indicate that epithelial-infection by parasites stimulates a broad range of effector functions in neutrophils and NK cell-mediated cytokine production that play immunomodulatory roles, demonstrating the potential of our system for advancing the study of human-parasite interactions.

Teaser

Novel engineered model of human intestinal tissue for study of dissemination and immune control of parasitic infections.
Inflammasome mediated neuronal-microglial crosstalk: a therapeutic substrate for the familialC9orf72variant of the frontotemporal dementia/amyotrophic lateral sclerosis
Authors: Trageser Kyle J. , Smith Chad , Yang Eun-Jeong , Iban-Arias Ruth , Oguchi Tatsunori , Sebastian-Valverde Maria , Iqbal Umar Haris , Wu Henry , Estill Molly , Rahim Md Al , Raval Urdhva , Herman Francis J , Zhang Yong Jie , Petrucelli Leonard , Pasinetti Giulio Maria
Published: January 2022

Intronic G4C2hexanucleotide repeat expansions (HRE) ofC9orf72are the most common cause of familial variants of frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS). G4C2HREs inC9orf72undergo non-canonical repeat-associated translation, producing dipeptide repeat (DPR) proteins, with various deleterious impacts on cellular homeostasis. While five different DPRs are produced, poly(glycine-arginine) (GR) is amongst the most toxic and is the only DPR to accumulate in the associated clinically relevant anatomical locations of the brain. Previous work has demonstrated the profound effects of a poly(GR) model ofC9orf72FTD/ALS, including motor impairment, memory deficits, neurodegeneration, and neuroinflammation. Neuroinflammation is hypothesized to be a driving factor in the disease course; microglia activation is present prior to symptom onset and persists throughout the disease. Here, using an established mouse model ofC9orf72FTD/ALS we investigate the contributions of the nod-like receptor pyrin-containing 3 (NLRP3) inflammasome in the pathogenesis of FTD/ALS. We find that inflammasome-mediated neuroinflammation is increased with microglial activation, cleavage of caspase-1, production of IL-1β and upregulation ofCxcl10in the brain ofC9orf72FTD/ALS mice. Excitingly, we find that genetic ablation ofNlrp3significantly improved survival, protected behavioral deficits and prevented neurodegeneration suggesting a novel mechanism involving HRE-mediated induction of innate immunity. The findings provide experimental evidence of the integral role of HRE in inflammasome-mediated innate immunity in theC9orf72variant of FTD/ALS pathogenesis and suggest the NLRP3 inflammasome as a therapeutic target.
Design in the DARK: Learning Deep Generative Models for De Novo Protein Design
Authors: Moffat Lewis , Kandathil Shaun M. , Jones David T.
Published: January 2022

Abstract

The design of novel protein sequences is providing paths towards the development of novel therapeutics and materials. At the forefront is the challenging field of de novo protein design, which looks to design protein sequences unlike those found in nature using general design methodologies. In this work, we develop a tool for de novo design, based on a deep generative sequence model, that rapidly samples novel protein sequences with diverse and ordered structures. To build this tool we develop a framework, called DARK, that trains the underlying generative model on an iteratively expanding set of synthetic sequences. The resulting model generalizes where models trained on natural sequences struggle and greatly improves on the efficiency of comparable sampling-based approaches. We further show how it can generate high quality candidates for de novo design problems and aid in the development of further novel design methods, in all, providing another step, amongst others, towards truly automated and intelligent protein design.
NGSEP 4: Efficient and Accurate Identification of Orthogroups and Whole-Genome Alignment
Authors: Tello Daniel , Gonzalez-Garcia Laura Natalia , Gomez Jorge , Zuluaga-Monares Juan Camilo , Garcia Rogelio , Angel Ricardo , Mahecha Daniel , Duarte Erick , del Rosario Leon Maria , Reyes Fernando , Escobar-Velásquez Camilo , Linares-Vásquez Mario , Cardozo Nicolas , Duitama Jorge
Published: January 2022

Whole-genome alignment allows researchers to understand the genomic structure and variations among the genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment, and visualization. Our results showed that the NGSEP algorithm for ortholog identification has competitive accuracy and better efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. Finally, our software includes a new graphical user interface. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.
Macrophages regulate gastrointestinal motility through complement component 1q
Authors: Pendse Mihir , Li Yun , Salinas Cristine N. , Quinn Gabriella , Vo Nguyen , Propheter Daniel C. , Dende Chaitanya , Crofts Alexander A. , Koo Eugene , Hassell Brian , Ruhn Kelly A. , Raj Prithvi , Obata Yuuki , Hooper Lora V.
Published: January 2022

Peristaltic movement of the intestine propels food down the length of the gastrointestinal tract to promote nutrient absorption. Interactions between intestinal macrophages and the enteric nervous system regulate gastrointestinal motility, yet we have an incomplete understanding of the molecular mediators of this crosstalk. Here we identify complement component 1q (C1q) as a macrophage product that regulates gut motility. Macrophages were the predominant source of C1q in the mouse intestine and most extraintestinal tissues. Although C1q mediates complement-mediated killing of bacteria in the bloodstream, we found that C1q was not essential for immune defense of the intestine. Instead, C1q-expressing macrophages were localized to the intestinal submucosal plexus where they closely associated with enteric neurons and expressed surface markers characteristic of nerve-adjacent macrophages in other tissues. Mice with a macrophage-specific deletion ofC1qashowed changes in enteric neuronal gene expression, increased peristaltic activity, and accelerated intestinal transit. Our findings identify C1q as a key regulator of gastrointestinal motility and provide enhanced insight into the crosstalk between macrophages and the enteric nervous system.
Selective Ablation of 3’ RNA ends and Processive RTs Facilitate Direct cDNA Sequencing of Full-length Host Cell and Viral Transcripts
Authors: Gallardo Christian M. , Nguyen Anh-Viet T. , Routh Andrew L. , Torbett Bruce E.
Published: January 2022

Alternative splicing (AS) is necessary for viral proliferation in host cells and a critical regulatory component of viral gene expression. Conventional RNA-seq approaches provide incomplete coverage of AS due to their short read-lengths and are susceptible to biases and artifacts introduced in prevailing library preparation methodologies. Moreover, viral splicing studies are often conducted separately from host cell transcriptome analysis, precluding an assessment of the viral manipulation of host splicing machinery. To address current limitations, we developed a quantitative full-length direct cDNA sequencing strategy to simultaneously profile viral and host cell transcripts. This nanopore-based approach couples processive reverse transcriptases with a novel one-step chemical ablation of 3’ RNA ends (termed CASPR) which decreases ribosomal RNA reads and enriches for poly-adenylated coding sequences. We extensively validate our approach using synthetic reference transcripts and show CASPR doubles the breadth of coverage per transcript and increases detection of long transcripts (>4kb), while being functionally equivalent to PolyA+ selection for transcript quantification. We used our approach to interrogate host cell and HIV-1 transcript dynamics during viral reactivation and identified novel putative HIV-1 host factors containing exon skipping or novel intron retentions and delineated the HIV-1 transcriptional state associated with these differentially regulated host factors.
Integrated pretraining with evolutionary information to improve RNA secondary structure prediction
Authors: Yan Zichao , Hamilton William , Blanchette Mathieu
Published: January 2022

Abstract

RNA secondary structure prediction is a fundamental task in computational and molecular biology. While machine learning approaches in this area have been shown to improve upon traditional RNA folding algorithms, performance remains limited for several reasons such as the small number of experimentally determined RNA structures and suboptimal use of evolutionary information. To address these challenges, we introduce a practical and effective pretraining strategy that enables learning from a larger set of RNA sequences with computationally predicted structures and in the meantime, tapping into the rich evolutionary information available in databases such as Rfam. Coupled with a flexible and scalable neural architecture that can navigate different learning scenarios while providing ease of integrating evolutionary information, our approach significantly improves upon state-of-the-art across a range of benchmarks, including both single sequence and alignment based structure prediction tasks, with particularly notable benefits on new, less well-studied RNA families. Our source code, data and packaged RNA secondary structure prediction software RSSMFold can be accessed at https://github.com/HarveyYan/RSSMFold.
Identifying systematic variation at the single-cell level by leveraging low-resolution population-level data
Authors: Rahmani Elior , Jordan Michael I. , Yosef Nir
Published: January 2022

A major limitation in single-cell genomics is a lack of ability to conduct cost-effective population-level studies. As a result, much of the current research in single-cell genomics focuses on biological processes that are broadly conserved across individuals, such as cellular organization and tissue development. This limitation prevents us from studying the etiology of experimental or clinical conditions that may be inconsistent across individuals owing to molecular variation and a wide range of effects in the population. In order to address this gap, we developed “kernel of integrated single cells” (Keris), a novel model-based framework to inform the analysis of single-cell gene expression data with population-level effects of a condition of interest. By inferring cell-type-specific moments and their variation across conditions using large tissue-level bulk data representing a population, Keris allows us to generate testable hypotheses at the single-cell level that would otherwise require collecting single-cell data from a large number of donors. Within the Keris framework, we show how the combination of low-resolution, large bulk data with small but high-resolution single-cell data enables the identification of changes in cell-subtype compositions and the characterization of subpopulations of cells that are affected by a condition of interest. Using Keris we estimate linear and non-linear age-associated changes in cell-type expression in large bulk peripheral blood mononuclear cells (PBMC) data. Combining with three independent single-cell PBMC datasets, we demonstrate that Keris can identify changes in cell-subtype composition with age and capture cell-type-specific subpopulations of senescent cells. This demonstrates the promise of enhancing single-cell data with population-level information to study compositional changes and to profile condition-affected subpopulations of cells, and provides a potential resource of targets for future clinical interventions.
Differential cellular stiffness contributes to tissue elongation on an expanding surface
Authors: Koyama Hiroshi , Suzuki Makoto , Yasue Naoko , Sasaki Hiroshi , Ueno Naoto , Fujimori Toshihiko
Published: January 2022

Pattern formation and morphogenesis of cell populations is essential for successful embryogenesis. Steinberg proposed the differential adhesion hypothesis (DAH), and differences in cell–cell adhesion and interfacial tension have proven to be critical for cell sorting. Standard theoretical models such as the vertex model consider not only cell–cell adhesion/tension but also area elasticity of apical cell surfaces and viscous friction forces. However, the potential contributions of the latter two parameters to pattern formation and morphogenesis remain to be determined. In this theoretical study, we analyzed the effect of both area elasticity and the coefficient of friction on pattern formation and morphogenesis. We assumed the presence of two cell populations, one population of which is surrounded by the other. Both populations were placed on the surface of a uniformly expanding environment analogous to growing embryos, in which friction forces are exerted between cell populations and their expanding environment. When the area elasticity or friction coefficient in the cell cluster was increased relative to that of the surrounding cell population, the cell cluster was elongated. In comparison with experimental observations, elongation of the notochord in mice is consistent with the hypothesis based on the difference in area elasticity but not the difference in friction coefficient. Because area elasticity is an index of cellular stiffness, we propose that differential cellular stiffness may contribute to tissue elongation within an expanding environment.
mucG, mucH, and mucI modulate production of mutanocyclin and reutericyclins in Streptococcus mutans B04Sm5
Authors: Baker Jonathon L. , Tang Xiaoyu , LaBonte Sandra , Uranga Carla , Edlund Anna
Published: January 2022

Streptococcus mutans is considered a primary etiologic agent of dental caries, which is the most common chronic infectious disease worldwide. S. mutans B04Sm5 was recently shown to produce reutericyclins and mutanocyclin through the muc biosynthetic gene cluster, and to utilize reutericyclins to inhibit the growth of neighboring commensal Streptococci. In this study, examination of S. mutans and muc phylogeny suggested evolution of an ancestral S. mutans muc into three lineages within one S. mutans clade, and then horizontal transfer of muc to other S. mutans clades. The roles of the mucG and mucH transcriptional regulators, and the mucI transporter, were also examined. mucH was demonstrated to encode a transcriptional activator of muc. mucH deletion reduced production of mutanocyclin and reutericyclins, and eliminated the impaired growth and inhibition of neighboring Streptococci phenotypes which are associated with reutericyclin production. ΔmucG had increased mutanocyclin and reutericyclin production, which impaired growth and increased the ability to inhibit neighboring Streptococci. However, deletion of mucG also caused reduced expression of mucD, mucE, and mucI. Deletion of mucI reduced mutanocyclin and reutericylin production, but enhanced growth, suggesting that mucI may not transport reutericyclin as its homolog does in Limosilactobacillus reuteri. Further research is needed to determine the roles of mucG and mucI, and to identify any co-factors affecting the activity of the mucG and mucH regulators. Overall, this study provided pangenome and phylogenetic analysis that serves as a resource for S. mutans research, and began elucidation of the regulation of reutericyclins and mutanocyclin production in S. mutans.

Importance

S. mutans must be able to outcompete neighboring organisms in its ecological niche in order to cause dental caries. S. mutans B04Sm5 inhibited the growth of neighboring commensal Streptococci through production of reutericyclins via the muc biosynthetic gene cluster. In this study, carriage of muc was examined across S. mutans, which showed that 35 of 244 RefSeq S. mutans genomes encoded muc and provided a valuable update to the S. mutans pangenome and phylogeny. The roles of the mucG and mucH transcriptional regulators, and the mucI transporter, were also examined. All 3 genes impacted production of mutanocyclin and reutericyclins, which affected the growth rates, transcriptomes, and the ability of the S. mutans strains to inhibit the growth of neighboring commensals.
Genomic and phylogenetic analysis of the first myovirus isolated from Oceanospirillaceae, representing a novel viral cluster prevalent in polar oceans
Authors: Zhang Wenjing , Liu Yundan , Xing Jinyan , Zheng Kaiyang , Li Qian , Gu Chengxiang , Wang Ziyue , Shao Hongbing , Guo Cui , He Hui , Wang Hualong , Sung Yeong Yik , Mok Wen Jye , Wong Li Lian , Liang Yantao , McMinn Andrew , Wang Min
Published: January 2022

The marine bacterial family Oceanospirillaceae, which is abundant in the deep-seas and polar oceans, is closely associated with algal blooms and petroleum hydrocarbons degradation. However, only a few Oceanospirillaceae-infecting phages have so far been reported. Here we report on a novel Oceanospirillum phage, vB_OsaM_PD0307, which is the first myovirus to be found that infects Oceanospirillaceae. vB_OsaM_PD0307 with a 44,421 bp linear dsDNA genome. Phylogenetic analysis and average nucleotide sequence identities suggest that vB_OsaM_PD0307 is different from other phage isolates and represents a novel genus-level myoviral cluster with two high-quality uncultured viral genomes, designed as Oceanospimyovirus. Additionally, the biogeographical distribution of the vB_OsaM_PD0307 cluster suggests that they are widespread in the oceans and abundant in polar areas. In summary, our findings expand the current understanding of the phylogenetic diversity, genomic characteristic and function of Oceanospimyovirus phages, and highlight the role of the vB_OsaM_PD0307 phage as a major ecological agent that can infect certain key bacterial groups associated with polar algal blooms.

Importance

Oceanospirillumphage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae and represents a novel viral genus, Oceanospimyovirus. This study provides insights into the genomic, phylogenetic, and ecological characteristics of myoviruses infecting Oceanospirillaceae and improves our understanding of the interactions between Oceanospirillaceae and their phages in the oceans.
The limits of metabolic heredity in protocells
Authors: Palmeira Raquel Nunes , Colnaghi Marco , Harrison Stuart A , Pomiankowski Andrew , Lane Nick
Published: January 2022

The universal core of metabolism could have emerged from thermodynamically favoured prebiotic pathways at the origin of life. Starting with H2and CO2, the synthesis of amino acids and mixed fatty acids, which self-assemble into protocells, is favoured under warm anoxic conditions. Here we address whether it is possible for protocells to evolve greater metabolic complexity, through positive feedbacks involving nucleotide catalysis. Using mathematical simulations to model metabolic heredity in protocells, based on branch points in proto-metabolic flux, we show that nucleotide catalysis can indeed promote protocell growth. This outcome only occurs when nucleotides directly catalyse CO2fixation. Strong nucleotide catalysis of other pathways (e.g. fatty acids, amino acids) generally unbalances metabolism and slows down protocell growth, and when there is competition between catalytic functions cell growth collapses. Autocatalysis of nucleotide synthesis can promote growth but only if nucleotides also catalyse CO2fixation; autocatalysis alone leads to the accumulation of nucleotides at the expense of CO2fixation and protocell growth rate. Our findings offer a new framework for the emergence of greater metabolic complexity, in which nucleotides catalyse broad-spectrum processes such as CO2fixation, hydrogenation and phosphorylation important to the emergence of genetic heredity at the origin of life.
Phenotypic and transcriptomic responses of the sun- and shade-loving plants to sunlight and dim-light conditions
Authors: Zhang Yu-Xin , Niu Yu-Qian , Wang Xin-Feng , Wang Zhen-Hui , Wang Meng-Li , Yang Ji , Wang Yu-Guo , Zhang Wen-Ju , Song Zhi-Ping , Li Lin-Feng
Published: January 2022

Elucidating how plant species respond to variable light conditions is important to understanding the ecological adaptation to heterogeneous natural habitats. However, the phenotypic responses and gene regulatory network of shade-loving plants under distinct light conditions have remained largely unclear. In this study, we assessed the differences in phenotypic and transcriptomic responses between Arabidopsis (sun-loving) and Panax ginseng (shade-loving) to sunlight and dim-light conditions. Our results showed that, compared to the Arabidopsis, ginseng plants not only exhibited a lower degree of phenotypic plasticity in response to distinct light conditions, but also showed higher photosynthetic efficiency under dim-light conditions. Further time-course transcriptome profiling and gene structural analyses revealed that differentially transcriptional regulation together with increased copy number of the photosynthesis-related genes (i.e., electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under dim-light conditions. In contrast, the loss-function and inactivation of phytochrome-interacting factors are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under the changing light conditions. Our study provides new insights on how shade-loving plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops.

Highlight

The shade-loving species Panax ginseng possesses lower phenotypic plasticity under distinct light conditions and shows high photosynthesis efficiency under dim-light condition.
LuminoCell: a versatile and affordable luminometer platform for monitoring in-cell luciferase-based reporters
Authors: Weissová Kamila , Fafílek Bohumil , Radaszkiewicz Tomasz , Celiker Canan , Macháčková Petra , Čechová Tamara , Šebestíková Jana , Hampl Aleš , Bryja Vítězslav , Krejčí Pavel , Bárta Tomáš
Published: January 2022

Luciferase reporter assays represent a simple and sensitive experimental system in cell and molecular biology to study multiple biological processes. However, the application of these assays is often limited by the costs of conventional luminometer instruments and the versatility of their use in different experimental conditions. Therefore, we aimed to develop a small, affordable luminometer allowing continuous measurement of luciferase activity, designed for inclusion into various kinds of tissue culture incubators. Here we introduce LuminoCell - an open-source platform for the construction of an affordable, sensitive, and portable luminometer capable of realtime monitoring in-cell luciferase activity. The LuminoCell costs $40, requires less than 1 hour to assemble, and it is capable of performing real-time sensitive detection of both magnitude and duration of the activity of major signalling pathways in cell cultures, including receptor tyrosine kinases (EGF, FGF), WNT/β-catenin, and NF-κB. Additionally, we show that the LuminoCell is suitable to be used in cytotoxicity assays as well as for monitoring periodic circadian gene expression.