bluuebunny/crossref_metadata_2025 huggingface dataset:
Pattern completion and disruption characterize contextual modulation in the visual cortex
Authors: Fu Jiakun , Shrinivasan Suhas , Baroni Luca , Ding Zhuokun , Fahey Paul G. , Pierzchlewicz Paweł , Ponder Kayla , Froebe Rachel , Ntanavara Lydia , Muhammad Taliah , Willeke Konstantin F , Wang Eric , Ding Zhiwei , Tran Dat T. , Papadopoulos Stelios , Patel Saumil , Reimer Jacob , Ecker Alexander S. , Pitkow Xaq , Antolik Jan , Sinz Fabian H. , Haefner Ralf M. , Tolias Andreas S. , Franke Katrin
Published: March 2023

Vision is fundamentally context-dependent, with neuronal responses influenced not just by local features but also by surrounding contextual information. In the visual cortex, studies using simple grating stimuli indicate that congruent stimuli - where the center and surround share the same orientation - are more inhibitory than when orientations are orthogonal, potentially serving redundancy reduction and predictive coding. Understanding these center-surround interactions in relation to natural image statistics is challenging due to the high dimensionality of the stimulus space, yet crucial for deciphering the neuronal code of real-world sensory processing. Utilizing large-scale recordings from mouse V1, we trained convolutional neural networks (CNNs) to predict and synthesize surround patterns that either optimally suppressed or enhanced responses to center stimuli, confirmed by in vivo experiments. Contrary to the notion that congruent stimuli are suppressive, we found that surrounds that completed patterns based on natural image statistics were facilitatory, while disruptive surrounds were suppressive. Applying our CNN image synthesis method in macaque V1, we discovered that pattern completion within the near surround occurred more frequently with excitatory than with inhibitory surrounds, suggesting that our results in mice are conserved in macaques. Further, experiments and model analyses confirmed previous studies reporting the opposite effect with grating stimuli in both species. Using the MICrONS functional connectomics dataset, we observed that neurons with similar feature selectivity formed excitatory connections regardless of their receptive field overlap, aligning with the pattern completion phenomenon observed for excitatory surrounds. Finally, our empirical results emerged in a normative model of perception implementing Bayesian inference, where neuronal responses are modulated by prior knowledge of natural scene statistics. In summary, our findings identify a novel relationship between contextual information and natural scene statistics and provide evidence for a role of contextual modulation in hierarchical inference
Dynamical flexible inference of nonlinear latent structures in neural population activity
Authors: Abbaspourazad Hamidreza , Erturk Eray , Pesaran Bijan , Shanechi Maryam M.
Published: March 2023

Inferring complex spatiotemporal dynamics in neural population activity is critical for investigating neural mechanisms and developing neurotechnology. These activity patterns are noisy observations of lower-dimensional latent factors and their nonlinear dynamical structure. A major unaddressed challenge is to model this nonlinear structure, but in a manner that allows for flexible inference, whether causally, non-causally, or in the presence of missing neural observations. We address this challenge by developing DFINE, a new neural network that separates the model into dynamic and manifold latent factors, such that the dynamics can be modeled in tractable form. We show that DFINE achieves flexible nonlinear inference across diverse behaviors and brain regions. Further, despite enabling flexible inference unlike prior neural network models of population activity, DFINE also better predicts the behavior and neural activity, and better captures the latent neural manifold structure. DFINE can both enhance future neurotechnology and facilitate investigations across diverse domains of neuroscience.
Optineurin deficiency impairs autophagy to cause interferon beta overproduction and increased survival of mice following viral infection
Authors: Fukushi Masaya , Ohsawa Ryosuke , Okinaka Yasushi , Oikawa Daisuke , Kiyono Tohru , Moriwaki Masaya , Irie Takashi , Oda Kosuke , Kamei Yasuhiro , Tokunaga Fuminori , Sotomaru Yusuke , Maruyama Hirofumi , Kawakami Hideshi , Sakaguchi Takemasa
Published: March 2023

Background

Optineurin (OPTN) is associated with several human diseases, including amyotrophic lateral sclerosis (ALS), and is involved in various cellular processes, including autophagy. Optineurin regulates the expression of interferon beta (IFNβ), which plays a central role in the innate immune response to viral infection. However, the role of optineurin in response to viral infection has not been fully clarified. It is known that optineurin-deficient cells produce more IFNβ than wild-type cells following viral infection. In this study, we investigate the reasons for, and effects of, IFNβ overproduction during optineurin deficiency bothin vitroandin vivo.

Methods

To investigate the mechanism of IFNβ overproduction, viral nucleic acids in infected cells were quantified by RT-qPCR and the autophagic activity of optineurin-deficient cells was determined to understand the basis for the intracellular accumulation of viral nucleic acids. Moreover, lethal viral infection experiments using optineurin-disrupted (Optn-KO) animals were performed.

Results

IFNβ overproduction following viral infection was observed not only in several types of optineurin-deficient cell lines but also inOptn-KO mice and human ALS patient cells carrying mutations inOPTN. IFNβ overproduction inOptn-KO cells was revealed to be caused by excessive accumulation of viral nucleic acids, which was a consequence of reduced autophagic activity caused by the loss of optineurin. Additionally, IFNβ overproduction inOptn-KO mice suppressed viral proliferation, resulting in increased mouse survival following lethal viral challenge.

Conclusion

Our findings indicate that the combination of optineurin deficiency and viral infection leads to IFNβ overproductionin vitroandin vivo. The effects of optineurin deficiency are elicited by viral infection, therefore, viral infection may be implicated in the development of optineurin-related diseases.
Targeted metagenomic sequencing for detection of vertebrate viruses in wastewater for public health surveillance
Authors: McCall Camille , Elworth Ryan A. Leo , Wylie Kristine M , Wylie Todd N , Dyson Katherine , Doughty Ryan , Treangen Todd , Hopkins Loren , Ensor Katherine B , Stadler Lauren B
Published: March 2023

Viruses of concern for quantitative wastewater monitoring are usually selected as a result of an outbreak and subsequent detection in wastewater. However, targeted metagenomics could proactively identify viruses of concern when used as an initial screening tool. To evaluate the utility of targeted metagenomics for wastewater screening, we used ViroCap, a panel of probes designed to target all known vertebrate viruses. Untreated wastewater was collected from wastewater treatment plants (WWTPs) and building-level manholes associated with vulnerable populations in Houston, TX. We evaluated differences in vertebrate virus detection between WWTP and building-level samples, classified human viruses in wastewater, and performed phylogenetic analysis on astrovirus sequencing reads to evaluate targeted metagenomics for subspecies level classification. Vertebrate viruses varied widely across building-level samples. Rarely detected and abundant viruses were identified in WWTP and building-level samples, including enteric, respiratory, and bloodborne viruses. Furthermore, full length genomes were assembled from astrovirus reads and two human astrovirus serotypes were classified in wastewater samples. This study demonstrates the utility of targeted metagenomics as an initial screening step for public health surveillance.
Immune profiling, microbiome, metabolomics, and gut physiology of a 1-year controlled human hookworm infection
Authors: Vacca Francesco , Lavender Brittany , Noble Sophia-Louise , Cait Alissa , Maclean Kate , Mamum John , Yumnam Bibek , Kawa Tama Te , Mules Thomas C , Ferrer-Font Laura , Tang Jeffry S. , Gasser Olivier , Gros Graham Le , Camberis Mali , Inns Stephen
Published: March 2023

The observation that experimental helminth infection can be associated with immunomodulation and suppression of inflammatory diseases at distal tissue sites, has been used as rationale for trialing helminths such asNecator americanusfor the treatment of inflammatory disorders in humans. However, the lack of sufficient knowledge of the immunological interplay between human host and parasite in a controlled infection setting limits ongoing clinical intervention studies. In this one-year longitudinal study, healthy volunteers were recruited and infected withN. americanus. Changes in immune responses, microbiome, plasma metabolome and gut physiology were examined over the course of the one-year period. All participants were successfully infected as confirmed by detectable eggs in the feces and adult worms visualized in the intestine. In general, individual variation in immune cells, serum cytokines, fecal microbiome and plasma metabolites were greater than changes induced by the infection. Nevertheless, eosinophils, serum IL-5, and fecal eosinophil degranulation markers transiently increased in the acute phase of infection. In addition, while we observed stability in microbial community composition through the course of infection, we found a difference in the microbial community composition of participants with moderate gastrointestinal symptoms. No significant changes were observed in gut physiology measured using SmartpillTM, except for a decrease in small bowel pH. Untargeted plasma metabolomics analysis of participant plasma over the course of infection revealed enrichment in tryptophan metabolism following infection which was associated with increased CTLA-4 expression on regulatory T cells (TREGS), CRTH2+T helper 2 cells (TH2) and CCR6+T helper 9 cells (TH9). In conclusion, hookworm infection is well tolerated and represents an innovative platform for investigating immunomodulatory properties of hookworm infection in a therapeutic clinical setting.

One Sentence Summary

Controlled human hookworm infection changes immune-linked metabolic pathways
Direction and distance dependency of reaching movements of lower limb
Authors: Oku Kyosuke , Tanaka Shinsuke , Kida Noriyuki
Published: March 2023

Efficient movement of the body is an important part of our daily lives, which we perform unconsciously. Such efficient movements have been investigated using reaching movements in the upper limb, and whose kinematics reportedly vary depending on the movement direction. However, the reaching movements of the lower limbs are not well understood. Therefore, we aimed to examine changes in the kinematics of the lower limb reaching movements to determine the mechanism of skilled motor ability in terms of direction and distance. Sixteen adults (10 males) were requested to reach targets projected on the floor in seven directions and at three distances, for a total of 21 points. We found that the reaching time slowed down for the contralateral side (right foot to left-sided target), and was caused by a slower start of the toe movement. To identify the cause of this delay, we analyzed the onset of movement at each joint and found that movement to the contralateral side began closer to the torso than movement to the ipsilateral side. The time-to-peak velocity was also calculated; the motion required to reach the target in the shortest time varied depending on the direction and distance. Acceleration phases that were not observed in the upper limb velocity profile were observed in the lower limb velocity profiles. These results suggest that movement kinematics vary with direction and distance, resulting in slower reaching time on the contralateral side.
Short-chain mono-carboxylates as negative modulators of allosteric transitions in GLIC, and impact of a pre-β5 strand (Loop Ω) double mutation on crotonate, not butyrate effect
Authors: Renterghem Catherine Van , Nemecz Ákos , Medjebeur Karima , Corringer Pierre-Jean
Published: March 2023

The bacterial model GLIC remains one of the best known among pentameric ligand-gated ion channels (pLGICs), regarding their structure. GLIC is activated at low extracellular pH, but no agonist compound is known. Van Renterghemet al. (2023) showed that short-chain di-carboxylates potentiate GLIC activity, with strict dependence on two carboxylate binding pockets, previously characterized by crystallography (Sauguetet al., 2013, Fouratiet al., 2015, 2020). An “in series” model was proposed, with compound binding at the inter-subunit pocket [homologous to the pLGICs orthotopic neutotransmitter binding site], and with involvement of the intra-subunit (or vestibular) pocket in coupling binding to gating.

Here we characterize saturated, mono-carboxylates as negative modulators of GLIC, as previously shown for crotonate (Alqazzazet al., 2016). Butyrate and crotonate have indistinguishable properties regarding negative modulation of WT GLIC. However, a double mutation in the pre-β5 strand (Loop Ω) converts crotonate, as well as caffeate, but not butyrate, into positive modulators. We perform a mutational analysis of residue dependency in the two pockets, with the pre-β5 strand either intact or mutated. We propose that positive modulation requires stringent conditions, with integrity of both pockets, whereas negative modulation is less labile. The vestibular pocket may be involved as an accessory binding site leading to negative, but not positive modulation. We propose that the pre-β5 strand is involved in ligand-elicited modulation of GLIC gating, not in pHo-controlled gating. Possible involvement in Eukaryote pLGICs of regions corresponding to the vestibular pocket and the pre-β5 strand/Loop Ω is discussed.

Key points summary

Using the bacterial proton-activated receptor-channel GLIC, we identify a locus in the pre-β5 strand (Loop Ω) whose mutation inverses the effect of the mono-carboxylate crotonate from negative to positive modulation of the allosteric transitions, suggesting an involvement of the pre-β5 strand in coupling the extracellular orthotopic receptor to pore gating in this pentameric ligand-gated ion channel.

As an extension to the previously proposed “in series” mechanism, we suggest that a orthotopic/orthosteric site – vestibular site – Loop Ω – β5-β6 “sandwich” - Pro-Loop/Cys-Loop series may be an essential component of orthotopic/orthosteric compound-elicited gating control in this pentameric ligand-gated ion channel, on top of which compounds targeting the vestibular site may provide modulation.
Uneven terrain versus dual-task walking: differential challenges imposed on walking behavior in older adults are predicted by cognitive and sensorimotor function
Authors: Shah Valay A , Cruz-Almeida Yenisel , Roy Arkaprava , Cenko Erta , Downey Ryan J , Ferris Daniel P , Hass Chris J , Reuter-Lorenz Patricia A. , Clark David J , Manini Todd M , Seidler Rachael D
Published: March 2023

Aging is associated with declines in walking function. To understand these mobility declines, many studies have obtained measurements while participants walk on flat surfaces in laboratory settings during concurrent cognitive task performance (dual-tasking). This may not adequately capture the real-world challenges of walking at home and around the community. Here, we hypothesized that uneven terrains in the walking path impose differential changes to walking speed compared to dual-task walking. We also hypothesized that changes in walking speed resulting from uneven terrains will be better predicted by sensorimotor function than cognitive function. Sixty-three community-dwelling older adults (65-93 yrs old) performed overground walking under varying walking conditions. Older adults were classified into two mobility function groups based on scores of the Short Physical Performance Battery. They performed uneven terrain walking across four surface conditions (Flat, Low, Medium, and High unevenness) and performed single and verbal dual-task walking on flat ground. Participants also underwent a battery of cognitive (cognitive flexibility, working memory, inhibition) and sensorimotor testing (grip strength, 2-pt discrimination, pressure pain threshold). Our results showed that walking speed decreased during both dual-task walking and across uneven terrain walking conditions compared to walking on flat terrain. Participants with lower mobility function had even greater decreases in uneven terrain walking speeds. The change in uneven terrain speed was associated with attention and inhibitory function. Changes in both dual-task and uneven terrain walking speeds were associated with 2-point tactile discrimination. This study further documents associations between mobility, executive functions, and somatosensation, highlights the differential costs to walking imposed by uneven terrains, and identifies that older adults with lower mobility function are more likely to experience these changes to walking function.
Epigenetic reprogramming of a distal developmental enhancer cluster drivesSOX2overexpression in breast and lung cancer
Authors: Abatti Luis E. , Lado-Fernández Patricia , Huynh Linh , Collado Manuel , Hoffman Michael M. , Mitchell Jennifer A.
Published: March 2023

Enhancer reprogramming has been proposed as a key source of transcriptional dysregulation during tumorigenesis, but the molecular mechanisms underlying this process remain unclear. Here, we identify an enhancer cluster required for normal development that is aberrantly activated in breast and lung carcinoma. Deletion of the SRR124–134 cluster disrupts transcription of theSOX2oncogene and dysregulates genome-wide chromatin accessibility in cancer cells. Analysis of primary tumors reveals a correlation between chromatin accessibility at this cluster andSOX2overexpression in breast and lung cancer patients. We demonstrate that FOXA1 is an activator and NFIB is a repressor of SRR124–134 activity andSOX2transcription in cancer cells, revealing a co-opting of the regulatory mechanisms involved in early development. Notably, we show that the conserved SRR124 and SRR134 regions are essential during mouse development, where homozygous deletion results in the lethal failure of esophageal-tracheal separation. These findings provide insights into how developmental enhancers can be reprogrammed during tumorigenesis and underscore the importance of understanding enhancer dynamics during development and disease.
A newPlasmodium vivaxreference genome for South American isolates
Authors: De Meulenaere Katlijn , Cuypers Bart , Gamboa Dionicia , Laukens Kris , Rosanas-Urgell Anna
Published: March 2023

Background

Plasmodium vivaxis the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, asP. vivaxis a genetically diverse parasite with geographical clustering.

Results

This study presents a new high-quality assembly of a South AmericanP. vivaxisolate, referred to as PvPAM. The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation invirgenes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Threedhfranddhpsdrug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions.

Conclusions

Our findings show that the PvPAM reference genome more accurately represents South AmericanP. vivaxisolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses onP. vivaxisolates from the South American continent.
Protein-specific signal peptides for mammalian vector engineering
Authors: O’Neill Pamela , Mistry Rajesh K , Brown Adam J. , James David C.
Published: March 2023

Expression of recombinant proteins in mammalian cell factories relies on synthetic assemblies of genetic parts to optimally control flux through the product biosynthetic pathway. In comparison to other genetic part-types, there is a relative paucity of characterized signal peptide components, particularly for mammalian cell contexts. In this study, we describe a toolkit of signal peptide elements, created using bioinformatics-led and synthetic design approaches, that can be utilized to enhance production of biopharmaceutical proteins in Chinese Hamster Ovary cell factories. We demonstrate, for the first time in a mammalian cell context, that machine learning can be used to predict how discrete signal peptide elements will perform when utilized to drive ER translocation of specific single chain protein products. For more complex molecular formats, such as multichain monoclonal antibodies, we describe how a combination ofin silicoand targeted design rule-basedin vitrotesting can be employed to rapidly identify product-specific signal peptide solutions from minimal screening spaces. The utility of this technology is validated by deriving vector designs that increase product titers ≥ 1.8x, compared to standard industry systems, for a range of products, including a difficult-to-express monoclonal antibody. The availability of a vastly expanded toolbox of characterized signal peptide parts, combined with streamlinedin silico/in vitrotesting processes, will permit efficient expression vector re-design to maximize titers of both simple and complex protein products.

GRAPHICAL ABSTRACT
Mycobacterial RNase E cleaves with a distinct sequence preference and controls the degradation rates of mostMycolicibacterium smegmatismRNAs
Authors: Zhou Ying , Sun Huaming , Vargas-Blanco Diego A. , Martini Maria Carla , Rapiejko Abigail R. , Chase Michael R. , Joubran Samantha R. , Davis Alexa B. , Dainis Joseph P. , Kelly Jessica M. , Ioerger Thomas R. , Roberts Louis A. , Fortune Sarah M. , Shell Scarlet S.
Published: March 2023

The mechanisms and regulation of RNA degradation in mycobacteria have been subject to increased interest following the identification of interplay between RNA metabolism and drug resistance. Mycobacteria encode multiple ribonucleases that are predicted to participate in mRNA degradation and/or processing of stable RNAs. RNase E is an endoribonuclease hypothesized to play a major role in mRNA degradation due to its essentiality in mycobacteria and its role in mRNA degradation in gram- negative bacteria. Here, we defined the impact of RNase E on mRNA degradation rates transcriptome- wide in the non-pathogenic modelMycolicibacterium smegmatis. RNase E played a rate-limiting role in the degradation of at least 89% of protein-coding genes, with leadered transcripts generally being more affected by RNase E repression than leaderless transcripts. There was an apparent global slowing of transcription in response to knockdown of RNase E, suggesting thatM. smegmatisregulates transcription in responses to changes in mRNA degradation. This compensation was incomplete, as the abundance of most transcripts increased upon RNase E knockdown. We assessed the sequence preferences for cleavage by RNase E transcriptome-wide in bothM. smegmatisandM. tuberculosis, and found a consistent bias for cleavage in C-rich regions. Purified RNase E had a clear preference for cleavage immediately upstream of cytidines, distinct from the sequence preferences of RNase E in gram-negatives. We furthermore report a high-resolution map of mRNA cleavage sites inM. tuberculosis, which occur primarily within the RNase E-preferred sequence context, confirming RNase E as a broad contributor toM. tuberculosistranscriptome structure.
Su(var)3-9 mediates age-dependent increase in H3K9 methylation on TDP-43 promoter triggering neurodegeneration
Authors: Marzullo Marta , Romano Giulia , Pellacani Claudia , Riccardi Federico , Ciapponi Laura , Feiguin Fabian
Published: March 2023

Aging progressively modifies the physiological balance of the organism increasing susceptibility to both genetic and sporadic neurodegenerative diseases. These changes include epigenetic chromatin remodeling events that may modify gene transcription. However, how aging interconnects with disease-causing genes is not well known. Here, we found that Su(var)3-9 causes increased methylation of histone H3K9 in the promoter region of TDP-43, the most frequently altered factor in amyotrophic lateral sclerosis (ALS), affecting the mRNA and protein expression levels of this gene through epigenetic modifications in chromatin organization that appear to be conserved in agedDrosophilabrains, mouse and human cells. Remarkably, augmented Su(var)3-9 activity causes a decrease in TDP-43 expression followed by early defects in locomotor activities. In contrast, decreasing Su(var)3-9 action promotes higher levels of TDP-43 expression and reinvigorates motility parameters in old flies, uncovering a novel role of this enzyme in regulating TDP-43 expression and locomotor senescence. The data indicate how conserved epigenetic mechanisms may link aging with neuronal diseases and suggest that Su(var)3-9 may play a role in the pathogenesis of ALS.
Free long chain fatty acid solitarily primes early postembryonic development inCaenorhabditis elegansunder starvation
Authors: Ruan Meiyu , Xu Fan , Li Na , Teng Fukang , Zhu Huanhu
Published: March 2023

Postembryonic development of animals is long considered an internal predetermined program, while macronutrient is essential only because they provide biomatters and energy to support this process. However, in this study, by using a nematodeCaenorhabditis elegansmodel, we surprisingly found that dietary supplementation of palmitic acid alone, but not other essential nutrients of abundance such as glucose or amino acid mixture, sufficiently initiated the early postembryonic development under complete macronutrient deprivation. Such a development was indicated by changes in morphology, cellular markers in multiple tissues, behaviors and the global transcription pattern. Mechanistically, palmitate doesn’t function as a biomatter/energy provider, but as a ligand to activate the nuclear hormone receptor NHR-49/80 and generate an obscure peroxisome-derived secretive hormone in the intestine. Such a hormonal signal was received by chemosensory neurons in the head in regulating the insulin-like neuropeptide secretion and its downstream nuclear receptor to orchestrate the global development. Moreover, the nutrient-sensing hub mTORC1 played a negative role in this process. In conclusion, our data indicate that free fatty acid acts as a prime nutrient signal to launch the early development inC. elegans;and implicate that specific nutrient rather than the internal genetic program is the first impetus of postembryonic development.
SafeMut: UMI-aware variant simulator incorporating allele-fraction overdispersion in read editing
Authors: Zhao Xiaofei , Guo Jingyu , Wang Sizhen
Published: March 2023

Next-generation sequencing (NGS) has been widely used for calling biological variants. The gold-standard methodology for accessing the ability of a computational method to call a specific variant is to perform NGS wet-lab experiments on samples known to harbor this variant. Nevertheless, wet-lab experiments are both labor-intensive and time-consuming, and rare variants may not be present in a sample of population. Moreover, these two issues are exacerbated in SafeSeqS which enabled liquid biopsy and minimum-residual disease (MRD) detection with cell-free DNA by using unique molecular identifier (UMI) to detect and/or correct NGS error. Hence, we developed the first UMI-aware NGS small-variant simulator named SafeMut which also considered the overdispersion of allele fraction. We used the tumor-normal paired sequencing runs from the SEQC2 somatic reference sets and cell-free DNA data sets to assess the performance of BamSurgeon, VarBen, and SafeMut. We observed that, unlike BamSurgeon and VarBen, the allele-fraction distribution of the variants simulated by SafeMut closely resembles such distribution generated by technical replicates of wet-lab experiments. SafeMut is able to provide accurate simulation of small variants in NGS data, thereby helping with the assessment of the ability to call these variants in a bioinformatics pipeline.
Extracellular vesicle-localized miR-203 mediates neural crest-placode communication required for trigeminal ganglia formation
Authors: Bernardi Yanel E , Sanchez-Vasquez Estefania , Piacentino Michael L. , Urrutia Hugo , Rossi Izadora , Saraiva Karina Lidianne Alcântara , Pereira-Neves Antonio , Ramirez Marcel Ivan , Bronner Marianne E. , de Miguel Natalia , Strobl-Mazzulla Pablo H.
Published: March 2023

While interactions between neural crest and placode cells are critical for the proper formation of the trigeminal ganglion, the mechanisms underlying this process remain largely uncharacterized. Here, we show that the microRNA-(miR)203, whose epigenetic repression is required for neural crest migration, is reactivated in coalescing and condensing trigeminal ganglion cells. Overexpression of miR-203 induces ectopic coalescence of neural crest cells and increases ganglion size. Reciprocally, loss of miR-203 function in placode, but not neural crest, cells perturbs trigeminal ganglion condensation. Demonstrating intercellular communication, overexpression of miR-203 in the neural crestin vitroorin vivorepresses a miR-responsive sensor in placode cells. Moreover, neural crest-secreted extracellular vesicles (EVs), visualized using pHluorin-CD63 vector, become incorporated into the cytoplasm of placode cells. Finally, RT-PCR analysis shows that small EVs isolated from condensing trigeminal ganglia are selectively loaded with miR-203. Together, our findings reveal a critical role in vivo for neural crest-placode communication mediated by sEVs and their selective microRNA cargo for proper trigeminal ganglion formation.

SIGNIFICANCE STRATEMENT

Cellular communication during early development plays a critical role. In this study, we demonstrate a unique role for a microRNA in cell-cell communication between the neural crest (NC) and placode cells (PC) during trigeminal ganglia (TG) formation. By utilizing loss and gain of function experiments in vivo, we demonstrate a requirement for miR-203 during cellular condensation to form the TG. We revealed that NC produces extracellular vesicles, selectively carrying miR-203, which is then taken up by the PC and regulates a sensor vector exclusively expressed in the placode. Taken together, our findings reveal a critical role in TG condensation for miR-203, produced by post-migratory NC and taken up by PC via extracellular vesicles.
Nanobodies against SARS-CoV-2 reduced virus load in the brain of challenged mice and neutralized Wuhan, Delta and Omicron Variants
Authors: Pavan María Florencia , Bok Marina , Juan Rafael Betanzos San , Malito Juan Pablo , Marcoppido Gisela Ariana , Franco Diego Rafael , Militello Daniela Ayelen , Schammas Juan Manuel , Bari Sara ,   Argentinian AntiCovid Consortium, Stone William B. , López Krisangel , Porier Danielle L. , Muller John , Auguste Albert J. , Yuan Lijuan , Wigdorovitz Andrés , Parreño Viviana , Ibañez Lorena Itatí
Published: March 2023

In this work, we developed llama-derived nanobodies (Nbs) directed to the receptor binding domain (RBD) and other domains of the Spike (S) protein of SARS-CoV-2. Nanobodies were selected after the biopanning of two VHH-libraries, one of which was generated after the immunization of a llama (lama glama) with the bovine coronavirus (BCoV) Mebus, and another with the full-length pre-fused locked S protein (S-2P) and the RBD from the SARS-CoV-2 Wuhan strain (WT). Most of the neutralizing Nbs selected with either RBD or S-2P from SARS-CoV-2 were directed to RBD and were able to block S- 2P/ACE2 interaction. Three Nbs recognized the N-terminal domain (NTD) of the S-2P protein as measured by competition with biliverdin, while some non-neutralizing Nbs recognize epitopes in the S2 domain. One Nb from the BCoV immune library was directed to RBD but was non-neutralizing. Intranasal administration of Nbs induced protection ranging from 40% to 80% against COVID-19 death in k18-hACE2 mice challenged with the WT strain. Interestingly, protection was not only associated with a significant reduction of virus replication in nasal turbinates and lungs, but also with a reduction of virus load in the brain. Employing pseudovirus neutralization assays, we were able to identify Nbs with neutralizing capacity against the Alpha, Beta, Delta and Omicron variants. Furthermore, cocktails of different Nbs performed better than individual Nbs to neutralize two Omicron variants (B.1.529 and BA.2). Altogether, the data suggest these Nbs can potentially be used as a cocktail for intranasal treatment to prevent or treat COVID-19 encephalitis, or modified for prophylactic administration to fight this disease.
A lymph node-to-tumour PDL1+macrophage circuit antagonizes dendritic cell immunotherapy
Authors: Sprooten Jenny , Vanmeerbeek Isaure , Datsi Angeliki , Govaerts Jannes , Borràs Daniel M , Naulaerts Stefan , Laureano Raquel S. , Calvet Anna , Kuballa Marc , Sabel Michael C. , Rapp Marion , Knobbe-Thomsen Christiane , Liu Peng , Zhao Liwei , Kepp Oliver , Kroemer Guido , Boon Louis , Tejpar Sabine , Borst Jannie , Schlenner Susan , Vleeschouwer Steven De , Sorg Rüdiger V. , Garg Abhishek D
Published: March 2023

Immune-checkpoint blockers (ICB) provide limited benefit against T cell-depleted tumours, calling for therapeutic innovation. Here, we aimed at designing a new type of dendritic cell (DC) vaccine by unbiased computational integration of multi-omics data from cancer patients. In a first attempt, a DC vaccine designed to present tumor antigens from cancer cells succumbing to immunogenic cancer cell death (ICD) and to elicit high type I interferon (IFN) responses failed to induce the regression of mouse tumors lacking T cell infiltrates. In lymph nodes (LNs), instead of activating CD4+and CD8+T cells, DCs stimulated immunosuppressive PD-L1+LN-associated macrophages (LAMs) via a type I IFN response. Moreover, DC vaccines of this type stimulated pre-existing, T cell-suppressive, PD-L1+tumour-associated macrophages (TAMs). This created a T cell-suppressive circuit of PD-L1+macrophages, spanning across LNs and tumours. Accordingly, DC vaccines synergised with PD-L1 blockade to deplete PD-L1+macrophages, suppress myeloid inflammation affecting the tumor bed and draining lymph nodes, and de-inhibit effector/stem-like memory T cells, eventually causing tumour regression. The synergistic interaction between the DC vaccine and PD-L1 blockade was lost when DCs were manipulated to loseIfnar1orCcr7or when macrophages were depleted. Interestingly, clinical DC vaccines also potentiated lymphocyte-suppressive PD-L1+TAMs in patients bearing T cell-depleted tumours. Altogether, our results reveal the existence of a novel PD-L1+LAM/TAM-driven immunosuppressive pathway that can be elicited by DC vaccines, yet can be subverted for improving the outcome of immunotherapy.
Reverse genetic screen identifies malaria parasite genes required for gametocyte-to-sporozoite development in its mosquito host
Authors: Ukegbu Chiamaka Valerie , Gomes Ana Rita , Giorgalli Maria , Campos Melina , Bailey Alexander J. , Besson Tanguy Rene Balthazar , Billker Oliver , Vlachou Dina , Christophides George K.
Published: March 2023

Malaria remains one of the most devastating infectious diseases. Reverse genetic screens offer a powerful approach to identify genes and molecular processes governing malaria parasite biology. However, sexual reproduction and complex regulation of gene expression and genotype-phenotype associations in the mosquito have hampered the development of screens in this key part of the parasite lifecycle. We designed a genetic approach in the rodent parasitePlasmodium berghei, which in conjunction with barcode sequencing allowed us to overcome the fertilization roadblock and screen for gametocyte-expressed genes required for parasite infection of the mosquitoAnopheles coluzzii. The results confirmed previous findings, validating our approach for scaling up, and identified new genes required for ookinete motility and mosquito midgut infection and for sporozoite development and oocyst egress and salivary gland infection. Our findings can assist efforts to study malaria transmission biology and develop new interventions to control disease transmission.
Unraveling the role ofSlc10a4in auditory processing and sensory motor gating: implications for neuropsychiatric disorders?
Authors: Ciralli Barbara , Malfatti Thawann , Hilscher Markus M. , Leao Richardson N. , Cederroth Christopher R. , Leao Katarina E. , Kullander Klas
Published: March 2023

Background

Psychiatric disorders, such as schizophrenia, are complex and challenging to study, partly due to the lack of suitable animal models. However, the absence of theSlc10a4gene, which codes for a monoaminergic and cholinergic associated vesicular transporter protein, in knockout mice (Slc10a4-/-), leads to the accumulation of extracellular dopamine. This makes them a potential animal model for schizophrenia, a disorder known to be associated with altered dopamine signaling in the brain.

Methods

The locomotion, auditory sensory filtering and prepulse inhibition (PPI) ofSlc10a4-/-mice were quantified and compared to wildtype (WT) littermates. Intrahippocampal electrodes were used to record auditory event-related potentials (aERPs) for quantifying sensory filtering in response to paired-clicks. The channel above aERPs phase reversal was chosen for reliably comparing results between animals, and aERPs amplitude and latency of click responses were quantified. WT andSlc10a4-/-mice were also administered subanesthetic doses of ketamine to provoke psychomimetic behavior.

Results

Baseline locomotion during auditory stimulation was similar betweenSlc10a4-/-mice and WT littermates. In WT animals, normal auditory gating was observed after i.p saline injections, and it was maintained under the influence of 5 mg/kg ketamine, but disrupted by 20 mg/kg ketamine. On the other hand,Slc10a4-/-mice did not show significant differences between N40 S1 and S2 amplitude responses in saline or low dose ketamine treatment. Auditory gating was considered preserved since the second N40 peak was consistently suppressed, but with increased latency. The P80 component showed higher amplitude, with shorter S2 latency under saline and 5 mg/kg ketamine treatment inSlc10a4-/-mice, which was not observed in WT littermates. Prepulse inhibition was also decreased inSlc10a4-/-mice when the longer interstimulus interval of 100 ms was applied, compared to WT littermates.

Conclusion

TheSlc10a4-/-mice responses indicate that cholinergic and monoaminergic systems participate in the PPI magnitude, in the temporal coding (response latency) of the auditory sensory gating component N40, and in the amplitude of aERPs P80 component. These results suggest thatSlc10a4-/-mice can be considered as potential models for neuropsychiatric conditions.
Ganglioside GD3 regulates neural stem cell quiescence and controls postnatal neurogenesis
Authors: Fuchigami Takahiro , Itokazu Yutaka , Yu Robert K.
Published: March 2023

The postnatal neural stem cell (NSC) pool hosts quiescent and activated radial glia-like NSCs contributing to neurogenesis throughout adulthood. However, the underlying regulatory mechanism during the transition from quiescent NSCs to activated NSCs in the postnatal NSC niche is not fully understood. Lipid metabolism and lipid composition play important roles in regulating NSC fate determination. Biological lipid membranes define the individual cellular shape and help maintain cellular organization and are highly heterogenous in structure and there exist diverse microdomains (also known as lipid rafts), which are enriched with sugar molecules, such as glycosphingolipids. An often overlooked but key aspect is that the functional activities of proteins and genes are highly dependent upon their molecular environments. We previously reported that ganglioside GD3 is the predominant species in NSCs and that the reduced postnatal NSC pools are observed in global GD3-synthase knockout (GD3S-KO) mouse brains. The specific roles of GD3 in determining the stage and cell-lineage determination of NSCs remain unclear, since global GD3S-KO mice cannot distinguish if GD3 regulates postnatal neurogenesis or developmental impacts. Here we show that inducible GD3 deletion in postnatal radial glia-like NSCs promotes the NSC activation, resulting in the loss of the long-term maintenance of the adult NSC pools. The reduced neurogenesis in the subventricular zone (SVZ) and the dentate gyrus (DG) of GD3S-conditional-knockout mice led to impaired olfactory and memory functions. Thus, our results provide convincing evidence that postnatal GD3 maintains the quiescent state of radial glia-like NSCs in the adult NSC niche.
Modeling and dissociation of intrinsic and input-driven neural population dynamics underlying behavior
Authors: Vahidi Parsa , Sani Omid G. , Shanechi Maryam M.
Published: March 2023

Neural dynamics can reflect intrinsic dynamics or dynamic inputs, such as sensory inputs or inputs from other regions. To avoid misinterpreting temporally-structured inputs as intrinsic dynamics, dynamical models of neural activity should account for measured inputs. However, incorporating measured inputs remains elusive in joint dynamical modeling of neural-behavioral data, which is important for studying neural computations of a specific behavior. We first show how training dynamical models of neural activity while considering behavior but not input, or input but not behavior may lead to misinterpretations. We then develop a novel analytical learning method that simultaneously accounts for neural activity, behavior, and measured inputs. The method provides the new capability to prioritize the learning of intrinsic behaviorally relevant neural dynamics and dissociate them from both other intrinsic dynamics and measured input dynamics. In data from a simulated brain with fixed intrinsic dynamics that performs different tasks, the method correctly finds the same intrinsic dynamics regardless of task while other methods can be influenced by the change in task. In neural datasets from three subjects performing two different motor tasks with task instruction sensory inputs, the method reveals low-dimensional intrinsic neural dynamics that are missed by other methods and are more predictive of behavior and/or neural activity. The method also uniquely finds that the intrinsic behaviorally relevant neural dynamics are largely similar across the three subjects and two tasks whereas the overall neural dynamics are not. These input-driven dynamical models of neural-behavioral data can uncover intrinsic dynamics that may otherwise be missed.
The Electrophysiological Markers of Statistically Learned Attentional Enhancement: Evidence for a Saliency Based Mechanism
Authors: Duncan Dock H. , van Moorselaar Dirk , Theeuwes Jan
Published: March 2023

It has been well established that attention can be sharpened through the process of statistical learning - whereby visual search is optimally adapted to the spatial probabilities of a target in visual fields. Specifically, attentional processing becomes more efficient when targets appear at high relatively to low probability locations. Statistically learned attentional enhancement has been shown to differ behaviorally from the more well studied top-down and bottom-up forms of attention; and while the electrophysiological characteristics of top-down and bottom-up attention have been well explored, relatively little work has been done to characterize the electrophysiological correlates of statistically learned attentional enhancement. In the current study, EEG data was collected while participants performed the additional singleton task with an unbalanced target distribution. Encephalographic data was then analyzed for two well-known correlates of attentional processing – alpha lateralization and the N2pc component. Our results showed that statistically learned attentional enhancement is not characterized by alpha lateralization, thereby differentiating it from top-down enhancement. Yet targets at high probability locations did reliably produce larger N2pc amplitudes, a known marker of increased bottom-up capture due to higher target-distractor contrasts. These results support an interpretation of the probability cuing effects where the improved processing of targets at expected locations is mediated by a saliency-based mechanism – boosting the salience of targets appearing at high-probability locations relative to those at low-probability locations.

Significance statement

Things are easier to find when you have a good idea of where they should be – e.g. shoes on the floor and birds in the sky. Expectations of where things are likely to be found can be implicitly learned without much, if any, awareness. Until now, little was known about how these implicit spatial biases change the representation of items in the brain. In the current work, we present EEG recordings which suggest that the brain may represent items in common locations as more salient than in other locations in space. These findings inform how the brain represents implicit search expectations; supporting a model where items in expected areas in space capture attention more frequently because they are represented by the brain as more salient.
The ancestry of Antennapedia-like homeobox genes
Authors: Copley Richard R.
Published: March 2023

I show that broad evolutionarily significant sub-groups of Antennapedia-like homeobox genes can be distinguished by consideration of 4 amino acids. The absence of proline at position 26 is a synapomorphy of the class; HOX-like homeodomains contain a 19,30 salt-bridge of inverted polarity with respect to the same residues in typical NK-like homeodomains, and residue 28 is highly conserved within but not necessarily between orthologous groups. None of these residues has an obvious role in sequence specific DNA recognition. The EH1 and hexapeptide sequence motifs outside the homeodomain are not well correlated with sub-type. From the discovery of a hexapeptide motif in a sponge NK-like gene, and identification of new instances of longer engrailed-like (EH2) variants of the hexapeptide, I infer that scattered motif distribution is unlikely to be due to convergent evolution, but rather multiple independent loss events. I reconcile these features and the species distribution of current genes to propose a scheme for the ordering of duplication events in the cnidarian-bilaterian stem group.