bluuebunny/crossref_metadata_2025 huggingface dataset:
To make a short story long: simultaneous short and long RNA profiling on Nanopore devices
Authors: MacKenzie Morgan , Tigert Susan , Lovato Debbie , Mir Hamza , Zahedi Kamyar , Barone Sharon L. , Brooks Marybeth , Soleimani Manoocher , Argyropoulos Christos
Published: December 2022

Sequencing of long coding RNAs informs about the abundance and the novelty in the transcriptome, while sequencing of short coding RNAs (e.g., microRNAs) or long non-coding RNAs informs about the epigenetic regulation of the transcriptome. Currently, each of these goals is addressed by separate sequencing experiments given the different physical characteristics of RNA species from biological samples. Sequencing of both short and long RNAs from the same experimental run has not been reported for long-read Nanopore sequencing to date and only recently has been achieved for short-read (Illumina) methods. We propose a library preparation method capable of simultaneously profiling short and long RNA reads in the same library on the Nanopore platform and provide the relevant bioinformatics workflows to support the goals of RNA quantification. Using a variety of synthetic samples we demonstrate that the proposed method can simultaneously detect short and long RNAs in a manner that is linear over 5 orders of magnitude for RNA abundance and three orders of magnitude for RNA length. In biological samples the proposed method is capable of profiling a wider variety of short and long non-coding RNAs when compared against the existing Smart-seq protocols for Illumina and Nanopore sequencing.
Quantifying the Fitness Benefit of Learning in Changing Environments
Authors: Arehart Emerson , Adler Frederick R.
Published: December 2022

The costs and benefits of learning for a foraging organism are difficult to quantify, and depend sensitively on the environment. We construct a minimal mathematical model of learning in which a forager learns the quality of different food types through experience. In our model, learning depends on two parameters: rate of memory updating and rate of exploration. Our method returns optimal learning parameters for environments in which the value and variance of food types may change in any fashion. We analyze the effect of five components of environmental change on the optimal memory and exploration parameters. The fitness outcomes from learning foragers are compared to the outcomes from following fixed strategies, explicitly quantifying the fitness benefit (or cost) of learning as a function of environmental change. We find that variance in resource values negatively biases foragers’ estimates for those values, potentially explaining experimental results showing that animals prefer less variable resources. Learning is beneficial only if memory and exploration are optimized. The benefit of learning is largely determined by the ratio between the overall expected value of taking one resource compared to the overall expected value of taking the other: As these two expectations diverge, the fitness benefit of learning decreases, and can even become negative. In many environments, sub-optimal learning performs as bad or even worse than following a fixed strategy.

Significance

Learning is commonly observed in foraging organisms. However, measuring the fitness benefits (and costs) of learning is difficult, and depends critically on the environment in which an organism lives. We build a minimal model of learning in the context of optimal foraging and optimal diet choice theory, with two learning parameters:α, corresponding to the duration of the forager’s memory, andϵ, corresponding to how much the forager explores the environment to learn more about it. We identify the optimalα,ϵfor different types of environmental change, and quantify the benefits and costs of learning. The benefit of learning is often surprisingly small, and in many environments, learning provides lower fitness than following a fixed strategy.
LIQ HD (Lick Instance Quantifier Home cage Device): An open-source tool for recording undisturbed two-bottle drinking behavior in a home cage environment
Authors: Petersen Nicholas , Adank Danielle N. , Raghavan Ritika , Winder Danny G. , Doyle Marie A.
Published: December 2022

Investigation of rodent drinking behavior has provided insight into drivers of thirst, circadian rhythms, anhedonia, and drug and ethanol consumption. Traditional methods of recording fluid intake involve weighing bottles, which is cumbersome and lacks temporal resolution. Several open-source devices have been designed to improve drink monitoring, particularly for two-bottle choice tasks. However, recent designs are limited by the use of infrared photobeam sensors and incompatibility with prolonged undisturbed use in ventilated home cages. Beam-break sensors lack accuracy for bout microstructure analysis and are prone to damage from rodents. Thus, we designed LIQ HD (Lick Instance Quantifier Home cage Device) with the goal of utilizing capacitive sensors to increase accuracy and analyze lick microstructure, building a device compatible with ventilated home cages, increasing scale with prolonged undisturbed recordings, and creating a design that is easy to build and use with an intuitive touchscreen graphical user interface. The system tracks two-bottle choice licking behavior in up to 18 rodent cages, or 36 single bottles, on a minute-to-minute timescale controlled by a single Arduino microcontroller. The data are logged to a single SD card, allowing for efficient downstream analysis. With sucrose, quinine, and ethanol two-bottle choice tasks, we validated that LIQ HD has superior accuracy compared to photobeam sensors. The system measures preference over time and changes in bout microstructure, with undisturbed recordings lasting up to 7 days. All designs and software are open-source to allow other researchers to build upon the system and adapt LIQ HD to their animal home cages.

Significance Statement

Two-bottle choice drinking tasks are traditionally performed by periodically weighing bottles, which is cumbersome and lacks temporal resolution. Several open-source tools have been developed to improve drink monitoring in various settings. However, no open-source devices have been designed specifically to investigate temporally precise two-bottle choice drinking behavior and bout microstructure during prolonged undisturbed tasks in mouse ventilated home cages at a large scale. Our design, LIQ HD (Lick Instance Quantifier Home cage Device), is a home cage compatible system that utilizes capacitive sensors for highly accurate lick detection during two-bottle choice tasks in up to 18 cages driven by a single Arduino microcontroller. The system is low-cost, easy to build, and controlled via touchscreen with an intuitive graphical user interface.
Identification of a Non-Canonical Ciliate Nuclear Genetic Code Where UAA and UAG Code for Different Amino Acids
Authors: McGowan Jamie , Kilias Estelle S. , Alacid Elisabet , Lipscombe James , Jenkins Benjamin H. , Gharbi Karim , Kaithakottil Gemy G. , Macaulay Iain C. , McTaggart Seanna , Warring Sally D. , Richards Thomas A. , Hall Neil , Swarbreck David
Published: December 2022

The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the “universal” genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3’UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.
Population variation in lipid depletion during parental care in male threespine sticklebacks (Gasterosteus aculeatus)
Authors: Scott Robert
Published: December 2022

I examined changes in stored lipid over the parental care interval in several populations of threespine stickleback (Gasterosteus aculeatus). Males from the limnetic populations and the marine population decreased in stored lipids over the progression of the nesting interval. Of the two benthic populations, one (Hotel Lake) did not decrease stored lipids over the parental care interval, as predicted, whereas the other (Crystal Lake) showed declining stored lipids over the parental care interval. Though food resources are likely high in the nesting area of Crystal Lake, the high density of conspecific cannibal groups in the littoral zone likely contributes to reduced foraging and elevated guarding/diversionary display behaviour and dependency on stored lipids to fuel those behaviours in the Crystal Lake (benthic) population. This study demonstrates the value of considering different ecological conditions on behavioural and energetic constraints among populations of threespine stickleback.
Evolutionary conservation of the structure and function of meiotic Rec114−Mei4 and Mer2 complexes
Authors: Daccache Dima , De Jonge Emma , Liloku Pascaline , Mechleb Karen , Haddad Marita , Corthaut Sam , Sterckx Yann G.-J. , Volkov Alexander N. , Bouuaert Corentin Claeys
Published: December 2022

Meiosis-specific Rec114−Mei4 and Mer2 complexes are thought to enable Spo11-mediated DNA double-strand-break (DSB) formation through a mechanism that involves DNA-dependent condensation. However, the structure, molecular properties, and evolutionary conservation of Rec114−Mei4 and Mer2 are unclear. Here, we present AlphaFold structures of Rec114−Mei4 and Mer2 complexes, supported by nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), and mutagenesis. We show that dimers composed of the Rec114 C-terminus form α-helical chains that cup an N-terminal Mei4 α-helix, and that Mer2 forms a parallel homotetrameric coiled coil. Both Rec114−Mei4 and Mer2 bind preferentially to branched DNA substrates, indicative of multivalent protein-DNA interactions. Indeed, the Rec114−Mei4 interaction domain contains two DNA-binding sites that point in opposite directions and drive condensation. The Mer2 coiled-coil domain bridges co-aligned DNA duplexes, likely through extensive electrostatic interactions along the length of the coiled coil. Finally, we show that the structure of Rec114−Mei4 and Mer2 are conserved across eukaryotes, while DNA-binding properties vary significantly. This work provides insights into the mechanism whereby Rec114−Mei4 and Mer2 complexes promote the assembly of the meiotic DSB machinery, and suggests a model where Mer2 condensation is the essential driver of assembly, with the DNA-binding activity of Rec114−Mei4 playing a supportive role.
Enhanced assembly of bacteriophage T7 produced in cell-free reactions under simulated microgravity
Authors: Lehr François-Xavier , Pavletić Bruno , Glatter Timo , Heimerl Thomas , Moeller Ralf , Niederholtmeyer Henrike
Published: December 2022

On-demand biomanufacturing has the potential to improve healthcare and self-sufficiency during space missions. Cell-free transcription and translation reactions combined with DNA blueprints can produce promising therapeutics like bacteriophages and virus-like particles. However, how space conditions affect the synthesis and self-assembly of such complex multi-protein structures is unknown. Here, we characterize the cell-free production of infectious bacteriophage T7 virions under simulated microgravity. Rotation in a 2D-clinostat increased the number of infectious particles compared to static controls. Quantitative analyses by mass spectrometry, immuno-dot-blot and real-time PCR showed no significant differences in protein and DNA contents, suggesting enhanced self-assembly of T7 phages in simulated microgravity. While the effects of genuine space conditions on the cell-free synthesis and assembly of bacteriophages remain to be investigated, our findings support the vision of a cell-free synthesis-enabled “astropharmacy”.
A scalable and robust system for Audience EEG recordings
Authors: Michalareas Georgios , Rudwan Ismat M.A. , Lehr Claudia , Gessini Paolo , Tavano Alessandro , Grabenhorst Matthias
Published: December 2022

The neural mechanisms that unfold when humans form a large group defined by an overarching context, such as audiences in theater or sports, are largely unknown and unexplored. This is mainly due to the lack of availability of a scalable system that can record the brain activity from a significantly large portion of such an audience simultaneously. Although the technology for such a system has been readily available for a long time, the high cost as well as the large overhead in human resources and logistic planning have prohibited the development of such a system. However, during the recent years reduction in technology costs and size have led to the emergence of low-cost, consumer-oriented EEG systems, developed primarily for recreational use. Here by combining such a low-cost EEG system with other off-the-shelve hardware and tailor-made software, we develop in the lab and test in a cinema such a scalable EEG hyper-scanning system. The system has a robust and stable performance and achieves accurate unambiguous alignment of the recorded data of the different EEG headsets. These characteristics combined with small preparation time and low-cost make it an ideal candidate for recording large portions of audiences.

Highlights

A scalable EEG hyper-scanning system for recording audiences and large groups is presented with the following characteristics.

Off-the-shelve, low cost components, namely a MUSE EEG headset, a Raspberry Pi computer and Photodiode.

A Python library, available to the public, has been specifically developed from first principles, optimized for facilitating robust recording over Bluetooth even when multiple EEG headsets are in close proximity.

The use of photodiodes provides unambiguous data alignment between the different systems.

A proof-of-concept system with 10 EEG headsets has been tested in the lab but also in naturalistic conditions, recording members of the audience in four different long movie screenings in the cinema of the German Film Museum.
Ythdf2 regulates cardiac remodeling through its m6A-mRNA target transcripts
Authors: Kmietczyk V. , Oelschläger J. , Varma E. , Hartl S. , Konstandin M. , Marx A. , Gupta P. , Loewenthal Z. , Kamuf-Schenk V. , Jürgensen L. , Stroh C. , Gorska A. , Jakobi T. , Frey N. , Völkers M.
Published: December 2022

m6A mRNA methylation controls cardiomyocyte function and increased overall m6A levels are a stereotyping finding in heart failure independent of the underlying etiology. However, it is largely unknown how the information is read by m6A reader proteins in heart failure. Here we show that the m6A reader protein Ythdf2 controls cardiac function and identified a novel mechanism how reader proteins control gene expression and cardiac function. Deletion of Ythdf2 in cardiomyocytesin vivoleads to cardiac hypertrophy, reduced heart function, and increased fibrosis during pressure overload as well as during aging. Similarly,in vitrothe knockdown of Ythdf2 results in cardiomyocyte growth and remodeling. Mechanistically, we identified the eucaryotic elongation factor 2 as a major target of Ythdf2 using cell type specific Ribo-seq data. Our study expands our understanding on the regulatory functions of m6A methylation in cardiomyocytes and how cardiac function is controlled by the m6A reader protein Ythdf2.
High Throughput Detection of Capillary Stalling Events with Bessel Beam Two-Photon Microscopy
Authors: Giblin John , Kura Sreekanth , Nunuez Juan Luis Ugarte , Zhang Juncheng , Kureli Gulce , Jiang John , Boas David A. , Chen Ichun A.
Published: December 2022

Disruptions in capillary flow have the potential to drive pathology across numerous diseases. But our understanding of the temporal and spatial dynamics of these events are hindered by slow volumetric imaging rates and the reliance on laborious manual analysis to process data. To address the challenges of increasing volumetric imaging speed, we use a custom-built Bessel beam two-photon microscope for efficient volumetric imaging of the capillary network. We demonstrate its ability to continuously monitor roughly 200 capillaries for capillary flow stoppages (i.e. stalling events) at a frame rate of approximately 0.5 Hz and develop a semi-automated correlation-based approach for identifying these stalling events. We applied our system and algorithm in a photothrombotic model of stroke and show elevated levels of stalling 1-week post-stroke in regions both within and outside of the stroke region, demonstrating that stalling may have impacts on stroke recovery that extend past the acute stage.
Controlled delivery of ultrasound through the head for effective and safe therapies of the brain
Authors: Riis Tom , Wilson Matthew , Kubanek Jan
Published: December 2022

Transcranial focused ultrasound provides noninvasive and reversible approaches for precise and personalized manipulations of brain circuits, with the potential to transform our understanding of brain function and treatments of brain dysfunction. However, the effectiveness and safety of these approaches have been limited by the human head, which attenuates and distorts ultrasound strongly and unpredictably. To address this lingering barrier, we have developed a “Relative Through-Transmit” (RTT) approach that directly measures and compensates for the attenuation and distortion of a given skull and scalp. We have implemented RTT in hardware and demonstrated that it accurately restores the operator’s intended intensities inside ex-vivo human skulls. Moreover, this functionality enabled effective and intensity-dependent transcranial modulation of nerves and effective release of defined doses of propofol inside the skull. RTT was essential for these new applications of transcranial ultrasound; when not applied, there were no significant differences from sham conditions. Moreover, RTT was safely applied in humans and accounted for all intervening obstacles including hair and ultrasound coupling. This method and hardware unlock the potential of ultrasound-based approaches to provide effective, safe, and reproducible precision therapies of the brain.
Having “multiple selves” helps learning agents explore and adapt in complex changing worlds
Authors: Dulberg Zack , Dubey Rachit , Berwian Isabel M. , Cohen Jonathan
Published: December 2022

Satisfying a variety of conflicting needs in a changing environment is a fundamental challenge for any adaptive agent. Here, we show that designing an agent in a modular fashion as a collection of subagents, each dedicated to a separate need, powerfully enhanced the agent’s capacity to satisfy its overall needs. We used the formalism of deep reinforcement learning to investigate a biologically relevant multi-objective task: continually maintaining homeostasis of a set of physiologic variables. We then conducted simulations in a variety of environments and compared how modular agents performed relative to standard monolithic agents (i.e., agents that aimed to satisfy all needs in an integrated manner using a single aggregate measure of success). Simulations revealed that modular agents: a) exhibited a form of exploration that was intrinsic and emergent rather than extrinsically imposed; b) were robust to changes in non-stationary environments, and c) scaled gracefully in their ability to maintain home-ostasis as the number of conflicting objectives increased. Supporting analysis suggested that the robustness to changing environments and increasing numbers of needs were due to intrinsic exploration and efficiency of representation afforded by the modular architecture. These results suggest that the normative principles by which agents have adapted to complex changing environments may also explain why humans have long been described as consisting of ‘multiple selves’.

Significance Statement

Adaptive agents must continually satisfy a range of distinct and possibly conflicting needs. In most models of learning, a monolithic agent tries to maximize one value that measures how well it balances its needs. However, this task is difficult when the world is changing and needs are many. Here, we considered an agent as a collection of modules each dedicated to a particular need and competing for control of action. Compared to the standard monolithic approach, modular agents were much better at maintaining homeostasis of a set of internal variables in simulated environments, both static and changing. These results suggest that having ‘multiple selves’ may represent an evolved solution to the universal problem of balancing multiple needs in changing environments.
Motion Impact Score for Detecting Spurious Brain-Behavior Associations
Authors: Kay Benjamin P. , Montez David F. , Marek Scott , Tervo-Clemmens Brenden , Siegel Joshua S. , Adeyemo Babatunde , Laumann Timothy O. , Metoki Athanasia , Chauvin Roselyne J. , Van Andrew N. , Suljic Vahdeta , Krimmel Samuel R. , Miller Ryland L. , Newbold Dillan J. , Zheng Annie , Seider Nicole A. , Scheidter Kristen M. , Monk Julia , Feczko Eric , Randolph Anita , Miranda-Dominguez Oscar , Moore Lucille A. , Perrone Anders J. , Earl Eric A. , Malone Stephen M. , Cordova Michaela , Doyle Olivia , Lynch Benjamin J. , Wilgenbusch James C. , Pengo Thomas , Graham Alice M. , Roland Jarod L. , Gordon Evan M. , Snyder Abraham Z. , Barch Deanna M. , Fair Damien A. , Dosenbach Nico U.F.
Published: December 2022

Between-participant differences in head motion introduce systematic bias to resting state fMRI brain-wide association studies (BWAS) that is not completely removed by denoising algorithms. Researchers who study traits, or phenotypes associated with in-scanner head motion (e.g. psychiatric disorders) need to know if trait-functional connectivity (FC) effects are biased by residual motion artifact in order to avoid reporting false positive results. We devised an adaptable method, Split Half Analysis of Motion Associated Networks (SHAMAN), to assign a motion impact score to specific trait-FC effects. The SHAMAN approach distinguishes between motion artifact causing overestimation or underestimation of trait-FC effects. SHAMAN was > 95% specific at sample sizes of n = 100 and above. SHAMAN was powered to detect motion overestimation scores 80% of the time at sample sizes of n = 5,000 but could detect motion underestimation scores only 50% of the time at n = 5000, making it most useful for researchers seeking to avoid overestimating trait-FC effects in large BWAS. We computed motion impact scores for trait-FC effect with 45 demographic, biophysical, cognitive, and personality traits from n = 7,270 participants in the Adolescent Brain Cognitive Development (ABCD) Study. After standard denoising with ABCD-BIDS and without motion censoring, 42% (19/45) of traits had significant (p < 0.05) motion overestimation scores and 38% (17/45) of traits had significant motion underestimation scores. Censoring at framewise displacement (FD) < 0.2 mm reduced the proportion of traits with significant motion overestimation scores from 42% to 2% (1/45) but did not decrease the number of traits with significant motion underestimation scores.
Histidine 73 methylation coordinatesβ-actin plasticity in response to key environmental factors
Authors: Schahl Adrien , Lagardère Louis , Walker Brandon , Ren Pengyu , Wioland Hugo , Ballet Maya , Jégou Antoine , Chavent Matthieu , Piquemal Jean-Philip
Published: December 2022

The functional importance of the methylation of histidine 73 (H73) in actin remains unclear. Focusing on cytoplasmicβ-actin, present in all mammalian cells, we use molecular dynamics simulations with a polarizable force field and adaptive sampling to examine the effects of H73 methylation. Our results show that methylation enhances nucleotide binding cleft opening, alters allosteric pathways connecting subdomains 2 and 4 (SD2 and SD4) in G-actin, and affects backdoor openings and inorganic phosphate release in F-actin, as validated by biochemical assays. These effects depend on the nucleotide and ions interacting with the actin. Together, our findings reveal how H73 methylation regulatesβ-actin plasticity and integrates environmental cues.
An important role for triglyceride in regulating spermatogenesis
Authors: Chao Charlotte F. , Pesch Yanina-Yasmin , Yu Huaxu , Wang Chenjingyi , Aristizabal Maria J. , Huan Tao , Tanentzapf Guy , Rideout Elizabeth J.
Published: December 2022

Drosophilais a powerful model to study how lipids affect spermatogenesis. Yet, the contribution of neutral lipids, a major lipid group which resides in organelles called lipid droplets (LD), to sperm development is largely unknown. Emerging evidence suggests LD are present in the testis and that loss of neutral lipid- and LD-associated genes causes subfertility; however, key regulators of testis neutral lipids and LD remain unclear. Here, we show LD are present in early-stage somatic and germline cells within theDrosophilatestis. We identified a role for triglyceride lipasebrummer(bmm) in regulating testis LD, and found that whole-body loss ofbmmleads to defects in sperm development. Importantly, these represent cell-autonomous roles forbmmin regulating testis LD and spermatogenesis. Because lipidomic analysis ofbmmmutants revealed excess triglyceride accumulation, and spermatogenic defects inbmmmutants were rescued by genetically blocking triglyceride synthesis, our data suggest thatbmm-mediated regulation of triglyceride influences sperm development. This identifies triglyceride as an important neutral lipid that contributes toDrosophilasperm development, and reveals a key role forbmmin regulating testis triglyceride levels during spermatogenesis.
A combined biochemical and cellular approach reveals Zn2+-dependent hetero- and homodimeric CD4 and Lck assemblies in T cells
Authors: Kocyła Anna , Czogalla Aleksander , Wessels Inga , Rink Lothar , Krężel Artur
Published: December 2022

The CD4 or CD8 co-receptors’ interaction with the protein-tyrosine kinase Lck is widely accepted as the initiator of the tyrosine phosphorylation cascade leading to T-cell activation. These co-receptors potentially enhance T-cell antigen sensitivity, but how they function is still debated. A critical question is: to what extent are co-receptors and signal-initiating Lck coupled? Our contribution concerns the small – but indispensable for CD4- and CD8-Lck formation – element Zn2+. The intracellular Zn2+pool is strictly buffered but undergoes dynamic changes, also reported during T-cell activation. Furthermore, the identical Zn2+-binding cysteinyl residues may alter co-receptor dimerization or heterodimerization with Lck. Following initial research demonstrating a significant difference in the affinity of Zn2+to CD4 and CD4-Lck in solution, we combined biochemical and cellular approaches to show that fluctuations of buffered Zn2+in physiological ranges indeed influence Zn(CD4)2and Zn(CD4)(Lck). This conclusion was supported by the simulation of complexes’ equilibria, demonstrating that Zn2+changes can alter the molar ratio between those complexes. In T cells, increased intracellular free Zn2+concentration causes higher CD4 partitioning in the plasma membrane by a still unknown mechanism. We additionally found that CD4 palmitoylation decreases the specificity of CD4-Lck formation in the reconstituted membrane model, suggesting that this reversible modification may also be involved. Our findings help elucidate co-receptor-Lck coupling stoichiometry and demonstrate that intracellular free Zn2+has a major role in the interplay between CD4 dimers and CD4-Lck assembly.
PXN/Paxillin Phase Separation Promotes Focal Adhesion Assembly and Integrin Signaling
Authors: Liang Peigang , Wu Yuchen , Zheng Shanyuan , Zhang Jiaqi , Yang Shuo , Wang Jinfang , Ma Suibin , Zhang Mengjun , Gu Zhuang , Liu Qingfeng , Jiang Wenxue , Xing Qiong , Wang Bo
Published: December 2022

Focal adhesions (FAs) are transmembrane protein assemblies mediating cell-matrix connection. Tools to manipulate the compositionally intricate and dynamic FAs are currently limited, rendering many fundamental hypotheses untestable. Although protein liquid-liquid phase separation (LLPS) has been tied to the organization and dynamics of FAs, the underlying mechanisms remain unclear. Here, we experimentally tune the LLPS of PXN/Paxillin, an essential scaffold protein of FAs, by utilizing light-inducible Cry2 system. In addition to nucleating FA components, light-triggered PXN LLPS potently activates integrin signaling and subsequently accelerates cell spreading. PXN favors homotypic interaction-driven LLPSin vitro. In cells, PXN condensates are associated with plasma membrane, and modulated by actomyosin contraction and client proteins of FAs. Interestingly, non-specific weak inter-molecular interactions, together with specific molecular interactions, underlie the multicomponent condensation of PXN, and are efficient to promote FA assembly and integrin signaling. Thus, our data establish an active role of PXN phase transition into a condensed membrane-associated compartment in promoting assembly/maturation of FAs.
Significantly reduced inflammatory foreign-body-response to neuroimplants and improved recording performance in young compared to adult rats
Authors: Sharon Aviv , Jankowski Maciej M. , Shmoel Nava , Erez Hadas , Spira Micha E.
Published: December 2022

The multicellular inflammatory encapsulation of implanted intracortical multielectrode arrays (MEA) is associated with severe deterioration of their field potentials’ (FP) recording performance, which thus limits the use of brain implants in basic research and clinical applications. Therefore, extensive efforts have been made to identify the conditions in which the inflammatory foreign body response (FBR) is alleviated, or to develop methods to mitigate the formation of the inflammatory barrier. Here, for the first time, we show that (1) in young rats (74±8 gr, 4 weeks old at the onset of the experiments), cortical tissue recovery following MEA implantation proceeds with ameliorated inflammatory scar as compared to adult rats (242 ±18 gr, 9 weeks old at the experimental onset); (2) in contrast to adult rats in which the Colony Stimulating factor 1 Receptor (CSF1R) antagonist chow eliminated ~95% of the cortical microglia but not microglia adhering to the implant surfaces, in young rats the microglia adhering to the implant were eliminated along with the parenchymal microglia population. The removal of microglia adhering to the implant surfaces was correlated with improved recording performance by in-house fabricated Perforated Polyimide MEA Platforms (PPMP). These results support the hypothesis that microglia adhering to the surface of the electrodes, rather than the multicellular inflammatory scar, is the major underlying mechanism that deteriorates implant recording performance, and that young rats provide an advantageous model to study months-long, multisite electrophysiology in freely behaving rats.
Soluble NS1 antagonizes IgG- and IgA-mediated monocytic phagocytosis of DENV infected cells
Authors: Waldran Mitchell J. , Wegman Adam D. , Bahr Lauren E. , Currier Jeffrey R. , Waickman Adam T.
Published: December 2022

Dengue virus (DENV) is endemic in over 100 countries, infecting an estimated 400 million individuals every year. Infection with DENV raises a significant antibody response, primarily consisting of antibodies targeting viral (structural) proteins. However, not all DENV antigens are part of the virion itself, as the DENV genome encodes several non-structural (NS) proteins. One of these, NS1, has been shown to be antigenic and is expressed on the membrane of DENV-infected cells. IgG and IgA isotype antibodies that bind NS1 are detectable in serum following DENV infection and are also capable of interacting with Fc receptors expressed on professional phagocytes. Our study aims to determine if NS1-binding IgG and IgA isotype antibodies contribute to the clearance of DENV-infected cells by professional phagocytes through antibody mediated phagocytosis/trogocytosis. Using an in vitro model of trogocytosis we observed that both IgG and IgA isotype antibodies can facilitate facilitating monocytic uptake of DENV NS1 expressing plasma membrane in an additive fashion. This process was dependent on the expression of FcγRI (CD64) and FcαR (CD89) for IgG and IgA mediated membrane uptake, respectively. Furthermore, this process was antagonized by the presence of soluble NS1, suggesting that the production of soluble NS1 by infected cells may serve as an immunological chaff, thereby antagonizing opsonization and clearance of infected cells by NS1-specific IgG and IgA isotype antibodies.
WRNIP1 PREVENTS G4/R-LOOP-ASSOCIATED GENOMIC INSTABILITY
Authors: Valenzisi Pasquale , Marabitti Veronica , Petrai Stefano , Giardinelli Francesca Rita , Pichierri Pietro , Franchitto Annapaola
Published: December 2022

Maintenance of genome integrity is essential for cell viability and depends on complete and accurate DNA replication. However, G4/R-loops may provide significant obstacles for DNA replication, as they can cause collisions between replication fork and the transcription machinery. Hence, cells require mechanisms to counteract the presence of persistent G4/R-loops, most of which remain poorly understood. Here, we demonstrate an involvement of the Werner helicase-interacting protein 1 (WRNIP1) in preventing DNA damage induced by G4/R-loop-associated transcription-replication conflicts. We discovered that the ubiquitin-binding domain of WRNIP1 is required to efficiently avoid pathological persistence of G4/R-loops upon replication stress. Also, we observed that G4s reside within R-loops and that WRNIP1 colocalises with these structures. Furthermore, WRNIP1 plays a role in restarting replication from transcription-induced fork stalling. More importantly, we characterized the interplay between WRNIP1 and the DNA helicase FANCJ in counteracting R-loop-dependent G4 formation in response to replication stress. Collectively, our findings propose a mechanisms whereby WRNIP1, contributing to stabilise FANCJ to G4 sites, mitigates the G4/R-loop-mediated transcription-replication conflicts and protects against DNA damage accumulation.
Targeted Kinase Degradation via the KLHDC2 Ubiquitin E3 Ligase
Authors: Kim Younghoon , Seo Christina , Jeon Eunhye , You Inchul , Hwang Kyubin , Kim Namkyoung , Choi Ha-Soon , Hinshaw Stephen M. , Gray Nathanael S. , Sim Taebo
Published: December 2022

Chemically induced protein degradation is a powerful strategy for perturbing cellular biochemistry. The predominant mechanism of action for protein degrader drugs involves induced proximity between the cellular ubiquitin conjugation machinery and the target. Unlike traditional small molecule enzyme inhibition, targeted protein degradation can clear an undesired protein from cells. We demonstrate here the use of peptide ligands for Kelch-Like Homology Domain Containing protein 2 (KLHDC2), a substrate adaptor protein and member of the cullin-2 (CUL2) ubiquitin ligase complex, for targeted protein degradation. Peptide-based bivalent compounds that can induce proximity between KLHDC2 and target proteins cause degradation of the targeted factors. The cellular activity of these compounds depends on KLHDC2 binding. This work demonstrates the utility of KLHDC2 for targeted protein degradation and exemplifies a strategy for the rational design of new peptide-based ligands useful for this purpose.
Heritability of de novo germline mutation reveals a contribution from paternal but not maternal genetic factors
Authors: Hwang Seongwon , Neville Matthew D. C. ,   Genomics England Research Consortium, Day Felix R. , Scally Aylwyn
Published: December 2022

De novo mutations (DNMs) in the germline have long been identified as a key element in the causes of developmental and other genetic disorders. Previous attempts to investigate genetic factors affecting DNMs have suffered from a lack of statistical power, due to the difficulty of obtaining a sufficient number of parent-offspring trios. Thus, the rare disease cohort of the UK’s 100k Genomes Project (100kGP), comprising more than 10,000 trios, represents an unprecedented opportunity to investigate the genetics of germline mutation. Here we estimate SNP heritability of DNM count in offspring, as a measure of the relative contribution of genetic factors to the variance of the trait, in a PCA-selected subset of the 100kGP cohort. We estimate separate SNP heritabilities for paternally and maternally transmitted mutations (based on parentally phased DNMs in offspring), computed using parental genetic variants at a range of minimum frequencies and a variety of methodologies. We estimate a heritability of 10-20% for paternal DNMs; by contrast, for maternal DNMs we find no significant evidence for non-zero heritability. We investigated the partitioning of heritability among genes with different expression profiles in different tissue or cell states, and found a relative heritability enrichment for genes expressed in gonadal tissues, particularly testis. Among germ cells in adult testes we observed relative enrichment of heritability in genes associated with the (undifferentiated) spermatogonial stem cell state.
Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements
Authors: Wirthlin Morgan E. , Schmid Tobias A. , Elie Julie E. , Zhang Xiaomeng , Shvareva Varvara A. , Rakuljic Ashley , Ji Maria B. , Bhat Ninad S. , Kaplow Irene M. , Schäffer Daniel E. , Lawler Alyssa J. , Annaldasula Siddharth , Lim Byungkook , Azim Eiman ,   Zoonomia Consortium, Meyer Wynn K. , Yartsev Michael M. , Pfenning Andreas R.
Published: December 2022

Vocal learning, the ability to modify vocal behavior based on experience, is a convergently evolved trait in birds and mammals. To identify genomic elements associated with vocal learning, we integrated new experiments conducted in the brain of the Egyptian fruit bat with analyses of the genomes of 222 placental mammals. We first identified an anatomically specialized region of the bat motor cortex containing direct monosynaptic projections to laryngeal motoneurons. Using wireless neural recordings of this brain region in freely vocalizing bats, we verified that single neuron activity in this region relates to vocal production. We profiled the open chromatin of this vocal-motor region, which we used to train machine learning models to identify enhancers associated with vocal learning across mammals. We found 201 proteins and 45 candidate enhancers that display convergent evolution associated with vocal learning, many of which overlapped loci associated with human speech disability. One such locus contains the neurodevelopmental transcription factorsTSHZ3andZNF536and multiple candidate vocal learning-associated enhancers, suggesting the co-evolution of protein and regulatory sequences underlying vocal learning.

One-Sentence Summary

Analyses of bat neural activity and epigenomic data in a brain region involved in vocal behavior were used to identify proteins and regulatory elements associated with vocal learning in mammals.
Coevolutionary dynamics via adaptive feedback in collective-risk social dilemma game
Authors: Liu Linjie , Chen Xiaojie , Szolnoki Attila
Published: December 2022

Human society and natural environment form a complex giant ecosystem, where human activities not only lead to the change of environmental states, but also react to them. By using collective-risk social dilemma game, some studies have already revealed that individual contributions and the risk of future losses are inextricably linked. These works, however, often use an idealistic assumption that the risk is constant and not affected by individual behaviors. We here develop a coevolutionary game approach that captures the coupled dynamics of cooperation and risk. In particular, the level of contributions in a population affects the state of risk, while the risk in turn influences individuals’ behavioral decision-making. Importantly, we explore two representative feedback forms describing the possible effect of strategy on risk, namely, linear and exponential feedbacks. We find that cooperation can be maintained in the population by keeping at a certain fraction or forming an evolutionary oscillation with risk, independently of the feedback type. However, such evolutionary outcome depends on the initial state. Taken together, a two-way coupling between collective actions and risk is essential to avoid the tragedy of the commons. More importantly, a critical starting portion of cooperators and risk level is what we really need for guiding the evolution toward a desired direction.
An approach to rapid distributed manufacturing of broad spectrum anti-viral griffithsin using cell-free systems to mitigate pandemics
Authors: Borhani Shayan G. , Levine Max Z. , Krumpe Lauren H. , Wilson Jennifer , Henrich Curtis J. , O’Keefe Barry R. , Lo Donald , Sittampalam G. Sitta , Godfrey Alexander G. , Lunsford R. Dwayne , Mangalampalli Venkata , Tao Dingyin , LeClair Christopher A. , Thole Aaron , Frey Douglas , Swartz James , Rao Govind
Published: December 2022

This study describes the cell-free biomanufacturing of a broad-spectrum antiviral protein, griffithsin (GRFT) such that it can be produced with consistent purity and potency in less than 24 hours. We demonstrate GRFT production using two independent cell-free systems, one plant and one microbial. Griffithsin purity and quality were verified using standard regulatory metrics. Efficacy was demonstratedin vitroagainst SARS-CoV-2 and HIV-1 and was nearly identical to that of GRFT expressedin vivo. The proposed production process is efficient and can be readily scaled up and deployed anywhere in the world where a viral pathogen might emerge. The current emergence of viral variants has resulted in frequent updating of existing vaccines and loss of efficacy for front-line monoclonal antibody therapies. Proteins such as GRFT with its efficacious and broad virus neutralizing capability provide a compelling pandemic mitigation strategy to promptly suppress viral emergence at the source of an outbreak.
Beta-triggered adaptive deep brain stimulation during reaching movement in Parkinson’s disease
Authors: He Shenghong , Baig Fahd , Merla Anca , Torrecillos Flavie , Perera Andrea , Wiest Christoph , Debarros Jean , Benjaber Moaad , Hart Michael G , Morgante Francesca , Hasegawa Harutomo , Samuel Michael , Edwards Mark , Denison Timothy , Pogosyan Alek , Ashkan Keyoumars , Pereira Erlick , Tan Huiling
Published: December 2022

Subthalamic nucleus (STN) beta-triggered adaptive deep brain stimulation (ADBS) has been shown to provide clinical improvement comparable to conventional continuous DBS (CDBS) in people with Parkinson’s disease (PD) with less energy delivered to the brain and less stimulation induced side-effects. However, several questions remain unanswered. First, there is a normal physiological reduction of STN beta band power just prior to and during voluntary movement. ADBS systems will therefore reduce or cease stimulation during movement and could therefore compromise motor performance compared to CDBS. Second, beta power was smoothed and estimated over time periods of 400ms or longer in most previous ADBS studies. A shorter smoothing period could have the advantage of being more sensitive to changes in beta power which could enhance motor performance. In this study, we addressed these two questions by evaluating the effectiveness of STN beta-triggered ADBS using a standard 400ms and a shorter 200ms smoothing window during reaching movements. Results from 13 people with PD showed that STN beta-triggered ADBS is effective in improving motor performance during reaching movements as it better preserves gamma oscillation than CDBS in people with PD, and that shortening the smoothing window does not result in any additional behavioural benefit. ADBS significantly improved tremor compared with no DBS but was not as effective as CDBS. When developing ADBS systems for PD, it might not be necessary to track very fast beta dynamics; combining beta, gamma, and motor decoding might be more beneficial with additional biomarkers needed for optimal treatment of tremor.
Diagnostic yield of genetic screening in a diverse, community-ascertained cohort
Authors: Rao Nandana D. , Kaganovsky Jailanie , Malouf Emily , Coe Sandy , Huey Jenna , Tsinajinne Darwin , Hassan Sajida , King Kristine , Fullerton Stephanie M. , Chen Annie T. , Shirts Brian H.
Published: December 2022

Background

Population screening for genetic risk of adult-onset preventable conditions has been proposed as an attractive public health intervention. Screening unselected individuals can identify many individuals who will not be identified through current genetic testing guidelines.

Methods

We sought to evaluate enrollment in and diagnostic yield of population genetic screening in a resource-limited setting among a diverse population. We developed a low-cost, short-read next-generation sequencing panel of 25 genes that had 98.4% sensitivity and 99.98% specificity compared to diagnostic panels. We used email invitations to recruit a diverse cohort of patients in the University of Washington Medical Center system unselected for personal or family history of hereditary disease. Participants were sent a saliva collection kit in the mail with instructions on kit use and return. Results were returned using a secure online portal. Enrollment and diagnostic yield were assessed overall, and across race and ethnicity groups.

Results

Overall, 40,857 people were invited and 2,899 (7.1%) enrolled. Enrollment varied across race and ethnicity groups, with the lowest enrollment among African American individuals (3.3%) and the highest among Multiracial or Other Race individuals (13.0%). Of 2,864 enrollees who received screening results, 106 actionable variants were identified in 103 individuals (3.6%). Of those who screened positive, 30.1% already knew about their results from prior genetic testing. The diagnostic yield was 74 new, actionable genetic findings (2.6%). The addition of more recently identified cancer risk genes increased the diagnostic yield of screening.

Conclusions

Population screening can identify additional individuals that could benefit from prevention, but challenges in recruitment and sample collection will reduce actual enrollment and yield. These should not be overlooked in intervention planning or in cost and benefit analysis.