bluuebunny/crossref_metadata_2025 huggingface dataset:
Honey bee functional genomics using symbiont-mediated RNAi
Authors: Lariviere Patrick J. , Leonard Sean P. , Horak Richard D. , Powell J. Elijah , Barrick Jeffrey E.
Published: May 2022

Bees are indispensable pollinators and model organisms for studying social behavior, development, and cognition. However, their eusociality makes it difficult to use standard forward genetic approaches to study gene function. To fill this gap, we engineered the bee gut bacteriumSnodgrassella alvito induce a host RNA interference response that reduces expression of a targeted gene. To employ this FUGUES (FUnctionalGenomicsUsingEngineeredSymbionts) procedure, a double-stranded RNA expression plasmid is cloned inEscherichia coliusing Golden Gate assembly and then transferred toS. alvi. Adult worker bees are then colonized with engineeredS. alvi. Finally, gene knockdown is verified through qRT-PCR, and bee phenotypes of interest can be further assessed. Expression of targeted genes is reduced by as much as 50-75% throughout the entire bee body by five days after colonization. This protocol can be accomplished in four weeks by bee researchers with microbiology and molecular cloning skills.
Engineered sensor bacteria evolve master-level gameplay through accelerated adaptation
Authors: Prakash Satya , Racovita Adrian , Varela Clenira , Walsh Mark , Galizi Roberto , Isalan Mark , Jaramillo Alfonso
Published: May 2022

Gene circuits enable cells to make decisions by controlling the expression of genes in reaction to specific environmental factors1. These circuits can be designed to encode logical operations2–7, but implementation of more complex algorithms has proved more challenging. Directed evolution optimizes gene circuits8without the need for design knowledge9, but adjusting multiple genes and conditions10in genotype searches poses challenges11. Here we show a multicellular sensor system, AdaptoCells, in Escherichia coli, that can evolve complex behavior through an accelerated adaptation to chemical environments. AdaptoCells recognize chemical patterns and act as a decision-making system. Using an iterative improvement method, we demonstrate that the AdaptoCells can evolve to achieve mastery in the game of tic-tac-toe, demonstrating an unprecedented level of complexity for engineered living cells. We provide an effective and straightforward way to encode complexity in gene circuits, allowing for fast adaptation in response to dynamic environments and leading to optimal decisions.
Individual prediction tendencies facilitate cortical speech tracking
Authors: Schubert Juliane , Schmidt Fabian , Gehmacher Quirin , Bresgen Annika , Weisz Nathan
Published: May 2022

Listening can be conceptualized as a process of active inference, in which the brain forms internal models to predict and integrate auditory information in a complex interaction of bottom-up and top-down processes. Whether inter-individual “prediction tendencies” shape listening experiences of real-world stimuli such as speech is, however, unknown. In the current study, we used a passive paradigm presenting tone sequences of varying entropy level, to independently quantify auditory prediction tendency (as the tendency to anticipate low-level acoustic features according to their contextual probability) for each individual. This measure was then used to predict the magnitude of cortical speech (envelope) tracking in a multi speaker listening task, where participants listened to audiobooks narrated by a target speaker in isolation or interfered by 1 or 2 distractors. Furthermore, rare semantic violations were introduced into the story, enabling us to also examine effects of word surprisal during continuous speech processing. Our results show that individual prediction tendency facilitates cortical speech tracking. Furthermore, we find interactions between individual prediction tendency and background noise as well as word surprisal in disparate brain regions. In sum, our findings suggest that individual prediction tendencies are generalizable across different listening situations and may serve as a valuable element to explain interindividual differences in natural listening experience.
Identification of Transient Intermediates During Spliceosome Activation by Single Molecule Fluorescence Microscopy
Authors: Fu Xingyang , Kaur Harpreet , Rodgers Margaret L. , Montemayor Eric J. , Butcher Samuel E. , Hoskins Aaron A.
Published: May 2022

Spliceosome activation is the process of creating the catalytic site for RNA splicing and occurs de novo on each intron following spliceosome assembly. Dozens of factors bind to or are released from the activating spliceosome including the Lsm2-8 heteroheptameric ring that binds the U6 small nuclear RNA (snRNA) 3’-end. Lsm2-8 must be released to permit active site stabilization by the Prp19-containing complex (NineTeen Complex, NTC); however, little is known about the temporal order of events and dynamic interactions that lead up to and follow Lsm2-8 release. We have used colocalization single molecule spectroscopy (CoSMoS) to visualize Lsm2-8 dynamics during activation of yeast spliceosomes. Lsm2-8 is recruited as a component of the tri-snRNP and is released after integration of the Prp19-containing complex (NineTeen Complex, NTC). Despite Lsm2-8 and the NTC being mutually exclusive in existing cryo-EM structures of yeast B complex spliceosomes, we identify a transient intermediate containing both and provide a kinetic framework for its formation and transformation during activation. Prior to assembly, the NTC rapidly and reversibly samples the spliceosome suggesting a mechanism for preventing NTC sequestration by defective spliceosomes that fail to properly activate. In complementary ensemble assays, we show that a base-pairing dependent ternary complex can form between Lsm2-8 and U2 and U6 helix II RNAs. Together our data suggest a Hfq-like function for Lsm2-8 in maintaining U2/U6 helix II integrity before it can be transferred to the NTC by transient formation of the spliceosome.

Significance Statement

The spliceosome active site is created de novo during activation and involves numerous conformational and compositional changes. Here, we define a kinetic pathway for yeast spliceosome activation using single molecule fluorescence that includes transient intermediates not previously identified. Real-time measurements allow us to uncover rapid, reversible sampling interactions of the NineTeen Complex (NTC) that may prevent its accumulation on defective spliceosomes. By analogy with bacterial Hfq, we propose that the homologous Lsm2-8 proteins stabilize U2/U6 helix II during activation before the helix is transferred to the NTC in a short-lived spliceosome containing both Lsm2-8 and the NTC. Our data demonstrate how single molecule studies of activation can reveal kinetically-competent intermediates and complement cryo-EM studies of stalled or inhibited complexes.
Toward Interpretable Digital Biomarkers of Walking and Reaching in Parkinson’s Disease
Authors: Ryu Jihye , Torres Elizabeth
Published: May 2022

Multimodal digital data registered with wearable biosensors has emerged as highly complementary of clinical pencil-and-paper criteria, offering new insights in ways to detect and diagnose various aspects of Parkinson’s disease. A pressing question is how to combine both the clinical knowledge of PD and the new technology to create interpretable digital biomarkers easily obtainable with off-the-shelf technology. Several challenges concerning disparity in biophysical units, anatomical differences across participants, sensor positioning, and sampling resolution are addressed in this work, along with identification of optimal parameters to automatically differentiate patients with PD from controls. We combine data from a multitude of biosensors registering signals from the central (EEG) and peripheral (magnetometry, kinematics) nervous systems, inclusive of the autonomic nervous system (EKG), as the participants perform natural tasks requiring different levels of intentional planning and automatic control. We find that magnetometer data during walking, across a variety of amplitude and timing signals provide optimal separation of PD from neurotypical controls. We conclude that considering multimodal signals, while differentiating across levels of intent in natural actions can be revealing of important features of PD that otherwise escape the naked eye. Further we add that clinical criteria combined with such optimal digital parameter spaces offer a far more complete picture of PD than using either one of these pieces of data alone.
Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
Authors: Tonkin-Hill Gerry , Gladstone Rebecca A , Pöntinen Anna K , Arredondo-Alonso Sergio , Bentley Stephen D , Corander Jukka
Published: May 2022

Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on Generalised Linear Regression that is robust to population structure, sampling bias and errors in the predicted presence/absence of genes. We demonstrate using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analysing several diverse bacterial genome datasets representing major human pathogens. Panstripe is freely available as an R package athttps://github.com/gtonkinhill/panstripe.
Comparison of dry and wet electrodes for detecting gastrointestinal activity patterns from body surface electrical recordings
Authors: Erickson Jonathan C. , Hassid Emily , Stepanyan Elen
Published: May 2022

Objective

Gastrointestinal motility patterns can be mapped via electrical signals measured non-invasively on the body surface. However, long-term monitoring (≥ 24 hr) may be hindered by skin-irritation inherent with traditional Ag/AgCl pre-gelled (“wet”) electrodes. Therefore, the aim of this work was to investigate the practical utility of using dry electrodes for GI body-surface electrical measurements.

Approach

To directly compare dry versus wet electrodes, we simultaneously recorded electrical signals from both types arranged in a 9 electrode (3 × 3) array during an ≈ 2.5 hr colonic meal-response study. Wavelet-based analyses were used to identify the signature post-meal colonic cyclic motor patterns. Signal quality was assessed for each electrode type through quantitative comparison of the dominant frequency, amplitude, signal-to-noise ratio (SNR), and signal energy vs time in the colonic frequency band. Blinded comparison of signal quality was carried out by four expert manual reviewers in order to assess the practical utility of each electrode type for identifying GI activity patterns.

Main results

Dry electrodes recorded high-quality GI signals comparable to that of wet electrodes, with dominant frequency in the range 2.85 - 3.25 cpm; peak-peak amplitudes of 120 ± 40µV, and SNR in the range 7.5 - 11 dB. The CWT colonic frequency band energy versus time correlation coefficient value was ≥ 0.71 for the majority of studies (6 out of 7) indicating very good agreement between dry and wet electrode signals overall. Whereas wet electrodes were rated by expert reviewers as having slightly better signal quality for identifying GI activity patterns, dry electrodes caused no skin irritation and were thus better-tolerated by all subjects.

Significance

Dry electrodes are a viable option for long-term GI monitoring studies, offering a potentially more comfortable alternative to conventional wet electrode systems.
Genome-wide translocation events drive the evolution ofCandida africana
Authors: Nnadi Nnaemeka Emmanuel , Giosa Domenico , Izam Yocy , Ubani Amaka , Ngene Anayochukwu , Ayanbimpe Grace Mebi , Enweani-Nwokelo Ifeoma Bessie , Aguiyi John Chinyere
Published: May 2022

Candida africanais emerging as an organism of interest. It is evolutionarily divergent fromCandida albicansbut has reduced virulence with a restricted ecological niche. This study aimed at comparing in silico the genome level to detect variations in the two species. Raw Illumina Hiseq data were downloaded from the European Nucleotide Archive (https://www.ebi.ac.uk/ena) with the accession numberSRR6669859and assembled using shovill (v. 1.0.9) the resulting genome was mapped against the haploid referenceCandida albicansSC5314_A22 strain using the D-GENIES webtool and contigs were reordered based on the reference, then gap-filled using GapFiller (v1-10), and annotated using MAKER-P. Synima and progressive Mauve were used to compare the annotated genomes ofCandida africanaandCandida albicansfor synteny. OrthoVenn2 webserver was used for the identification and comparison of orthologous clusters. Microsynteny variations within the genomes were determined using the GEvo. The study revealed the presence of insertions, deletions, and hypervariable regions within the genome ofCandidia africana, showing a high level of synteny withCandida albicans. The genome ofCandida africanais 14.04Mbp with a BUSCO score of 99.66%. The two species form a total of 5146 orthologous protein clusters and shared a total of 5124 protein,C. africanahas a unique cluster protein cluster whileC. albicanshave 18 unique Protein clusters. The genome ofC. africanahas lots of structural variations and the presence of gene losses and gains. These genetic variations possibly play a role in the reduced virulence potential observed inC. africana.
Similarities and differences in molecular epidemiology of third-generation cephalosporin-resistant Escherichia coli carried by dogs living in urban and nearby rural settings and associated behavioural risk factors
Authors: Sealey Jordan E. , Hammond Ashley , Mounsey Oliver , Gould Virginia C. , Reyher Kristen K. , Avison Matthew B.
Published: May 2022

Synopsis

Objectives

Our aims were to compare faecal third-generation cephalosporin-resistant (3GC-R) Escherichia coli isolates from dogs living in a city and in a rural area ~30 km away; to compare isolates from dogs, cattle, and humans in these regions; to determine risk factors associated with 3GC-R E. coli carriage in these two cohorts of dogs.

Methods

600 dogs were included, with faecal samples processed to recover 3GC-R E. coli using 2 mg/L cefotaxime. WGS was by Illumina; risk factor analyses were multivariable linear regression using the results of an owner-completed survey.

Results

3GC-R E. coli were excreted by 20/303 rural and 31/297 urban dogs. Dog/human sharing was evident for the dominant canine 3GC-R sequence type, ST963(blaCMY-2). Cattle/dog sharing was evident for CTX-M-14 and CTX-M-32-producing E. coli from rural dogs, including sharing of plasmid pMOO-32, which is common on cattle farms in the area. Feeding raw meat was associated with carrying 3GC-R E. coli in rural dogs, but not in urban dogs, where swimming in rivers was a weak risk factor.

Conclusions

Given clear zoonotic potential for resistant canine E. coli, our work suggests interventions that may reduce this threat. In rural dogs, carriage of 3GC-R E. coli, particularly CTX-M producers, was phylogenetically associated with interaction with local cattle and epidemiologically associated with feeding raw meat. In urban dogs, sources of 3GC-R E. coli appear to be more varied and include environments such as rivers.
Functional antibodies exhibit light chain coherence
Authors: Jaffe David B. , Shahi Payam , Adams Bruce A. , Chrisman Ashley M. , Finnegan Peter M. , Raman Nandhini , Royall Ariel E. , Tsai FuNien , Vollbrecht Thomas , Reyes Daniel S. , McDonnell Wyatt J.
Published: May 2022

The vertebrate adaptive immune system modifies the genome of individual B cells to encode antibodies binding particular antigens1. In most mammals, antibodies are composed of a heavy and a light chain which are sequentially generated by recombination of V, D (for heavy chains), J, and C gene segments. Each chain contains three complementarity-determining regions (CDR1-3), contributing to antigen specificity. Certain heavy and light chains are preferred for particular antigens2–21. We considered pairs of B cells sharing the same heavy chain V gene and CDRH3 amino acid sequence and isolated from different donors, also known as public clonotypes22,23. We show that for naive antibodies (not yet adapted to antigens), the probability that they use the same light chain V gene is ∼10%, whereas for memory (functional) antibodies it is ∼80%. This property of functional antibodies is a phenomenon we call light chain coherence. We also observe it when similar heavy chains recur within a donor. Thus, though naive antibodies appear to recur by chance, the recurrence of functional antibodies reveals surprising constraint and determinism in the processes of V(D)J recombination and immune selection. For most functional antibodies, the heavy chain determines the light chain.
Altered basal ganglia output during self-restraint
Authors: Gu Bon-Mi , Berke Joshua D
Published: May 2022

Suppressing actions is essential for flexible behavior. Multiple neural circuits involved in behavioral inhibition converge upon a key basal ganglia output nucleus, the substantia nigra pars reticulata (SNr). To examine how changes in basal ganglia output contribute to self-restraint, we recorded SNr neurons during a proactive behavioral inhibition task. Rats responded to Go! cues with rapid leftward or rightward movements, but also prepared to cancel one of these movement directions on trials when a Stop! cue might occur. This action restraint – visible as direction-selective slowing of reaction times – altered both rates and patterns of SNr spiking. Overall firing rate was elevated before the Go! cue, and this effect was driven by a subpopulation of direction-selective SNr neurons. In neural state space, this corresponded to a shift away from the restrained movement. SNr neurons also showed more variable inter-spike-intervals during proactive inhibition. This corresponded to more variable state-space trajectories, which may slow reaction times via reduced preparation to move. These findings open new perspectives on how basal ganglia dynamics contribute to movement preparation and cognitive control.
Identifying Proteasome 26S Subunit, ATPase (PSMC) Family Genes as the Prognostic Indicators and Therapeutic Targets in Lung Adenocarcinoma
Authors: Ullah Md. Asad , Islam Nafisa Nawal , Moin Abu Tayab , Park Su Hyun , Kim Bonglee
Published: May 2022

This study explored the prognostic and therapeutic potentials of multiple Proteasome 26S Subunit, ATPase (PSMC) family of genes (PSMC1-5) in lung adenocarcinoma (LUAD) diagnosis and treatment. All the PSMCs were found to be differentially expressed (upregulated) at the mRNA and protein levels in LUAD tissues. The promoter and multiple coding regions of PSMCs were reported to be differentially and distinctly methylated, which may serve in the methylation-sensitive diagnosis of LUAD patients. Multiple somatic mutations (alteration frequency: 0.6-2%) were observed along the PSMCs coding regions in LUAD tissues that could assist in the high-throughput screening of LUAD patients. A significant association between PSMCs overexpression and LUAD patients’ poor overall and relapse-free survival (p<0.05, HR:>1.3) and individual cancer stages (p<0.001) was discovered, which justifies PSMCs as the ideal targets for LUAD diagnosis. Multiple immune cells and modulators (i.e., CD274, IDO1) were found to be associated with PSMCs expression in LUAD tissues that could aid in formulating PSMC-based diagnostic measures and therapeutic interventions for LUAD. Functional enrichment analysis of neighbor genes of PSMCs in LUAD tissues revealed different genes (i.e., SLIRP, PSMA2, NUDSF3) previously known to be involved in oncogenic processes and metastasis co-expressed with PSMCs, which could also be investigated further. Overall, this study recommends that PSMCs and their transcriptional and translational products are potential candidates for LUAD diagnostic and therapeutic measure discovery. However, further laboratory research is needed to validate the findings of this experiment.
Three-Dimensional Mitochondria Reconstructions of Murine Cardiac Muscle Changes in Size Across Aging
Authors: Vue Zer , Neikirk Kit , Vang Larry , Garza-Lopez Edgar , Christensen Trace A. , Shao Jianqiang , Lam Jacob , Beasley Heather K. , Marshall Andrea G. , Crabtree Amber , Josephs B , Rodriguez Benjamin , Kirk Benjamin , Bacevac Serif , Barongan Taylor , Shao Bryanna , Stephens Dominique C. , Kabugi Kinuthia , Koh Ho-Jin , Koh Alice , Evans Chantell S. , Taylor Brittany , Reddy Anilkumar K. , Miller-Flemming Tyne , Actkins Ky’Era V. , Zaganjor Elma , Daneshgar Nastaran , Murray Sandra A. , Mobley Bret C. , Damo Steven , Gaddy Jennifer A. , Riggs Blake , Wanjalla Celestine , Kirabo Annet , McReynolds Melanie , Gomez Jose A. , Phillips Mark A. , Exil Vernat , Dai Dao-Fu , Hinton Antentor
Published: May 2022

ABSTRACT

With sparse treatment options, cardiac disease remains a significant cause of death among humans. As a person ages, mitochondria break down and the heart becomes less efficient. Heart failure is linked to many mitochondria-associated processes, including endoplasmic reticulum stress, mitochondrial bioenergetics, insulin signaling, autophagy, and oxidative stress. The roles of key mitochondrial complexes that dictate the ultrastructure, such as the mitochondrial contact site and cristae organizing system (MICOS), in aging cardiac muscle are poorly understood. To better understand the cause of age-related alteration in mitochondrial structure in cardiac muscle, we used transmission electron microscopy (TEM) and serial block facing-scanning electron microscopy (SBF-SEM) to quantitatively analyze the 3D networks in cardiac muscle samples of male mice at aging intervals of 3 months, 1 year, and 2 years. Here, we present the loss of cristae morphology, the inner folds of the mitochondria, across age. In conjunction with this, the 3D volume of mitochondria decreased. These findings mimicked observed phenotypes in murine cardiac fibroblasts with CRISPR/Cas9 knockout ofMitofilin, Chchd3, Chchd6(some members of the MICOS complex), andOpa1, which showed poorer oxidative consumption rate and mitochondria with decreased mitochondrial length and volume. In combination, these data show the need to explore if loss of the MICOS complex in the heart may be involved in age-associated mitochondrial and cristae structural changes.
Intrauterine inflammation leads to some sex and age-specific behavior and molecular differences in mice
Authors: Cristancho Ana G. , Tulina Natalia , Anton Lauren , Barila Guillermo , Elovitz Michal A.
Published: May 2022

Background

Prenatal inflammation is associated with long-term adverse neurobehavioral outcomes in exposed children. Sex-specific differences in behavior have been observed in anxiety and learning; however, whether these differences manifest differently by age is unknown. This study assesses possible behavioral changes from in utero inflammation as a function of age in neonatal, juvenile, and adult animals. We also tested if the observed behavioral differences correlated to neonatal sex-specific neurogenesis gene expression changes in the hippocampus to suggest a mechanism for observed behavioral differences.

Methods

CD-1 timed pregnant dams were injected in utero with lipopolysaccharide (LPS, 50μg/animal) or saline at embryonic day 15 (E15). Neonatal behavioral testing was performed on postnatal day (P) 5 on male and female pups born at term using the Ultrasonic Vocalization test (USV). Juvenile and mature animals of each sex were tested in Open Field (OF) and Barnes Maze (BM) on P28 and P67 (OF), and 32-36 and 70-75 (BM). A commercially available array designed to assess the expression of genes involved in mammalian neurogenesis was utilized for profiling gene expression in the hippocampal tissue isolated from LPS and saline-exposed P7 pups.

Results

There were no differences in stress responses measured by neonatal USV between LPS- and saline-exposed groups of either sex. In contrast, exposure to prenatal inflammation caused a male-specific increase in anxiety in mature but not juvenile animals. Juvenile LPS-exposed females had decreased movement in OF that was not present in adult animals. In addition, we observed improved memory retrieval in response to in utero LPS in the juvenile animals of both sexes. However, there was an impairment of long-term memory in adult LPS-exposed females. Finally, gene expression analyses revealed that LPS induced sex-specific changes in genes involved in hippocampal neurogenesis.

Conclusions

Intrauterine exposure to inflammation has age and sex-specific effects on anxiety and learning. These differences are not apparent in the neonatal period but begin to be evident in juvenile animals and evolve in adult animals. These sex-specific differences in learning may be correlated to sex-specific disruption of the expression of genes associated with neurogenesis in the hippocampus.
Detection of local growth patterns in longitudinally imaged low-grade gliomas
Authors: Gui Chloe , Kai Jason , Khan Ali R. , Lau Jonathan C. , Megyesi Joseph F.
Published: May 2022

Background

Diffuse low-grade gliomas (LGGs) are primary brain tumors with infiltrative, anisotropic growth related to surrounding white and grey matter structures. In this study, we illustrate the use of deformation-based morphometry (DBM) as a simple and objective method to study the local change in growth patterns of LGGs.

Methods

An imaging pipeline was developed involving the creation of patient-specific average templates and nonlinear registration of pre-treatment follow-up MRIs to the average template. Jacobian maps were derived and analyzed to identify areas of tissue expansion and contraction over time.

Results

Our analysis demonstrates that tissue expansion occurs primarily around the edges of the tumor, while the lesion core and areas adjacent to obstacles, such as the skull, show no significant growth. Tumors also appeared to grow faster and predominantly in areas of white matter. Regions of the brain surrounding the lesion showed slight contraction over time, likely representing compression due to mass effect of the tumor.

Conclusions

We demonstrate that DBM is a useful clinical tool to understand the long-term clinical course of an individual’s tumor and identify areas of rapid growth, which can explain the clinical signs and symptoms, predict future symptoms, and guide targeted diagnostics and therapy.

Highlights

Low-grade glioma expansion occurs primarily around the edges of the tumor.

Tumor cores and tissue next to obstacles show no significant growth over time.

DBM provides a clinically valuable assessment of local tumor growth and activity.
The association between working memory precision and the nonlinear dynamics of frontal and parieto-occipital EEG activity
Authors: Chang Wen-Sheng , Liang Wei-Kuang , Li Dong-Han , Muggleton Neil G. , Balachandran Prasad , Huang Norden E. , Juan Chi-Hung
Published: May 2022

Electrophysiological working memory (WM) research has shown that distinct brain areas communicate through macroscopic oscillatory activities across multiple frequency bands. Such cross-frequency interactions generate nonlinear amplitude modulations (AM) in the observed signal. Traditionally, the AM of a signal is expressed as coupling strength between the signal and a pre-specified modulator at a lower frequency. Therefore, the idea of AM and coupling cannot be separately studied. This EEG study shows that the AM of parieto-occipital alpha/beta power and the coupling between frontal theta phase and parieto-occipital alpha/beta AM provide different information on WM processing. Thirty-three participants completed a color recall task with simultaneous EEG recording. The results showed that individual differences in WM precision are associated with frontal theta power enhancement and parieto-occipital alpha/beta power suppression. Furthermore, the AM of parieto-occipital alpha/beta power predicted WM precision after presenting a target-defining probe array. The phase-amplitude coupling (PAC) between frontal theta phase and parieto-occipital alpha/beta AM increased with WM load during the processing of incoming stimuli, but they did not predict the subsequent recall performance. These results indicate that the frontoparietal PAC reflects the executive control for selecting relevant WM representations, but whether the memorized information can be retrieved depends on the subsequent amplitude variation of parieto-occipital alpha/beta power. In conclusion, individuals with higher working memory precision are associated with enhanced frontal theta power and parieto-occipital alpha/beta power suppression.
Growth and adaptation mechanisms of tumour spheroids with time-dependent oxygen availability
Authors: Murphy Ryan J. , Gunasingh Gency , Haass Nikolas K. , Simpson Matthew J.
Published: May 2022

Tumours are subject to external environmental variability. However,in vitrotumour spheroid experiments, used to understand cancer progression and develop cancer therapies, have been routinely performed for the past fifty years in constant external environments. Furthermore, spheroids are typically grown in ambient atmospheric oxygen (normoxia), whereas mostin vivotumours exist in hypoxic environments. Therefore, there are clear discrepancies betweenin vitroandin vivoconditions. We explore these discrepancies by combining tools from experimental biology, mathematical modelling, and statistical uncertainty quantification. Focusing on oxygen variability to develop our framework, we reveal key biological mechanisms governing tumour spheroid growth. Growing spheroids in time-dependent conditions, we identify and quantify novel biological adaptation mechanisms, including unexpected necrotic core removal, and transient reversal of the tumour spheroid growth phases.
Functional Comparison Between Endogenous and Synthetic Notch Systems
Authors: Khamaisi Bassma , Luca Vincent C. , Blacklow Stephen C. , Sprinzak David
Published: May 2022

The Notch pathway converts receptor-ligand interactions at the cell surface into a transcriptional response in the receiver cell. In recent years, synthetic Notch systems (SynNotch) that respond to different inputs and transduce different transcriptional responses have been engineered. One class of synNotch systems uses antibody-antigen interactions at the cell surface to induce the proteolytic cleavage cascade of the endogenous Notch autoregulatory core and the consequent release of a synNotch intracellular domain (ICD), converting surface antigen detection into a cellular response. However, whereas the activation of endogenous Notch requires ubiquitylation and subsequent endocytosis of the ligand ICD, these synNotch systems do not seem to have such a requirement because the synNotch ligands completely lack an ICD. This observation raises questions about existing models for the Notch activation mechanism. Here, we test how different structural and biochemical factors affect the dependence of endogenous and synthetic Notch activation on ligand ICD. We compare the behavior of antibody-antigen synNotch (aa-synNotch) to that of endogenous Notch, and to a synNotch system that uses induced FKBP-FRB dimerization with rapamycin (ff-synNotch), which still requires a ligand ICD. We found that differences in receptor-ligand affinity, in the identity of the transmembrane domain, or in the presence or absence of extracellular EGF repeats cannot explain the differences in ligand ICD requirement that distinguishes aa-synNotch from endogenous Notch or ff-synNotch. These findings suggest that the aa-SynNotch systems bypass the ligand ICD requirement because antigen-antibody pairs are able to promote other adhesive cell-cell interactions that provide the mechanical tension needed for ligand activation.
GNL3 is an evolutionarily-conserved stem cell gene influencing cell proliferation, animal growth, and regeneration in the hydrozoan Hydractinia
Authors: Quiroga-Artigas Gonzalo , de Jong Danielle , Schnitzler Christine E.
Published: May 2022

Nucleostemin (NS) is a vertebrate gene preferentially expressed in stem and cancer cells, which acts to regulate cell cycle progression, genome stability, and ribosome biogenesis. NS and its paralogous gene, GNL3-like (GNL3L), arose in the vertebrate clade after a duplication event from their orthologous gene, G protein Nucleolar 3 (GNL3). Research on invertebrate GNL3, however, has been limited. To gain a greater understanding of the evolution and functions of the GNL3 gene, we have performed studies in the hydrozoan cnidarian Hydractinia symbiolongicarpus, a colonial hydroid that continuously generates pluripotent stem cells throughout its life cycle and presents impressive regenerative abilities. We show that Hydractinia GNL3 is expressed in stem and germline cells. The knockdown of GNL3 reduces the number of mitotic and S-phase cells in Hydractinia larvae of different ages. Genome editing of Hydractinia GNL3 via CRISPR/Cas9 resulted in colonies with reduced growth rates, polyps with impaired regeneration capabilities, gonadal morphological defects, and low sperm motility. Collectively, our study shows that GNL3 is an evolutionarily-conserved stem cell and germline marker involved in cell proliferation, animal growth, regeneration, and sexual reproduction in Hydractinia, and sheds new light into the evolution of GNL3 and of stem cell systems.
Decoding reward–curiosity conflict in decision-making from irrational behaviors
Authors: Konaka Yuki , Naoki Honda
Published: May 2022

Humans and animals are not always rational. They not only rationally exploit rewards but also explore an environment, even if reward is less expected, owing to their curiosity. However, the mechanism of such curiosity-driven irrational behavior is largely unknown. Here, we developed a novel decision-making model for a two-choice task based on the free energy principle, which is a theory integrating recognition and action selection. The model successfully described irrational behaviors depending on the curiosity level. We then proposed a machine learning method to decode temporal curiosity from behavioral data, which enables us to quantitatively compare estimated curiosity and neural activities. By applying it to rat behavioral data, we found that the irrational choices sticking to one option was reflected to the negative curiosity level. Our decoding approach can be a fundamental tool for identifying the neural basis for reward-curiosity conflicts. Specifically, it could be effective in diagnosing mental disorders.
Homogeneous inhibition is optimal for the phase precession of place cells in the CA1 field
Authors: Vandyshev G.K. , Mysin I.E.
Published: May 2022

Place cells are hippocampal neurons encoding the position of an animal in space. Studies of place cells are essential to understanding the processing and transmission of information by neural networks of the brain. An important characteristic of place cell spike trains is phase precession. When an animal is running through the place field, the discharges of the place cells shift from the ascending phase of the theta rhythm through the minimum to the descending phase. The role of excitatory inputs to CA1 pyramidal neurons along the Schaffer collaterals and the perforant pathway in phase precession is described, but the role of inputs from local interneurons to CA1 pyramidal cell is poorly understood. We have set the goal the contribution of field CA1 interneurons to the phase precession of place cells using mathematical methods. The CA1 field was chosen because it provides the largest set of experimental data required to build and verify the model. We have solved the optimization problem and found the parameters of the excitatory and inhibitory inputs to the pyramidal neuron of the CA1 field so that the neuron generates a spike train with the effect of phase precession. We have discovered that the uniform inhibition of field CA1 pyramidal neurons best explains the effect of phase precession. Among interneurons, axo-axonal neurons make the greatest contribution to the inhibition of pyramidal cells.
Portable low-cost macroscopic mapping system for all-optical cardiac electrophysiology
Authors: Heinson Yuli W. , Han Julie L. , Entcheva Emilia
Published: May 2022

Significance

All-optical cardiac electrophysiology enables the visualization and control of key parameters relevant to the detection of cardiac arrhythmias. Mapping such responses in human induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs) is of great interest for cardiotoxicity and personalized medicine applications.

Aim

We introduce and validate a very low-cost compact mapping system for macroscopic all-optical electrophysiology in layers of hiPSC-CMs.

Approach

The system uses oblique trans-illumination, low-cost cameras, light-emitting diodes and off-the-shelf components (total < $15,000) to capture voltage, calcium and mechanical waves under electrical or optical stimulation.

Results

Our results corroborate the equivalency of electrical and optogenetic stimulation of hiPSC-CMs, and Vm – [Ca2+]i similarity in conduction under pacing. Green-excitable optical sensors are combinable with blue optogenetic actuators (Chanelrhodopsin2) only under very low green light (< 0.05mW/mm2). Measurements in warmer culture medium yield larger spread of action potential duration and higher conduction velocities compared to Tyrode’s solution at room temperature.

Conclusions

As multiple optical sensors and actuators are combined, our results can help handle the “spectral congestion” and avoid parameter distortion. We illustrate the utility of the system for uncovering the action of cellular uncoupling agents and show extensibility to an epi-illumination mode for future imaging of thicker native or engineered tissues.
Inhibition of mutant RAS-RAF interaction by mimicking structural and dynamic properties of phosphorylated RAS
Authors: Ilter Metehan , Kaşmer Ramazan , Jalalypour Farzaneh , Atilgan Canan , Topcu Ozan , Karakaş Nihal , Sensoy Ozge
Published: May 2022

Undruggability of RAS proteins has necessitated alternative strategies for the development of effective inhibitors. In this respect, phosphorylation has recently come into prominence as this reversible post-translational modification attenuates sensitivity of RAS towards RAF. As such, in this study, we set out to unveil the impact of phosphorylation on dynamics of HRASWT and aim to invoke similar behavior in HRASG12D mutant by means of small therapeutic molecules. To this end, we performed molecular dynamics (MD) simulations using phosphorylated HRAS and showed that phosphorylation of Y32 distorted Switch I, hence the RAS/RAF interface. Consequently, we targeted Switch I in HRASG12D by means of approved therapeutic molecules and showed that the ligands enabled detachment of Switch I from the nucleotide-binding pocket. Moreover, we demonstrated that displacement of Switch I from the nucleotide-binding pocket was energetically more favorable in the presence of the ligand. Importantly, we verified computational findings in vitro where HRASG12D/RAF interaction was prevented by the ligand in HEK293T cells that expressed HRASG12D mutant protein. Therefore, these findings suggest that targeting Switch I, hence making Y32 accessible might open up new avenues in future drug discovery strategies that target mutant RAS proteins.
FBXW7β isoform drives transcriptional activation of a proinflammatory TNF cluster in normal and malignant pro-B cells
Authors: Yang Scarlett Y. , Hayer Katharina E. , Fazelinia Hossein , Spruce Lynn A. , Asnani Mukta , Black Kathryn L. , Naqvi Ammar S. , Pillai Vinodh , Barash Yoseph , Elenitoba-Johnson Kojo S. J. , Thomas-Tikhonenko Andrei
Published: May 2022

Non-canonical exon usage plays many important roles in cellular phenotypes, but its contribution to human B-cell development remains sketchily understood. To fill this gap, we collected various B-cell fractions from bone marrow and tonsil donors, performed RNA-seq, and examined transcript variants. We identified 150 genes that harbor local splicing variations in all pairwise comparisons. One of them encodes FBXW7, an E3 ubiquitin ligase implicated as a cancer driver in several blood cancers. Surprisingly, we discovered that in normal human pro-B cells, the predominant transcript utilized an alternative first exon to produce the poorly characterized FBXW7β isoform, previously thought to be restricted to neural tissues. The FBXW7β transcript was also abundant in cell lines and primary samples of pediatric B-cell acute lymphoblastic leukemia (B-ALL), which originates in the bone marrow. When overexpressed in a heterologous cell system, this transcript yielded the expected protein product, as judged by anti-FLAG immunoblotting and mass spectrometry. Furthermore, in REH B-ALL cells, FBXW7β mRNA was the only FBXW7 isoform enriched in the polyribosome fraction. To shed light on possible functions of FBXW7β, we utilized gain- and loss-of-function approaches and identified an FBXW7β-dependent inflammatory gene signature, apparent in a subset of B-ALL with high FBXW7β expression. This signature contained several members of the TNF superfamily, including those comprising the HLA Class III cluster (LTB, LST1, NCR3, LTA, and NFKBIL1). Our findings suggest that FBXW7β expression drives proinflammatory responses, which could contribute to normal B-cell development, leukemogenesis and responses to anti-cancer therapies.

Key points

Previously thought to be restricted to neural tissues, FBXW7β is the predominant FBXW7 isoform in normal and malignant human pro-B cells.

FBXW7β promotes transcriptional activation of a proinflammatory gene cluster that contains TNF superfamily members.
The language network reliably ‘tracks’ naturalistic meaningful non-verbal stimuli
Authors: Sueoka Yotaro , Paunov Alexander , Ivanova Anna , Tanner Alyx , Blank Idan A. , Fedorenko Evelina
Published: May 2022

The language network, comprised of brain regions in the left frontal and temporal cortex, responds robustly and reliably during language comprehension but shows little or no response during many non-linguistic cognitive tasks (e.g., Fedorenko & Blank, 2020). However, one domain whose relationship with language remains debated is semantics—our conceptual knowledge of the world. Given that the language network responds strongly to meaningful linguistic stimuli, could some of this response be driven by the presence of rich conceptual representations encoded in linguistic inputs? In this study, we used a naturalistic cognition paradigm to test whether the cognitive and neural resources that are responsible for language processing are also recruited for processing semantically rich non-verbal stimuli. To do so, we measured BOLD responses to a set of ∼5-minute-long video and audio clips that consisted of meaningful event sequences but did not contain any linguistic content. We then used the inter-subject correlation (ISC) approach (Hasson et al., 2004) to examine the extent to which the language network ‘tracks’ these stimuli, i.e. exhibits stimulus-related variation. Across all the regions of the language network, non-verbal meaningful stimuli elicited reliable ISCs. These ISCs were higher than the ISCs elicited by semantically impoverished non-verbal stimuli (e.g., a music clip), but substantially lower than the ISCs elicited by linguistic stimuli. Our results complement earlier findings from controlled experiments (e.g., Ivanova et al., 2021) in providing further evidence that the language network shows some sensitivity to semantic content in non-verbal stimuli.
Direct N-Me Aziridination Reaction Enables Pinpointing C=C Bonds in Lipids with Mass Spectrometry
Authors: Feng Guifang , Gao Ming , Fu Rongrong , Wan Qiongqiong , Wang Tianze , Zhang Zhourui , Chen Suming
Published: May 2022

The biological functions of lipids largely depend on their chemical structures. The position of C=C bonds is an essential attribute that determines the structures of unsaturated lipids. Here, we developed a new type of chemical derivatization method for C=C bond using aziridination reaction. This new cyclization method for the C=C bonds in lipids based on the direct N-Me aziridination reaction of olefins using N-methyl-O-tosylhydroxylamine (TsONHCH3) as the aminating reagent. When combined with the tandem MS analysis, this novel activation approach for C=C bonds enables the accurate identification their positions in different kinds of unsaturated lipids. Furthermore, an integrated workflow has been established for comprehensively identifying the C=C bond positional isomers of lipids in complicated biological sample. This work provided a new chemical approach for the structural lipidomics.
Small-amplitude head oscillations result from a multimodal head stabilization reflex in hawkmoths
Authors: Chatterjee Payel , Mohan Umesh , Sane Sanjay P.
Published: May 2022

In flying insects, head stabilization is an important reflex which helps to reduce motion blur during fast aerial maneuvers. This reflex is multimodal and requires the integration of visual and antennal mechanosensory feedback, each operating as a negative-feedback control loop. As in any negative-feedback system, the head stabilization system possesses inherent oscillatory dynamics that depends on the rates and latencies of the sensorimotor components constituting the reflex. Consistent with this expectation, we observed small amplitude oscillations in the head motion (or head wobble) of the Oleander hawkmoth Daphnis nerii. We show here that these oscillations emerge from the inherent dynamics of the multimodal reflex that underlies gaze stabilization, and the amplitude of the head wobble is a function of both the visual feedback and antennal mechanosensory feedback from the Johnston’s organs. The head wobble is thus an outcome of a multimodal, dynamically-stabilized head positioning reflex.
Mircubactin B rescues the lethal effect of cell wall biosynthesis mutations in Bacillus subtilis
Authors: Kepplinger Bernhard , Wen Xin , Tyler Andrew Robert , Kim Byung-Yong , Brown James , Banks Peter , Dashti Yousef , Mackenzie Eilidh Sohini , Wills Corinne , Kawai Yoshikazu , Waldron Kevin John , Allenby Ellis Nicholas Edward , Wu Ling Juan , Hall Michael John , Errington Jeff
Published: May 2022

Growth of most rod-shaped bacteria is accompanied by the insertion of new peptidoglycan into the cylindrical cell wall. This insertion, which helps maintain and determine the shape of the cell, is guided by a complex protein machinery called the rod complex or elongasome. Although most of the proteins in this complex are essential under normal growth conditions, cell viability can be rescued, for reasons that are not understood, by the presence of a high (mM) Mg2+ concentration. We screened for natural product compounds that could rescue the growth of mutants affected in rod-complex function. By screening >2,000 extracts from a diverse collection of actinobacteria, we identified a new compound, mirubactin B, related to the known iron siderophore mirubactin A, which rescued growth in the low micromolar range, and this activity was confirmed by synthesising mirubactin B. The compound also displayed toxicity at higher concentrations, and this effect appears related to iron homeostasis. However, several lines of evidence suggest that the mirubactin B rescuing activity is not due simply to iron sequestration. The results demonstrate a novel antibacterial compound and add to growing evidence that bacterial siderophores have a range of activities beyond simple iron sequestration.