bluuebunny/crossref_metadata_2025 huggingface dataset:
Three-dimensional volumetric muscle reconstruction of the
Australopithecus afarensis
pelvis and limb, with estimations of limb leverage
Authors: Wiseman Ashleigh L. A.
Published: June 2023

To understand how an extinct species may have moved, we first need to reconstruct the missing soft tissues of the skeleton, which rarely preserve, with an understanding of segmental volume and muscular composition within the body. The
Australopithecus afarensis
specimen AL 288-1 is one of the most complete hominin skeletons. Despite 40+ years of research, the frequency and efficiency of bipedal movement in this specimen is still debated. Here, 36 muscles of the pelvis and lower limb were reconstructed using three-dimensional polygonal modelling, guided by imaging scan data and muscle scarring. Reconstructed muscle masses and configurations guided musculoskeletal modelling of the lower limb in comparison with a modern human. Results show that the moment arms of both species were comparable, hinting towards similar limb functionality. Moving forward, the polygonal muscle modelling approach has demonstrated promise for reconstructing the soft tissues of hominins and providing information on muscle configuration and space filling. This method demonstrates that volumetric reconstructions are required to know where space must be occupied by muscles and thus where lines of action might not be feasible due to interference with another muscle. This approach is effective for reconstructing muscle volumes in extinct hominins for which musculature is unknown.
Rearing in strontium-enriched water induces vaterite otoliths in the Japanese rice fish,
Oryzias latipes
Authors: Murase Iki , Kawamoto Tatsuhiko , Akizawa Norikatsu , Irie Takahiro
Published: June 2023

Sagittal otoliths, typically composed of aragonite, are frequently laid down rather as vaterite during growth in hatchery-reared fish populations. Sagittal vateritization is believed to impair individual hearing/balancing abilities, but the causal mechanism remains unclear. Here we experimentally demonstrated that rearing in Sr-rich water induces sagittal vateritization in the HdrR-II1 inbred strain of the Japanese rice fish,
Oryzias latipes
. Both sagittae were partly vateritized in 70% of individuals subjected to the Sr
2+
treatment (
n
= 10), whereas fish reared in normal tap water showed no sagittal vateritization (
n
= 8). Our result is consistent with the theoretical prediction that vaterite becomes thermodynamically more stable than aragonite as the Sr
2+
concentration in solution increases. A vateritic layer develops surrounding the original aragonitic sagitta in vateritized otoliths, some of which take on a comma-like shape. Electron probe microanalysis demonstrates that the vateritized phase is characterized by lower Sr
2+
and higher Mg
2+
concentrations than the aragonitic phase. It is unlikely that increased environmental Sr
2+
is responsible for the sagittal vateritization in farmed fish. However, our findings likely help to establish an
in vivo
assay using
O. latipes
to understand the physiological process underlying the sagittal vateritization in farmed fish.
Recent advances and future challenges in gene therapy for hearing loss
Authors: Amariutei Ana E. , Jeng Jing-Yi , Safieddine Saaid , Marcotti Walter
Published: June 2023

Hearing loss is the most common sensory deficit experienced by humans and represents one of the largest chronic health conditions worldwide. It is expected that around 10% of the world's population will be affected by disabling hearing impairment by 2050. Hereditary hearing loss accounts for most of the known forms of congenital deafness, and over 25% of adult-onset or progressive hearing loss. Despite the identification of well over 130 genes associated with deafness, there is currently no curative treatment for inherited deafness. Recently, several pre-clinical studies in mice that exhibit key features of human deafness have shown promising hearing recovery through gene therapy involving the replacement of the defective gene with a functional one. Although the potential application of this therapeutic approach to humans is closer than ever, substantial further challenges need to be overcome, including testing the safety and longevity of the treatment, identifying critical therapeutic time windows and improving the efficiency of the treatment. Herein, we provide an overview of the recent advances in gene therapy and highlight the current hurdles that the scientific community need to overcome to ensure a safe and secure implementation of this therapeutic approach in clinical trials.
Data-driven reduction and decomposition with time-axis clustering
Authors: Barwey S. , Raman V.
Published: June 2023

A new approach for modal decomposition through re-interpretation of unsteady dynamics, termed time-axis clustering, is developed in this work and is demonstrated on an experimental turbulent reacting flow dataset consisting of simultaneously measured planar OH-PLIF and PIV fields in a model combustor. The method executes a K-Means clustering algorithm on an alternative representation of the input snapshot dataset: the dataset is interpreted here as a collection of one-dimensional time series, where each time series represents the time evolution of some flow quantity of interest (QoI) at a fixed point in physical space (i.e. pixel locations). The clustering algorithm in the modal decomposition context produces (a) spatial modes (called time-axis modes) that identify localized regions of dynamical similarity in physical space and (b) temporal coefficients that represent average trajectories of the flow QoI conditioned on the regions in physical space identified by the corresponding spatial mode. Due to the non-overlapping nature of K-Means clusters, visualization of the modes provides a unique pathway for flow feature extraction based on dynamical similarity. Ultimately, this work shows how time-axis clustering provides a promising avenue for domain-localized data-based modelling of complex fluid flows.
Human locomotion over obstacles reveals real-time prediction of energy expenditure for optimized decision-making
Authors: Daniels Katherine A. J. , Burn J. F.
Published: June 2023

Despite decades of evidence revealing a multitude of ways in which animals are adapted to minimize the energy cost of locomotion, little is known about how energy expenditure shapes adaptive gait over complex terrain. Here, we show that the principle of energy optimality in human locomotion can be generalized to complex task-level locomotor behaviours requiring advance decision-making and anticipatory control. Participants completed a forced-choice locomotor task requiring them to choose between discrete multi-step obstacle negotiation strategies to cross a ‘hole’ in the ground. By modelling and analysing mechanical energy cost of transport for preferred and non-preferred manoeuvres over a wide range of obstacle dimensions, we showed that strategy selection was predicted by relative energy cost integrated across the complete multi-step task. Vision-based remote sensing was sufficient to select the strategy associated with the lowest prospective energy cost in advance of obstacle encounter, demonstrating the capacity for energetic optimization of locomotor behaviour in the absence of online proprioceptive or chemosensory feedback mechanisms. We highlight the integrative hierarchic optimizations that are required to facilitate energetically efficient locomotion over complex terrain and propose a new behavioural level linking mechanics, remote sensing and cognition that can be leveraged to explore locomotor control and decision-making.
Developmental biomechanics and age polyethism in leaf-cutter ants
Authors: Püffel Frederik , Meyer Lara , Imirzian Natalie , Roces Flavio , Johnston Richard , Labonte David
Published: June 2023

Many social insects display age polyethism: young workers stay inside the nest, and only older workers forage. This behavioural transition is accompanied by genetic and physiological changes, but the mechanistic origin of it remains unclear. To investigate if the mechanical demands on the musculoskeletal system effectively prevent young workers from foraging, we studied the biomechanical development of the bite apparatus in
Atta vollenweideri
leaf-cutter ants. Fully matured foragers generated peak
in vivo
bite forces of around 100 mN, more than one order of magnitude in excess of those measured for freshly eclosed callows of the same size. This change in bite force was accompanied by a sixfold increase in the volume of the mandible closer muscle, and by a substantial increase of the flexural rigidity of the head capsule, driven by a significant increase in both average thickness and indentation modulus of the head capsule cuticle. Consequently, callows lack the muscle force capacity required for leaf-cutting, and their head capsule is so compliant that large muscle forces would be likely to cause damaging deformations. On the basis of these results, we speculate that continued biomechanical development post eclosion may be a key factor underlying age polyethism, wherever foraging is associated with substantial mechanical demands.
Association between arginine vasopressin receptor 1A (
AVPR1A
) polymorphism and inequity aversion
Authors: Tanaka Hiroki , Nishina Kuniyuki , Shou Qiulu , Takahashi Hidehiko , Sakagami Masamichi , Matsuda Tetsuya , Inoue-Murayama Miho , Takagishi Haruto
Published: June 2023

Although numerous studies have focused on brain functions related to inequity aversion, few have examined its genetic basis. Here, we show the association between estimated inequity aversion and polymorphisms in three genes associated with human sociality. Non-student adult participants took part in five economic game experiments on different days. Disadvantageous inequity aversion (DIA) and advantageous inequity aversion (AIA) were calculated from behavioural responses using Bayesian estimation. We investigated the association between genetic polymorphisms in the oxytocin receptor (
OXTR
rs53576), arginine vasopressin receptor 1A (
AVPR1A
RS3) and opioid receptor mu 1 (
OPRM1
rs1799971) and inequity aversion. Regarding
AVPR1A
RS3, participants with the SS genotype had higher AIA than those with the SL or LL genotypes, but no association was found for DIA. Moreover, we observed no aversion associations for
OXTR
rs53576 or
OPRM1
rs1799971. The results suggest that
AVPR1A
plays an important role in aversion when one's own gain is greater than that of others. Our findings may provide a solid theoretical basis for future studies on the relationship between genetic polymorphisms and inequity aversion.
Artificial light at night causes conflicting behavioural and morphological defence responses in a marine isopod
Authors: Bullough Kathryn , Gaston Kevin J. , Troscianko Jolyon
Published: June 2023

Encroachment of artificial light at night (ALAN) into natural habitats is increasingly recognized as a major source of anthropogenic disturbance. Research focussed on variation in the intensity and spectrum of ALAN emissions has established physiological, behavioural and population-level effects across plants and animals. However, little attention has been paid to the structural aspect of this light, nor how combined morphological and behavioural anti-predator adaptations are affected. We investigated how lighting structure, background reflectance and the three-dimensional properties of the environment combined to affect anti-predator defences in the marine isopod
Ligia oceanica.
Experimental trials monitored behavioural responses including movement and background choice, and also colour change, a widespread morphological anti-predator mechanism little considered in relation to ALAN exposure. We found that behavioural responses of isopods to ALAN were consistent with classic risk-aversion strategies, being particularly exaggerated under diffuse lighting. However, this behaviour was disconnected from optimal morphological strategies, as diffuse light caused isopods to become lighter coloured while seeking out darker backgrounds. Our work highlights the potential for the structure of natural and artificial light to play a key role in behavioural and morphological processes likely to affect anti-predator adaptations, survival, and ultimately wider ecological effects.
Mismatches between phenotype and environment shape fitness at hyperlocal scales
Authors: Alujević Karla , Streicher Jeffrey W. , Garcia Raquel A. , Riesgo Ana , Taboada Sergio , Logan Michael L. , Clusella-Trullas Susana
Published: June 2023

In the era of human-driven climate change, understanding whether behavioural buffering of temperature change is linked with organismal fitness is essential. According to the ‘cost–benefit’ model of thermoregulation, animals that live in environments with high frequencies of favourable thermal microclimates should incur lower thermoregulatory costs, thermoregulate more efficiently and shunt the associated savings in time and energy towards other vital tasks such as feeding, territory defence and mate acquisition, increasing fitness. Here, we explore how thermal landscapes at the scale of individual territories, physiological performance and behaviour interact and shape fitness in the southern rock agama lizard (
Agama atra
). We integrated laboratory assays of whole organism performance with behavioural observations in the field, fine-scale estimates of environmental temperature, and paternity assignment of offspring to test whether fitness is predicted by territory thermal quality (i.e. the number of hours that operative temperatures in a territory fall within an individual's performance breadth). Male lizards that occupied territories of low thermal quality spent more time behaviourally compensating for sub-optimal temperatures and displayed less. Further, display rate was positively associated with lizard fitness, suggesting that there is an opportunity cost to engaging in thermoregulatory behaviour that will change as climate change progresses.
Too many big promises: What is holding back cyanobacterial research and applications?
Authors: Schmelling Nicolas M. , Bross Moritz
Published: June 2023

Climate change as a global crisis demands a shift from a fossil fuel-based economy to-wards sustainable solutions. Cyanobacteria are promising organisms for the truly sustainable, carbon-neutral production of various chemicals. However, so far, proof of concepts for large-scale cyanobacterial productions that produce industrial-relevant amounts of desired products are lacking. To systematically address this topic, a comprehensive overview that identifies current obstacles and solutions is missing.

We conducted a quantitative survey among researchers in the cyanobacterial community. This work investigates individual experiences and challenges in the field of cyanobacteria, as well as information about specific protocols. Additionally, qualitative interviews with academic experts were conducted. Their answers were compared, and highlights were summarised.

In this work, we provide for the first time a comprehensive overview of current trends and challenges as perceived by researchers in the field of cyanobacteria. Based on the results of the survey and interviews, we formulate a set of recommendations on how to improve the working conditions within the cyanobacteria research community.
C1q Enables Influenza HA Stem Binding Antibodies to Block Viral Attachment and Broadens the Antibody Escape Repertoire
Authors: Kosik Ivan , Santos Jefferson Da Silva , Angel Matthew , Hu Zhe , Holly Jaroslav , Gibbs James S. , Gill Tanner , Kosikova Martina , Li Tiansheng , Bakhache William , Dolan Patrick T. , Xie Hang , Andrews Sarah F. , Gillespie Rebecca A. , Kanekiyo Masaru , McDermott Adrian B. , Pierson Theodore C. , Yewdell Jonathan W.
Published: June 2023

Broadly neutralizing, anti-hemagglutinin stem antibodies (Abs) are a promising universal influenza vaccine target. While anti-stem Abs are not believed to block viral attachment, we show that C1q confers attachment inhibition and boosts fusion and neuraminidase inhibition, greatly enhancing virus neutralization activity in vitro and in mice challenged with influenza virus via the respiratory route. These effects reflect increased steric interference and not increased Ab avidity. Remarkably, C1q greatly expands the anti-stem Ab viral escape repertoire to include residues throughout the hemagglutinin. Some substitutions cause antigenic alterations in the globular region or modulate HA receptor avidity. We also show that C1q enhances the neutralization activity of non-RBD anti-SARS-CoV-2 Spike Abs, an effect dependent on Spike density on the virion surface. Together, our findings show that first, Ab function must be considered in a physiological context and second, inferring the exact selection pressure for Ab-driven viral evolution is risky business, at best.
Functional glycoproteomics by integrated network assembly and partitioning
Authors: Griffin Matthew E. , Thompson John W. , Xiao Yao , Sweredoski Michael J. , Aksenfeld Rita B. , Jensen Elizabeth H. , Koldobskaya Yelena , Schacht Andrew L. , Kim Terry D. , Choudhry Priya , Lomenick Brett , Garbis Spiros D. , Moradian Annie , Hsieh-Wilson Linda C.
Published: June 2023

The post-translational modification (PTM) of proteins by O-linked β-N-acetyl-D-glucosamine (O-GlcNAcylation) is widespread across the proteome during the lifespan of all multicellular organisms. However, nearly all functional studies have focused on individual protein modifications, overlooking the multitude of simultaneous O-GlcNAcylation events that work together to coordinate cellular activities. Here, we describeNetworking ofInteractors andSubstratEs (NISE), a novel, systems-level approach to rapidly and comprehensively monitor O-GlcNAcylation across the proteome. Our method integrates affinity purification-mass spectrometry (AP-MS) and site-specific chemoproteomic technologies with network generation and unsupervised partitioning to connect potential upstream regulators with downstream targets of O-GlcNAcylation. The resulting network provides a data-rich framework that reveals both conserved activities of O-GlcNAcylation such as epigenetic regulation as well as tissue-specific functions like synaptic morphology. Beyond O-GlcNAc, this holistic and unbiased systems-level approach provides a broadly applicable framework to study PTMs and discover their diverse roles in specific cell types and biological states.
Mycobiome analyses of critically ill COVID-19 patients
Authors: Weaver Danielle , Gago Sara , Bassetti Matteo , Giacobbe Daniele Roberto , Prattes Juergen , Hoenigl Martin , Reizine Florian , Guegan Hélène , Gangneux Jean-Pierre , Bromley Michael John , Bowyer Paul
Published: June 2023

Rationale

COVID-19-associated pulmonary aspergillosis (CAPA) is a life-threatening complication in patients with severe COVID-19. Previously, acute respiratory distress syndrome in patients with COVID-19 has been associated with lung fungal dysbiosis, evidenced by reduced microbial diversity andCandidacolonisation. Increased fungal burden in the lungs of critically ill COVID-19 patients is linked to prolonged mechanical ventilation and increased mortality. However, specific mycobiome signatures associated with severe COVID-19 in the context of survival and antifungal drug prophylaxis have not yet been determined and such knowledge could have an important impact on treatment.

Objectives

To understand the composition of the respiratory mycobiome in critically ill COVID-19 patients with and without CAPA and the impact of antifungal use in patient outcome.

Methods

We performed a multi-national study of 39 COVID-19 patients in intensive care units (ICU) with and without CAPA. Respiratory mycobiome was profiled using ITS1 sequencing andAspergillus fumigatusburden was further validated using qPCR. Fungal communities were investigated using alpha diversity, beta diversity, taxa predominance and taxa abundances.

Results

Respiratory mycobiomes of COVID-19 patients were dominated byCandidaandAspergillus.There was no significant association with corticosteroid use or CAPA diagnosis and respiratory fungal communities. IncreasedA. fumigatusburden was associated with mortality and, the use of azoles at ICU admission was linked with an absence ofA. fumigatus.

Conclusions

Our findings suggest that mould-active antifungal treatment at ICU admission may be linked with reducedA. fumigatus-associated mortality in severe COVID-19. However, further studies are warranted on this topic.
Demographic inference for spatially heterogeneous populations using long shared haplotypes
Authors: Forien Raphaël , Ringbauer Harald , Coop Graham
Published: June 2023

We introduce a modified spatial Λ-Fleming-Viot process to model the ancestry of individuals in a population occupying a continuous spatial habitat divided into two areas by a sharp discontinuity of the dispersal rate and effective population density. We derive an analytical formula for the expected number of shared haplotype segments between two individuals depending on their sampling locations. This formula involves the transition density of a skew diffusion which appears as a scaling limit of the ancestral lineages of individuals in this model. We then show that this formula can be used to infer the dispersal parameters and the effective population density of both regions, using a composite likelihood approach, and we demonstrate the efficiency of this method on a range of simulated data sets.
Dynamics in the assembly of the 30S ribosomal subunit investigated by coarse-grained simulations
Authors: Liu Xin , Zhang Zhiyong
Published: June 2023

The ribosome is a large biomolecular complex responsible for protein synthesis. InEscherichia coli(E. coli), a complete ribosome is composed of a 30S small subunit and a 50S large subunit. For about half a century, the 30S subunit has been a key model system for studying thein vitroassembly of the ribosome, and an assembly map has been proposed. However, structural details in the assembly of this protein-RNA complex remain elusive. In this paper, we have conducted a series of coarse-grained simulations following the order of the assembly map, in order to investigate conformational dynamics during the assembly process of the 30S subunit. It has been found that, the tertiary structure of the naked 16S rRNA is very unstable, and that is the case after binding of the early-assembly proteins. The mid-assembly proteins can significantly restrict the mobility of the 16S rRNA and make the latter close to the native structure. The final binding of the late-assembly proteins would fully obtain the collective motion of the 16S rRNA. In particular, proteins S9 and S3 may have more important contributions to the assembly of the 30S subunit than other S proteins. Our strategy of coarse-grained simulations can be generally used to study assembly dynamics of large biomolecular complexes as long as the assembly map is available.
Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data
Authors: Fu Xiaohang , Lin Yingxin , Lin David M , Mechtersheimer Daniel , Wang Chuhan , Ameen Farhan , Ghazanfar Shila , Patrick Ellis , Kim Jinman , Yang Jean YH
Published: June 2023

Recent advances in subcellular imaging transcriptomics platforms have enabled high-resolution spatial mapping of gene expression, while also introducing significant analytical challenges in accurately identifying cells and assigning transcripts. Existing methods grapple with cell segmentation, frequently leading to fragmented cells or oversized cells that capture contaminated expression. To this end, we present BIDCell, a self-supervised deep learning-based framework with biologically-informed loss functions that learn relationships between spatially resolved gene expression and cell morphology. BIDCell incorporates cell-type data, including single-cell transcriptomics data from public repositories, with cell morphology information. Using a comprehensive evaluation framework consisting of metrics in five complementary categories for cell segmentation performance, we demonstrate that BIDCell outperforms other state-of-the-art methods according to many metrics across a variety of tissue types and technology platforms. Our findings underscore the potential of BIDCell to significantly enhance single-cell spatial expression analyses, including cell-cell interactions, enabling great potential in biological discovery.
Cortical Activity Associated With Acute Development of Phantom Auditory Percepts via Unilateral Deprivation
Authors: Ginnan Gregory , Rampp Stefan , Schaette Roland , Buchfelder Michael , Müller-Voggel Nadia
Published: June 2023

Subjective tinnitus describes the experience of hearing phantom sounds (e.g., tones, buzzing, noise). While the majority of those who report having experienced phantom sounds claim that these percepts have not lasted but are transient, some experience this chronically, with others even describing their tinnitus as severe enough to negatively impact their well-being and daily lives. Currently, no permanent solution has been discovered for preventing or curing tinnitus. This is due to several factors, including an insufficient understanding of the mechanisms at play that give rise to such auditory sensations, as well as a lack of research investigating the corresponding changes in neural activity associated with the onset and development of tinnitus. Taking advantage of the high spatial and temporal resolution of magnetoencephalography (MEG), we measured cortical activity associated with the development of acute tinnitus-like percepts induced via unilateral auditory deprivation. Over the course of four days, participants continuously wore a silicone earplug in one ear, which led to the experience of phantom sounds in 15 of 16 participants. Frequency analysis of source-localized continuous MEG data revealed a significant increase of gamma power in primary auditory cortices (A1) during the tinnitus condition (p=0.02), which most likely reflects the neuronal processing correlated with tinnitus perception.
Label-free quantification LC-mass spectrometry proteomic analysis of blood plasma in healthy dogs
Authors: Doulidis Pavlos G. , Kuropka Benno , Frizzo Ramos Carolina , Rodríguez-Rojas Alexandro , Burgener Iwan A.
Published: June 2023

Bloodwork is a widely used diagnostic tool in veterinary medicine, as diagnosis and therapeutic interventions often rely on blood biomarkers. However, biomarkers available in veterinary medicine often lack sensitivity or specificity. Mass spectrometry (MS)-based proteomics technology has been extensively used in biological fluids and offers excellent potential for a more comprehensive characterization of the plasma proteome in veterinary medicine. In this study, we aimed to identify and quantify plasma proteins in a cohort of healthy dogs and compare two techniques for depleting high-abundance plasma proteins to enable the detection of lower-abundance proteins. We utilized surplus lithium-heparin plasma from 30 healthy dogs, which were subdivided into five groups of pooled plasma from 6 randomly selected individuals each. Our goal was to identify and quantify plasma proteins via label-free quantification LC-mass spectrometry. Additionally, we employed different methods to deplete the most abundant proteins. Firstly, we used a commercial kit for the depletion of high-abundance plasma proteins. Secondly, we employed an in-house method to remove albumin using Blue-Sepharose. Among all the samples, some of the most abundant proteins identified were apolipoprotein A and B, albumin, alpha-2-macroglobulin, fibrinogen beta chain, fibronectin, complement C3, serotransferrin, and coagulation Factor V. However, neither of the depletion techniques achieved significant depletion of high-abundant proteins. Nevertheless, the two different depletion methods exhibited substantial differences in the fold-change of many proteins, suggesting partial depletion that did not contribute to an increase in the number of detected proteins. Despite this limitation, we were able to detect and quantify many clinically relevant proteins. The determination of the healthy canine proteome is a crucial first step in establishing a reference proteome for canine plasma. This reference proteome can later be utilized to identify protein markers associated with different diseases, thereby contributing to the diagnosis and prognosis of various pathologies.
A large-scale sORF screen identifies putative microproteins and provides insights into their interaction partners, localisation and function
Authors: Schlesinger Dörte , Dirks Christopher , Luzon Carmen Navarro , Lafranchi Lorenzo , Eirich Jürgen , Elsässer Simon J
Published: June 2023

The human genome contains thousands of potentially coding short open reading frames (sORFs). A growing set of microproteins translated from these sORFs are known to have important cellular functions. However, the majority remains uncharacterised. Thus, larger screens to find functional microproteins have become more vital. Here, we performed a high-throughput CRISPR/Cas9 knock-out screen with a customised library of 11,776 sORFs, curated from literature and databases to identify microproteins essential for cancer cell line growth. 16/17 tested candidates displayed a reproducible knockout phenotype. We selected our top six hits, consisting of 11 to 63 amino acids. Various of these candidates localised to distinct subcellular compartments and the majority showed specific interaction partners. Endogenous tagging demonstrated translation of an sORF in the CENPBD2P pseudogene that bears no resemblance to the CENPBD2P name-giving CENPB DNA binding domains. For two candidates, uORFs in the DSE and NUTF2 genes, the microprotein suppliedin transameliorated the growth defect of the respective knock-out. RNA-seq analysis revealed however that gene expression changes in the knock-out could only partially be rescued. Overall, we identified various putative microproteins and a microprotein-producing pseudogene that might be involved in cancer cell growth, but also illustrate the limitations and caveats of sORF functional screening and characterisation.
The effects of prefrontal tDCS on working memory associate with the magnitude of the individual electric field in the brain
Authors: Razza Lais B. , De Smet Stefanie , Van Hoornweder Sybren , De Witte Sara , Luethi Matthias S. , Baeken Chris , Brunoni Andre R. , Vanderhasselt Marie-Anne
Published: June 2023

Transcranial direct current stimulation (tDCS) over the prefrontal cortex has the potential to enhance working memory by means of a weak direct current applied to the scalp. However, its effects are highly variable and possibly dependent on individual variability in cortical architecture and head anatomy. Unveiling sources of heterogeneity might improve fundamental and clinical application of tDCS in the field. Therefore, we investigated sources of tDCS variability of prefrontal 1.5mA tDCS, 3mA tDCS and sham tDCS in 40 participants (67.5% women, mean age 24.7 years) by associating simulated electric field (E-field) magnitude in brain regions of interest (dorsolateral prefrontal cortex, anterior cingulate cortex (ACC) and subgenual ACC) and working memory performance. Emotional and non-emotional 3-back paradigms were used. In the tDCS protocol analysis, effects were only significant for the 3mA group, and only for the emotional tasks. In the individual E-field magnitude analysis, faster responses in non-emotional, but not in the emotional task, were associated with stronger E-fields in all brain regions of interest. A follow-up analysis showed that people with higher (vs. lower) E-fields magnitude in the left DLPFC were faster in the both tasks, and more accurate in the emotional task. Concluding, individual E-field distribution might explain part of the variability of prefrontal tDCS effects on working memory performance and in clinical samples. Our results suggest that tDCS effects can be more consistent or improved by applying personalizing current intensity, although this hypothesis should be confirmed by further studies.
The homeodomain drives favorable DNA binding energetics of prostate cancer target ONECUT2
Authors: Chatterjee Avradip , Gallent Brad , Katiki Madhusudhanarao , Qian Chen , Harter Matthew R. , Freeman Michael R. , Murali Ramachandran
Published: June 2023

The ONECUT transcription factors feature a CUT and a homeodomain, evolutionarily conserved elements that bind DNA cooperatively, but the process remains mechanistically enigmatic. Using an integrative DNA binding analysis of ONECUT2, a driver of aggressive prostate cancer, we show that the homeodomain energetically stabilizes the ONECUT2-DNA complex through allosteric modulation of CUT. Further, evolutionarily conserved base-interactions in both the CUT and homeodomain are necessary for the favorable thermodynamics. We have identified a novel arginine pair unique to the ONECUT family homeodomain that can adapt to DNA sequence variations. Base interactions in general, including by this arginine pair, are critical for optimal DNA binding and transcription in a prostate cancer model. These findings provide fundamental insights into DNA binding by CUT-homeodomain proteins with potential therapeutic implications.

One-Sentence Summary

Base-specific interactions regulate homeodomain-mediated stabilization of DNA binding by the ONECUT2 transcription factor.
Structure-based virtual screening identifies small molecule inhibitors of O-fucosyltransferase SPINDLY
Authors: Aizezi Yalikunjiang , Zhao Hongming , Zhang Zhenzhen , Bi Yang , Yang Qiuhua , Guo Guangshuo , Zhang Hongliang , Guo Hongwei , Jiang Kai , Wang Zhi-Yong
Published: June 2023

Protein O-glycosylation is a nutrient-signaling mechanism that plays essential roles in maintaining cellular homeostasis across different species. In plants, SPINDLY (SPY) and SECRET AGENT (SEC) catalyze posttranslational modifications of hundreds of intracellular proteins by O-fucose and O-linked N-acetylglucosamine, respectively. SPY and SEC play overlapping roles in cellular regulation and loss of both SPY and SEC causes embryo lethality in Arabidopsis. Using structure-based virtual screening of chemical libraries followed byin vitroandin plantaassays, we identified aSPYO-fucosyltransferaseinhibitor (SOFTI). Computational analyses predicted that SOFTI binds to the GDP-fucose-binding pocket of SPY and competitively inhibits GDP-fucose binding.In vitroassays confirmed that SOFTI interacts with SPY and inhibits its O-fucosyltransferase activity. Docking analysis identified additional SOFTI analogs that showed stronger inhibitory activities. SOFTI treatment of Arabidopsis seedlings decreased protein O-fucosylation and caused phenotypes similar to thespymutants, including early seed germination, increased root hair density, and defect in sugar-dependent growth. By contrast, SOFTI had no visible effect on thespymutant. Similarly, SOFTI inhibited sugar-dependent growth of tomato seedlings. These results demonstrate that SOFTI is a specific SPY O-fucosyltransferase inhibitor and a useful chemical tool for functional studies of O-fucosylation and potentially for agricultural management.
Population ecology and potential biogeochemical impacts of ssDNA and dsDNA soil viruses along a permafrost thaw gradient
Authors: Trubl Gareth , Roux Simon , Borton Mikayla A. , Varsani Arvind , Li Yueh-Fen , Sun Christine , Jang Ho Bin , Woodcroft Ben J. , Tyson Gene W. , Wrighton Kelly C. , Saleska Scott R. , Eloe-Fadrosh Emiley A. , Sullivan Matthew B. , Rich Virginia I.
Published: June 2023

Climate change is disproportionately warming northern peatlands, which may release large carbon stores via increased microbial activity. While there are many unknowns about such microbial responses, virus roles are especially poorly characterized with studies to date largely restricted to “bycatch” from bulk metagenomes. Here, we used optimized viral particle purification techniques on 20 samples along a highly contextualized peatland permafrost thaw gradient, extracted and sequenced viral particle DNA using two library kits to capture single-stranded (ssDNA) and double-stranded (dsDNA) virus genomes (40 total viromes), and explored their diversity and potential ecosystem impacts. Both kits recovered similar dsDNA virus numbers, but only one also captured thousands of ssDNA viruses. Combining these data, we explored population-level ecology using genomic representation from 9,560 viral operational taxonomic units (vOTUs); nearly a 4-fold expansion from permafrost-associated soils, and 97% of which were novel when compared against large datasets from soils, oceans, and the human gut.In silicopredictions identified putative hosts for 44% (4,149 dsDNA + 17 ssDNA) of the identified vOTUs spanning 2 eukaryotic, 12 archaeal, and 30 bacterial phyla. The recovered vOTUs encoded 1,684 putative auxiliary metabolic genes (AMGs) and other metabolic genes carried by ∼10% of detected vOTUs, of which 46% were related to carbon processing and 644 were novel. These AMGs grouped into five functional categories and 11 subcategories, and nearly half (47%) of the AMGs were involved in carbon utilization. Of these, 112 vOTUs encoded 123 glycoside hydrolases spanning 15 types involved in the degradation of polysaccharides (e.g., cellulose) to monosaccharides (e.g., galactose), or further monosaccharide degradation, which suggests virus involvement in myriad metabolisms including fermentation and central carbon metabolism. These findings expand the scope of viral roles in microbial carbon processing and suggest viruses may be critical for understanding the fate of soil organic carbon in peatlands.
Programmable RNA-guided endonucleases are widespread in eukaryotes and their viruses
Authors: Jiang Kaiyi , Lim Justin , Sgrizzi Samantha , Trinh Michael , Kayabolen Alisan , Yutin Natalya , Koonin Eugene V. , Abudayyeh Omar O. , Gootenberg Jonathan S.
Published: June 2023

TnpB proteins are RNA-guided nucleases that are broadly associated with IS200/605 family transposons in prokaryotes. TnpB homologs, named Fanzors, have been detected in genomes of some eukaryotes and large viruses, but their activity and functions in eukaryotes remain unknown. We searched genomes of diverse eukaryotes and their viruses for TnpB homologs and identified numerous putative RNA-guided nucleases that are often associated with various transposases, suggesting they are encoded in mobile genetic elements. Reconstruction of the evolution of these nucleases, which we rename Horizontally-transferred Eukaryotic RNA-guided Mobile Element Systems (HERMES), revealed multiple acquisitions of TnpBs by eukaryotes and subsequent diversification. In their adaptation and spread in eukaryotes, HERMES proteins acquired nuclear localization signals, and genes captured introns, indicating extensive, long term adaptation to functioning in eukaryotic cells. Biochemical and cellular evidence show that HERMES employ non-coding RNAs encoded adjacent to the nuclease for RNA-guided cleavage of double-stranded DNA. HERMES nucleases contain a re-arranged catalytic site of the RuvC domain, similar to a distinct subset of TnpBs, and lack collateral cleavage activity. We demonstrate that HERMES can be harnessed for genome editing in human cells, highlighting the potential of these widespread eukaryotic RNA-guided nucleases for biotechnology applications.
Implicit motor adaptation patterns in a redundant motor task manipulating a stick with both hands
Authors: Kobayashi Toshiki , Nozaki Daichi
Published: June 2023

The remarkable ability of the motor system to adapt to novel environments has traditionally been investigated using kinematically non-redundant tasks, such as planar reaching movements. This limitation prevents the study of how the motor system achieves adaptation by altering the movement patterns of our redundant body. To address this issue, we developed a redundant motor task in which participants reached for targets with the tip of a virtual stick held with both hands. Despite the redundancy of the task, participants consistently employed a stereotypical strategy of flexibly changing the tilt angle of the stick depending on the direction of tip movement. Thus, this baseline relationship between tip-movement direction and stick-tilt angle constrained both the physical and visual movement patterns of the redundant system. Our task allowed us to systematically investigate how the motor system implicitly changed both the tip-movement direction and the stick-tilt angle in response to imposed visual perturbations. Both types of perturbations, whether directly affecting the task (tip-movement direction) or not (stick-tilt angle around the tip), drove adaptation, and the patterns of implicit adaptation were guided by the baseline relationship. Consequently, tip-movement adaptation was associated with changes in stick-tilt angle, and intriguingly, even seemingly ignorable stick-tilt perturbations significantly influenced tip-movement adaptation, leading to tip-movement direction errors. These findings provide a new understanding that the baseline relationship plays a crucial role not only in how the motor system controls movement of the redundant system, but also in how it implicitly adapts to modify movement patterns.
Defining the molecular correlate of arteriolar hyalinosis in kidney disease progression by integration of single cell transcriptomic analysis and pathology scoring
Authors: Menon Rajasree , Otto Edgar A. , Barisoni Laura , Melo Ferreira Ricardo , Limonte Christine P. , Godfrey Bradley , Eichinger Felix , Nair Viji , Naik Abhijit S. , Subramanian Lalita , D’Agati Vivette , Henderson Joel M. , Herlitz Leal , Kiryluk Krzysztof , Moledina Dennis G. , Moeckel Gilbert W. , Palevsky Paul M. , Parikh Chirag R. , Randhawa Parmjeet , Rosas Sylvia E. , Rosenberg Avi Z. , Stillman Isaac , Toto Robert , Torrealba Jose , Vazquez Miguel A. , Waikar Sushrut S. , Alpers Charles E. , Nelson Robert G. , Eadon Michael T. , Kretzler Matthias , Hodgin Jeffrey B. ,   Kidney Precision Medicine Project (KPMP),   Nephrotic Syndrome Study Network (NEPTUNE)
Published: June 2023

Arteriolar hyalinosis in kidneys is an independent predictor of cardiovascular disease, the main cause of mortality in chronic kidney disease (CKD). The underlying molecular mechanisms of protein accumulation in the subendothelial space are not well understood. Using single cell transcriptomic data and whole slide images from kidney biopsies of patients with CKD and acute kidney injury in the Kidney Precision Medicine Project, the molecular signals associated with arteriolar hyalinosis were evaluated. Co-expression network analysis of the endothelial genes yielded three gene set modules as significantly associated with arteriolar hyalinosis. Pathway analysis of these modules showed enrichment of transforming growth factor beta / bone morphogenetic protein (TGFβ / BMP) and vascular endothelial growth factor (VEGF) signaling pathways in the endothelial cell signatures. Ligand-receptor analysis identified multiple integrins and cell adhesion receptors as over-expressed in arteriolar hyalinosis, suggesting a potential role of integrin-mediated TGFβ signaling. Further analysis of arteriolar hyalinosis associated endothelial module genes identified focal segmental glomerular sclerosis as an enriched term. On validation in gene expression profiles from the Nephrotic Syndrome Study Network cohort, one of the three modules was significantly associated with the composite endpoint (> 40% reduction in estimated glomerular filtration rate (eGFR) or kidney failure) independent of age, sex, race, and baseline eGFR, suggesting poor prognosis with elevated expression of genes in this module. Thus, integration of structural and single cell molecular features yielded biologically relevant gene sets, signaling pathways and ligand-receptor interactions, underlying arteriolar hyalinosis and putative targets for therapeutic intervention.
Decoding Phase Separation of Prion-Like Domains through Data-Driven Scaling Laws
Authors: Maristany M. Julia , Aguirre Gonzalez Anne , Espinosa Jorge R. , Huertas Jan , Collepardo-Guevara Rosana , Joseph Jerelle A.
Published: June 2023

Proteins containing prion-like low complexity domains (PLDs) are common drivers of the formation of biomolecular condensates and are prone to misregulation due to amino acid mutations. Here, we exploit the accuracy of our residue-resolution coarse-grained model, Mpipi, to quantify the impact of amino acid mutations on the stability of 140 PLD mutants from six proteins (hnRNPA1, TDP43, FUS, EWSR1, RBM14, and TIA1). Our simulations reveal the existence of scaling laws that quantify the range of change in the critical solution temperature of PLDs as a function of the number and type of amino acid sequence mutations. These rules are consistent with the physicochemical properties of the mutations and extend across the entire family tested, suggesting that scaling laws can be used as tools to predict changes in the stability of PLD condensates. Our work offers a quantitative lens into how the emergent behavior of PLD solutions varies in response to physicochemical changes of single PLD molecules.
Fluorochrome-dependent specific changes in spectral profiles using different compensation beads or human cells in full spectrum cytometry
Authors: Shevchenko Yaroslava , Lurje Isabella , Tacke Frank , Hammerich Linda
Published: June 2023

Full spectrum flow cytometry is a powerful tool for immune monitoring on a single-cell level and with currently available machines, panels of 40 or more markers per sample are possible. However, with an increased panel size, spectral unmixing issues arise, and appropriate single stain reference controls are required for accurate experimental results and to avoid unmixing errors. In contrast to conventional flow cytometry, full spectrum flow cytometry takes into account even minor differences in spectral signatures and requires the full spectrum of each fluorochrome to be identical in the reference control and the fully stained sample to ensure accurate and reliable results. In general, using the cells of interest is considered optimal, but certain markers may not be expressed at sufficient levels to generate a reliable positive control. In this case, compensation beads show some significant advantages as they bind a consistent amount of antibody independent of its specificity. In this study, we evaluated two types of manufactured compensation beads for use as reference controls for full spectrum cytometry and compared them to human and murine primary leukocytes. While most fluorochromes show the same spectral profile on beads and cells, we demonstrate that specific fluorochromes show a significantly different spectral profile depending on which type of compensation beads is used, and some fluorochromes should be used on cells exclusively. Finally, we provide a list of appropriate reference controls for 30 of the most commonly used and commercially available fluorochromes.