bluuebunny/crossref_metadata_2025 huggingface dataset:
Immediate predation risk alters the relationship between potential and realised selection on male traits in the Trinidad guppy Poecilia reticulata
Authors: Glavaschi Alexandra , Cattelan Silvia , Devigili Alessandro , Pilastro Andrea
Published: April 2022

Predation risk perception can alter mating behaviours in males and females, but the consequences for sexual selection remain underexplored. We have previously shown that in experimental populations of Trinidadian guppies Poecilia reticulata the opportunity for sexual selection (i.e. the variance in male reproductive fitness) was higher following exposure to a simulated risk of predation than in a no-risk condition. We build upon this result by exploring whether imminent predation risk affects: 1) the relationship between the opportunity for sexual selection and the actual strength of selection on male traits and 2) the traits contributing to male fitness, and he shape of selection on these traits. While predation risk increased the variance in male fitness, realised selection on traits remained unaffected. Pre- and postcopulatory traits follow complex patterns of nonlinear and correlational selection in both treatments. Differences in selection gradients deviate from predictions based on evolutionary responses to predation, the most notable being stronger selection on courtship rate under predation risk. Our results demonstrate that the operation of sexual selection can be altered by perception of an imminent predation risk and reinforce the notion that both trait-based and variance-based metrics should be employed for an informative quantification.
A paracrine circuit of IL-1β/IL-1R1 between myeloid and tumor cells drives glioblastoma progression
Authors: Chen Zhihong , Giotti Bruno , Kaluzova Milota , Herting Cameron J. , Pinero Gonzalo , Vallcorba Montse Puigdelloses , Cristea Simona , Ross James L. , Ackley James , Maximov Victor , Szulzewsky Frank , Marquez-Ropero Mar , Angione Angelo , Nichols Noah , Tsankova Nadejda , Michor Franziska , Shayakhmetov Dmitry M. , Gutmann David H. , Tsankov Alexander M. , Hambardzumyan Dolores
Published: April 2022

Monocytes and monocyte-derived macrophages (MDM) from blood circulation infiltrate and promote glioblastoma growth. Here we discover that glioma cells induce the expression of potent pro-inflammatory cytokine IL-1β in MDM, which engages IL-1R1 in glioma cells, activates NF-κB pathway, and subsequently leads to the induction of monocyte chemoattractant proteins (MCPs). Thus, a feedforward paracrine circuit of IL-1β/IL-1R1 between the tumors and MDM creates an interdependence driving glioblastoma progression. Locally antagonizing IL-1β/IL-1R1 leads to reduced MDM infiltration, diminished tumor growth, reduced exhausted CD8+T cells, and thereby extends the survival of tumor-bearing mice. In contrast to IL-1β, IL-1a exhibits anti-tumor effects. Genetic deletion ofIl1ais associated with decreased recruitment of lymphoid cells and loss of interferon (IFN) signaling in various immune populations and subsets of malignant cells. IL-1β antagonism of IL-1β should be considered as an effective anti-glioblastoma therapy.

Graphical Abstract
Genetically encoded sensors for analysing neurotransmission among synaptically-connected neurons
Authors: Shindo Yutaka , Ashida Keita , Masamoto Kazuto , Takuwa Hiroyuki , Takahashi Manami , Higuchi Makoto , Ide Ryuto , Hotta Kohji , Oka Kotaro
Published: April 2022

Anatomical connectome mapping in small areas of the nervous system as well as large-scale detection of neuronal activity patterns have been respectively achieved; however, it is still challenging to evaluate the functional connections among anatomically-connected neurons in a large-scale nervous system. We have developed a novel method to visualize neurotransmission named Split Protein HEmispheres for REconstitution (Sphere). By splitting a sensor into two fragments and expressing them in pre- and postsynaptic neurons separately, functional neurotransmitter sensors can be reconstituted only at the synapses between those neurons. We developed a Sphere-SF-iGluSnFR to measure glutamate levels, and further demonstrated that this system is functional in cultured cells, worms, and mouse brains. Moreover, this system is applicable to sensors other than glutamate, and colour variants have also been developed. This could allow for brain-wide imaging of functional synaptic transmission among particular neurons and identification of important neuronal circuits in the nervous system.
Flexible color segmentation of biological images with the R package recolorize
Authors: Weller Hannah I. , Van Belleghem Steven M. , Hiller Anna E. , Lord Nathan P.
Published: April 2022

Color is an important source of biological information in fields ranging from disease ecology to sexual selection. Despite its importance, most metrics for color are restricted to point measurements. Methods for moving beyond point measurements rely on color maps, where every pixel in an image is assigned to one of a set of discrete color classes (color segmentation). Manual methods for color segmentation are slow and subjective, while existing automated methods often fail due to biological variation in pattern, technical variation in images, and poor scalability for batch clustering. As a result, color segmentation is the common bottleneck step for a majority of existing downstream analyses. Here we presentrecolorize, an R package for color segmentation that succeeds in many cases where existing methods fail.Recolorizehas three major components: (1) an effective two-part clustering algorithm where color distributions are binned and combined according to perceived similarity in a frequency-independent manner; (2) a toolkit for minor manual adjustments to automatic output where needed; and (3) flexible export options. This paper illustrates how to userecolorizeand compares it to existing methods, including examples where we segment formerly intractable images, and demonstrates the downstream use of methods that rely on color maps.
Structural and Preliminary Biochemical Characterization of MppQ, a PLP-Dependent Aminotransferase from Streptomyces hygroscopicus
Authors: Vuksanovic Nemanja , Serrano Dante A. , Schwabacher Alan W. , Silvaggi Nicholas R.
Published: April 2022

MppQ is an enzyme of unknown function from Streptomyces hygroscopicus that is involved in the biosynthesis of the nonproteinogenic amino acid L-enduracididine (L-End). Since L-End is a component of several peptides showing high activity against methicillin-resistant Staphylococcus aureus (MRSA), a complete understanding of its biosynthetic pathway is of utmost importance for developing chemoenzymatic routes for syntheses of novel antibiotics. In this work, we report high-resolution X-ray crystal structures of MppQ complexed with pyridoxal-5’-phosphate (PLP) and pyridoxamine-5’-phosphate (PMP). The structure of MppQ shares a fold with known Type I PLP-dependent aminotransferases, consisting of an N-terminal extension, large domain, and a small domain. We also report the first functional characterization of MppQ, which we incubated with enzymatically produced 2-ketoenduracidine and observed conversion to L-End via mass spectroscopy. Additionally, we have observed that MppQ has a relatively high affinity for 2-ketoarginine, a shunt product in the L-End biosynthetic pathway, indicating a possible role of MppQ in increasing efficiency of L-End biosynthesis by converting 2-ketoarginine back to the starting material, L-arginine.
The trustworthiness and impact of trial preprints for COVID-19 decision-making: A methodological study
Authors: Zeraatkar Dena , Pitre Tyler , Leung Gareth , Cusano Ellen , Argawal Arnav , Khalid Faran , Escamilla Zaira , Cooper Matthew , Ghadimi Maryam , Wang Ying , Verdugo Francisca , Rada Gabriel , Kum Elena , Qasim Anila , Bartoszko Jessica J , Siemieniuk Reed , Patel Chirag J , Guyatt Gordon , Brignardello-Petersen Romina
Published: April 2022

Purpose: To assess the trustworthiness and impact of preprint trial reports during the COVID-19 pandemic.
Data sources: WHO COVID-19 database and the L-OVE COVID-19 platform by the Epistemonikos Foundation (up to August 3rd, 2021)
Design: We compare the characteristics of COVID-19 trials with and without preprints, estimate time to publication of COVID-19 preprint reports, describe discrepancies in key methods and results between preprint and published trial reports, report the number of retracted preprints and publications, and assess whether including versus excluding preprint reports affects meta-analytic estimates and the certainty of evidence. For the effects of eight therapies on mortality and mechanical ventilation, we performed meta-analyses including preprints and excluding preprints at 1 month, 3 months, and 6 months after the first trial addressing the therapy became available either as a preprint or publication (120 meta-analyses in total).
Results: We included 356 trials, 101 of which are only available as preprints, 181 as journal publications, and 74 as preprints first and subsequently published in journals. Half of all preprints remain unpublished at six months and a third at one year. There were few important differences in key methods and results between trial preprints and their subsequent published reports. We identified four retracted trials, three of which were published in peer-reviewed journals. With two exceptions (2/60; 3.3%), point estimates were consistent between meta-analyses including versus excluding preprints as to whether they indicated benefit, no appreciable effect, or harm. There were nine comparisons (9/60; 15%) for which the rating of the certainty of evidence differed when preprints were included versus excluded, for four of these comparisons the certainty of evidence including preprints was higher and for five of these comparisons the certainty of evidence including preprints was lower.
Limitations: The generalizability of our results is limited to COVID-19. Preprints that are subsequently published in journals may be the most rigorous and may not represent all trial preprints.
Conclusion: We found no compelling evidence that preprints provide less trustworthy results than published papers. We show that preprints remain the only source of findings of many trials for several months, for a length of time that is unacceptable in a health emergency. We show that including preprints may affect the results of meta-analyses and the certainty of evidence. We encourage evidence users to consider data from preprints in contexts in which decisions are being made rapidly and evidence is being produced faster than can be peer-reviewed.
Self-supervised neural network improves tri-exponential intravoxel incoherent motion model fitting in non-alcoholic fatty liver disease
Authors: Troelstra Marian A. , van Dijk Anne-Marieke , Witjes Julia J. , Mak Anne Linde , Zwirs Diona , Runge Jurgen H. , Verheij Joanne , Beuers Ulrich H. , Nieuwdorp Max , Holleboom Adriaan G. , Nederveen Aart J. , Gurney-Champion Oliver J.
Published: April 2022

Neural network generated intravoxel incoherent motion (IVIM) parameter maps are visually more detailed, less noisy and have a higher test-retest repeatability than conventional least-squares (LSQ) generated images. Recent literature suggests that tri-exponential models may fit liver IVIM data more accurately than conventional bi-exponential models, warranting investigation into the use of a neural network (NN) to estimate tri-exponential IVIM parameters. Here, we developed a tri-exponential IVIM unsupervised physics-informed deep neural network (IVIM3-NET), assessed its performance in non-alcoholic fatty liver disease (NAFLD) and compared outcomes with bi-exponential LSQ and NN fits and tri-exponential LSQ fits. Scanning was performed using a 3.0T free-breathing multi-slice diffusion-weighted single-shot echo-planar imaging sequence with 18 b-values. Images were analysed for visual quality, comparing the bi- and tri-exponential IVIM models for LSQ fits and NN fits using parameter-map signal-to-noise ratios (SNR) and adjusted R2. IVIM parameters were compared to histological fibrosis, disease activity and steatosis grades. Parameter map quality improved with bi- and tri-exponential NN approaches, with average parameter-map SNR increasing from 3.38 to 5.59 and 2.45 to 4.01 for bi- and tri-exponential LSQ and NN models respectively. In 33 out of 36 patients, the tri-exponential model exhibited higher adjusted R2 values than the bi-exponential model. Correlating IVIM data to liver histology showed that the bi- and tri-exponential NN outperformed both LSQ models for the majority of IVIM parameters (10 out of 15 significant correlations). Overall, our results support the use of a tri-exponential IVIM model in NAFLD. We show that the IVIM3-NET can be used to improve image quality compared to a tri-exponential LSQ fit and provides promising correlations with histopathology.
Overactive mitochondrial DNA replisome causes neonatal heart failure via ferroptosis
Authors: Landoni Juan C. , Laalo Tuomas , Goffart Steffi , Kivelä Riikka , Skube Karlo , Nieminen Anni I. , Wickström Sara A. , Stewart James , Suomalainen Anu
Published: April 2022

Increasing mitochondrial DNA (mtDNA) replication and amount have been proposed as therapeutic approaches for mitochondrial dysfunction, but also as a mechanism of premature aging. We addressed this fascinating paradox by enhancing mtDNA replication via two mechanisms: increasing both mtDNA replication licensing and processivity. We crossed mice overexpressing Twinkle helicase (boosting mtDNA replication initiation) with mtDNA mutator mice (exonuclease-deficient mtDNA replicase, increasing mtDNA mutagenesis and replication processivity). The former model is asymptomatic by two years of age, whereas the latter manifests with progeroid symptoms at six months. Surprisingly, the double transgenics demonstrate postnatally halted growth and devastating cardiomyopathy, fatal within weeks. The mice show high mtDNA replication preventing cardiac maturation and the postnatal shift to oxidative metabolism, causing ferroptotic cardiomyocyte death. Our findings emphasize the critical importance of mtDNA replisome regulation for perinatal cardiac maturation. Furthermore, the data implicate ferroptosis as a cell death mechanism for neonatal mitochondrial cardiomyopathies.
Colouring coral larvae for tracking dispersal
Authors: Doropoulos Christopher , Roff George
Published: April 2022

Ecologists have long sought to understand larval dispersal characteristics of benthic marine invertebrates. Direct quantification of coral larvae dispersal has proven challenging, in part due to their complex life-history, minute size, and widespread dispersal at the scale of kilometres. Instead, indirect methods such as particle modelling, chemical signatures, and genetic correlation are often used in dispersal studies.

Here, we develop a direct method of quantifying larval dispersal by applying vital stains to coral larvae, allowing differentiation and direct tracking of millions of larvae from the pelagic dispersal stage through to the sedentary stages of attachment and metamorphosis on coral reefs.

Neutral red and Nile blue stains were extremely effective at staining coral larvae, while alizarin red and calcein blue showed no visible results. Differences in toxicity to vital stains was noted among species, withAcroporaspp. exhibiting decreased larval survival and settlement, while Merulinidae spp. were unaffected. By experimenting with different incubation times and concentrations, our results indicate that neutral red can be effectively applied for short periods (<20 minutes) at low concentrations (1-100 mg l-1), whereas Nile blue requires longer stain times (>60 minutes) at higher concentrations (100-1000 mg l-1).

The strong colour of both neutral red and Nile blue stains was retained by newly settled larvae in lab settings upwards of five days following settlement, providing a direct method of differentiating between newly settled larvae on reefs. Field-validation of Nile blue applied to coral larvae from wild-captured coral slicks demonstrates the efficacy of staining across a diverse range of coral taxa.

Vital staining provides a simple, rapid (<60 mins), and low cost (<AUD$0.00001 per larva) method of colouring coral larvae that allows for direct tracking of dispersal and recruitment in studies of reef connectivity and restoration.
Effect of LSD and music on the time-varying brain dynamics
Authors: Adamska Iga , Finc Karolina
Published: April 2022

Rationale

Psychedelics are getting closer to being widely used in clinical treatment. Music is known as a key element of psychedelic-assisted therapy due to its psychological effects, specifically on the emotion, meaning-making and sensory processing. However, there is still a lack of understanding in how psychedelics influence brain activity in experimental settings involving music listening.

Objectives

The main goal of our research is to investigate the effect of music, as a part of “setting”, on the brain states dynamics after lysergic acid diethylamide (LSD) intake.

Methods

We used an open dataset, where a group of 15 participants underwent two functional MRI scanning sessions under LSD and placebo influence. Every scanning session contained three runs: two resting-state runs separated by one run with music listening. We applied K-Means clustering to identify the repetitive patterns of brain activity, so-calledbrain states. For further analysis, we calculated states’ dwell time, fractional occupancy and transition probability.

Results

The interaction effect of music and psychedelics led to change in the time-varying brain activity of the task-positive state. LSD, regardless of the music, affected the dynamics of the state of combined activity of DMN, SOM and VIS networks. Crucially, we observed that the music itself could potentially have a long-term influence on the resting-state, in particular on states involving task-positive networks.

Conclusions

This study indicates that music, as a crucial element of “setting”, can potentially have an influence on the subject’s resting-state during psychedelic experience. Further studies should replicate these results on a larger sample size.
A Self-Purifying Microfluidic System for Identifying Drugs Acting Against Adult Schistosomes
Authors: Girod Vincent , Ghoris Marie-José , Caby Stéphanie , Melnyk Oleg , Dissous Colette , Senez Vincent , Vicogne Jérôme
Published: April 2022

The discovery of novel antihelminthic molecules to combat the development and spread of schistosomiasis, a disease caused by several Schistosoma flatworm species, mobilizes significant research efforts worldwide. In the absence of reliable and practical biochemical assays for measuring the viability of adult worms, the antischistosomicidal activity of molecules is usually evaluated by a detailed microscopic observation of worm mobility and/or integrity upon drug exposure. These assays have the disadvantage of being inacurate, subjective, biased by the limited in vitro worm viability and difficult to integrate at high density. We describe here a self-purifiying microfluidic system enabling the selection of healthy adult worms and the identification of molecules acting on the parasite. The worms are assayed in a dynamic environment that eliminates unhealthy worms that cannot attach firmly to the chip walls prior to being exposed to the drug. The detachment of the worms is also used as second step readout for identifying active compounds. We have validated this new fluidic screening approach using the two major antihelmintic drugs, Praziquantel and Artemisinin. The reported dynamic system is simple to produce and to parallelize. Importantly, it enables a quick, sensitive and reliable detection of antischistosomal compounds in no more than one day. This system can potentially be modified in the future to better mimic the natural habitat of the parasite.
Cognitive dysfunction and anxiety resulting from synaptic downscaling, hippocampal atrophy and ventricular enlargement with intracerebroventricular streptozotocin injection in male Wistar rats
Authors: Roy Avishek , Sharma Sakshi , Nag Tapas Chandra , Katyal Jatinder , Gupta Yogendra Kumar , Jain Suman
Published: April 2022

Insulin-resistant brain state is proposed to be the early sign of Alzheimer’s disease(AD), which can be studied in intracerebroventricular streptozotocin (ICV-STZ) rodent model. ICV-STZ is reported to induce sporadic AD with the majority of the disease hallmarks as phenotype. On the other hand, Available experimental evidence has used varying doses of STZ (<1 to 3mg/kg) and studied its effect for different study durations, ranging from 14-270 days. Though these studies suggest 3mg/kg of ICV-STZ to be the optimum dose for progressive pathogenesis, the reason for such is elusive.

Here we sought to investigate the mechanism of action of 3mg/kg ICV-STZ on cognitive and non-cognitive aspects at a follow-up interval of two weeks for two months. On 60th day, we examined layer thickness, cell density, ventricular volume, spine density, protein expression related to brain metabolism and mitochondrial function by histological examination. Findings suggest progressive loss of spatial, episodic, avoidance memory with increase in anxiety in a span of two month. Furthermore, hippocampal neurodegeneration, ventricular enlargement, diffused amyloid plaque deposition, loss of spine in dentate gyrus and imbalance in energy homeostasis was found on 60th day post injection. Interestingly, AD rats showed a uniform fraction of time spent in four quadrants of water maze with change in strategy when they were exposed to height. Our findings reveal that ICV-STZ injection at a dose of 3mg/kg can cause cognitive and neuropsychiatric abnormalities due to structural loss both at neuronal as well as synaptic level, which is tightly associated with change in neuronal metabolism.
The genetic architectures of vine and skin maturity in tetraploid potato
Authors: Caraza-Harter Maria V. , Endelman Jeffrey B.
Published: April 2022

Potato vine and skin maturity, which refer to foliar senescence and adherence of the tuber periderm, respectively, are both important to production and therefore breeding. Our objective was to investigate the genetic architectures of these traits in a genome-wide association panel of 586 genotypes, and through joint linkage mapping in a half-diallel subset (N = 397). Skin maturity was measured by image analysis after mechanized harvest 120 days after planting. To correct for the influence of vine maturity on skin maturity under these conditions, the former was used as a covariate in the analysis. The genomic heritability based on a 10K SNP array was 0.33 for skin maturity vs. 0.46 for vine maturity. Only minor QTL were detected for skin maturity, the largest being on chromosome 9 and explaining 8% of the variation. As in many previous studies, S. tuberosum Cycling DOF Factor 1 (CDF1) had a large influence on vine maturity, explaining 33% of the variation in the panel as a bi-allelic SNP and 44% in the half-diallel as a multi-allelic QTL. From the estimated effects of the parental haplotypes in the half-diallel and prior knowledge of the allelic series for CDF1, the CDF1 allele for each haplotype was predicted and ultimately confirmed through whole-genome sequencing. The ability to connect statistical alleles from QTL models with biological alleles based on DNA sequencing represents a new milestone in genomics-assisted breeding for tetraploid species.
All-optical visualization of specific molecules in the ultrastructural context of brain tissue
Authors: M’Saad Ons , Kasula Ravikiran , Kondratiuk Ilona , Kidd Phylicia , Falahati Hanieh , Gentile Juliana E. , Niescier Robert F. , Watters Katherine , Sterner Robert C. , Lee Seong , Liu Xinran , De Camilli Pietro , Rothman James E. , Koleske Anthony J. , Biederer Thomas , Bewersdorf Joerg
Published: April 2022

Understanding the molecular anatomy and neural connectivity of the brain requires imaging technologies that can map the 3D nanoscale distribution of specific proteins in the context of brain ultrastructure. Light and electron microscopy (EM) enable visualization of either specific labels or anatomical ultrastructure, but combining molecular specificity with anatomical context is challenging. Here, we present pan-Expansion Microscopy of tissue (pan-ExM-t), an all-optical mouse brain imaging method that combines ∼24-fold linear expansion of biological samples with fluorescent pan-staining of protein densities (providing EM-like ultrastructural context), and immunolabeling of protein targets (for molecular imaging). We demonstrate the versatility of this approach by imaging the established synaptic markers Homer1, Bassoon, PSD-95, Synaptophysin, the astrocytic protein GFAP, myelin basic protein (MBP), and anti-GFP antibodies in dissociated neuron cultures and mouse brain tissue sections. pan-ExM-t reveals these markers in the context of ultrastructural features such as pre and postsynaptic densities, 3D nanoarchitecture of neuropil, and the fine structures of cellular organelles. pan-ExM-t is adoptable in any neurobiological laboratory with access to a confocal microscope and has therefore broad applicability in the research community.

Highlights

pan-ExM-t visualizes proteins in the context of synaptic ultrastructure

Lipid labeling in pan-ExM-t reveals organellar and cellular membranes

All-optical, easily accessible alternative to correlative light/electron microscopy

High potential for high throughput connectomics studies
Breast cancer stem cell-derived tumors escape from γδ T cell immunosurveillance in vivo by modulating γδ T cell ligands
Authors: Raute Katrin , Strietz Juliane , Andrieux Geoffroy , Thomas Oliver S. , Kistner Klaus M. , Zintchenko Marina , Aichele Peter , Zhou Houjiang , Weber Wilfried , Boerries Melanie , Swamy Mahima , Maurer Jochen , Minguet Susana
Published: April 2022

Triple negative breast cancer (TNBC) lacks targeted therapy options. TNBC is enriched in breast cancer stem cells (BCSCs), which play a key role in metastasis, chemoresistance, relapse and mortality. γδ T cells hold great potential in immunotherapy against cancer, and might be an alternative to target TNBC. γδ T cells are commonly observed to infiltrate solid tumors and have an extensive repertoire of tumor sensing, recognizing stress-induced molecules and phosphoantigens (pAgs) on transformed cells. We show that patient-derived triple negative BCSCs are efficiently recognized and killed by ex vivo expanded γδ T cells from healthy donors. Orthotopically xenografted BCSCs, however, were refractory to γδ T cell immunotherapy. Mechanistically, we unraveled concerted differentiation and immune escape: xenografted BCSCs lost stemness, expression of γδ T cell ligands, adhesion molecules and pAgs, thereby evading immune recognition by γδ T cells. Indeed, neither pro-migratory engineered γδ T cells, nor anti-PD-1 checkpoint blockade significantly prolonged overall survival of tumor-bearing mice. BCSC immune escape was independent of the immune pressure exerted by the γδ T cells, and could be pharmacologically reverted by Zoledronate or IFN-α treatment. These results pave the way for novel combinatorial immunotherapies for TNBC.
Kidins220 regulates the development of B cells bearing the λ light chain
Authors: Schaffer Anna-Maria , Fiala Gina J. , Hils Miriam , Natali Eriberto Noel , Babrak Lmar , Herr Laurenz A. , Rizzi Marta , Miho Enkelejda , Schamel Wolfgang , Minguet Susana
Published: April 2022

The ratio between Igκ and Igλ light chain (LC)-expressing B cells varies considerably between species. We recently identified Kinase D-interacting substrate of 220 kDa (Kidins220) as an interaction partner of the BCR. In vivo ablation of Kidins220 in B cells resulted in a marked reduction of λLC-expressing B cells. Kidins220 knockout B cells fail to open and recombine the genes of the λLC locus, even in genetic scenarios where the κLC genes cannot be rearranged or where the κLC confers autoreactivity. κLC gene recombination and expression in Kidins220-deficient B cells is normal. Kidins220 regulates the development of λLC B cells by enhancing the survival of developing B cells and thereby extending the time-window in which the λLC locus opens and the genes are rearranged and transcribed. Further, our data suggest that Kidins220 guarantees optimal pre-BCR and BCR signaling to induce λLC locus opening and gene recombination during B cell development and receptor editing.

One Sentence Summary

We demonstrate that the scaffold protein Kidins220 regulates the development of λLC B cells by supporting B cell precursor survival and optimizing pre-BCR and BCR signaling to open, recombine, and transcribe the genes of the λLC locus.
Socially learned arbitrary call use in a wild primate
Authors: Deshpande Adwait , Zuberbuhler Klaus
Published: April 2022

Human speech is an unusually flexible form of primate communication. A limited repertoire of phonemes is assembled into morphemes whose combinations are linked to referents by social learning in culturally specific ways. Non-human primate vocal utterances, in contrast, are drastically less flexible at every level, i.e., acoustic diversity, combinatoriality and referential function. Here, we were interested in whether primate vocal behaviour, despite its inflexible nature, is still amenable to social learning, a well-documented, powerful mechanism in many other aspects of primate behaviour. We provided wild vervet monkeys with social learning opportunities to operate a food dispensing apparatus by uttering specific vocalisations, ‘move-grunts’, that were contextually inappropriate. In two separate experiments, subjects witnessed how another group member produced move-grunts whilst operating a food dispenser. In experiment 1, subjects only heard playbacks of the calls, followed by food release; in experiment 2, they witnessed a complete demonstration video of conspecific including the calls, followed by food release. None of the subjects learned the task in experiment 1, but 1 of 39 subjects, a juvenile female, succeeded in experiment 2 by producing move-grunts at the food dispenser to obtain food rewards. We discuss our results and behavioural observations in relation to the current theory and its eventual implications for reconstructing the evolutionary pathway to human speech.
Re-engineering ofCUP1promoter and Cup2/Ace1 transactivator to convertSaccharomyces cerevisiaeinto a whole-cell eukaryotic biosensor capable of detecting 10 nM of bioavailable copper
Authors: Žunar Bojan , Mosrin Christine , Bénédetti Héléne , Vallée Béatrice
Published: April 2022

While copper is an essential micronutrient and a technologically indispensable heavy metal, it is toxic at high concentrations, harming the environment and human health. Currently, copper is monitored with costly and low-throughput analytical techniques that do not evaluate bioavailability, a crucial parameter which can be measured only with living cells. We overcame these limitations by building upon yeastS. cerevisiae’s native copper response and constructed a promising next-generation eukaryotic whole-cell copper biosensor. We combined a dual-reporter fluorescent system with an engineeredCUP1promoter and overexpressed Cup2 transactivator, constructing through four iterations a total of 16 variants of the biosensor, with the best one exhibiting a linear range of 10-8to 10-3M of bioavailable copper. Moreover, this variant distinguishes itself by superior specificity, detection limit, and linear range, compared to other currently reported eukaryotic and prokaryotic whole-cell copper biosensors. By re-engineering the transactivator, we altered the system’s sensitivity and growth rate, while assessing the performance of Cup2 with heterologous activation domains. Thus, in addition to presenting the next-generation whole-cell copper biosensor, this work urges for an iterative design of eukaryotic biosensors and paves the way toward higher sensitivity through transactivator engineering.

Graphical abstract
Chromatin regulates genome-wide transcription factor binding affinities
Authors: Neikes Hannah K. , Lindeboom Rik G.H. , Gräwe Cathrin , Lamers Lieke A. , Baltissen Marijke P. , Jansen Pascal W.T.C. , van Heeringen Simon J. , Logie Colin , Teichmann Sarah A. , Vermeulen Michiel
Published: April 2022

Transcription factor binding across the genome is regulated by DNA sequence and chromatin features. However, it is not yet possible to quantify the impact of chromatin context on genome-wide transcription factor binding affinities. Here we report the establishment of a method to determine genome-wide absolute apparent binding affinities of transcription factors to native, chromatinized DNA. Our experiments revealed that DNA accessibility is the main determinant of transcription factor binding in the genome, which largely restricts nanomolar affinity binding of YY1, SP1 and MYC/MAX to promoters, while FOXA1 also interacts with non-promoter elements with high affinity. Furthermore, whereas consensus DNA binding motifs for transcription factors are important to establish very high-affinity binding sites, these motifs are not always strictly required to generate nanomolar affinity interactions in the genome. Finally, we uncovered transcription factor concentration dependent binding to specific gene classes, suggesting transcription factor concentration dependent effects on gene expression and cell fate. Importantly, our method adds a quantitative dimension to transcription factor biology which enables stratification of genomic targets based on transcription factor concentration and prediction of transcription factor binding sites under non-physiological conditions, such as disease associated overexpression of (onco)genes.
GoFish: A low-cost, open-source platform for closed-loop behavioural experiments on fish
Authors: Ajuwon Victor , Cruz Bruno F. , Carriço Paulo ,   Champalimaud Foundation Scientific Hardware Platform, Kacelnik Alex , Monteiro Tiago
Published: April 2022

Fish are the most species-rich vertebrate group, displaying vast ecological, anatomical and behavioural diversity, and therefore are of major interest for the study of behaviour and its evolution. Despite this, with respect to other vertebrates, fish are relatively underrepresented in behavioural research. This is partly due to the difficulty of implementing stimuli, manipulanda, and data recording underwater, meaning that this is frequently done with gates to control subjects, physical displays as stimuli, and visual annotation of videos to record data. To overcome these restrictions we developed GoFish, a fully-automated platform for behavioural experiments. GoFish includes real-time video tracking of subjects, presentation of stimuli in a computer screen, an automatic feeder device, and closed-loop control of task contingencies and data acquisition. The design and software components of the platform are freely available, while the hardware is widely available and relatively inexpensive. The control software, Bonsai, is user-friendly and supported by a growing community of users. As an illustration and test of its use, we present the results of 2 experiments on discrimination learning, reversal, and choice in goldfish (Carassius auratus). GoFish enables the relatively easy implementation of high-throughput tasks and the acquisition of rich behavioural data. Our platform has the potential to become a widely used tool that facilitates complex behavioural experiments in aquatic species.
A computational modeling of primary-microRNA expression
Authors: Zheng Hansi , Wang Saidi , Li Xiaoman , Hu Haiyan
Published: April 2022

MicroRNAs (miRNAs) play crucial roles in gene regulation. Most studies so far focus on mature miRNAs, which leaves many gaps in our knowledge in primary miRNAs (pri-miRNA). To fill these gaps, we attempted to model the expression of pri-miRNAs in 1829 primary cell types and tissues in this study. We demonstrated that the expression of their associated mRNAs could model the expression of the pri-miRNAs well. These associated mRNAs are different from their corresponding target mRNAs and are enriched with specific functions. The majority of the associated mRNAs of a miRNA are shared across conditions, although a fraction of the associated mRNAs are condition-specific. Our study shed new light on the understanding of miRNA biogenesis and general gene transcriptional regulation.
Differential pathogenesis of SARS-CoV-2 variants of concern in human ACE2-expressing mice
Authors: Natekar Janhavi Prasad , Pathak Heather , Stone Shannon , Kumari Pratima , Sharma Shaligram , Arora Komal , Rothan Hussin Alwan , Kumar Mukesh
Published: April 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a pandemic resulting in millions of deaths worldwide. Increasingly contagious variants of concern (VoC) have fueled recurring global infection waves. A major question is the relative severity of disease caused by the previous and currently circulating variants of SARS-CoV-2. In this study, we evaluated the pathogenesis of SARS-CoV-2 variants in human ACE-2-expressing (K18-hACE2) mice. Eight-week-old K18-hACE2 mice were inoculated intranasally with a representative virus from the original B.1 lineage, or the emerging B.1.1.7 (alpha), B.1.351 (beta), B.1.617.2 (delta) or B.1.1.529 (omicron) lineages. We also infected a group of mice with the mouse-adapted SARS-CoV-2 (MA10). Our results demonstrate that B.1.1.7, B.1.351 and B.1.617.2 viruses are significantly more lethal than B.1 strain in K18-hACE2 mice. Infection with B.1.1.7, B.1.351 and B.1.617.2 variants resulted in significantly higher virus titers in the lungs and brain of mice compared to the B.1 virus. Interestingly, mice infected with the B.1.1.529 variant exhibited less severe clinical signs and high survival rate. We found that B.1.1.529 replication was significantly lower in the lungs and brain of infected mice in comparison to other VoC. Transcription levels of cytokines and chemokines in the lungs of the B.1.1.529-infected mice were significantly less when compared to those challenged with the B.1.1.7 virus. Together, our data provide insights into the pathogenesis of the previous and circulating SARS-CoV-2 VoC in mice.
Drug addiction mutations unveil a methylation ceiling in EZH2-mutant lymphoma
Authors: Kwok Hui Si , Freedy Allyson M. , Siegenfeld Allison P. , Morriss Julia W. , Waterbury Amanda L. , Kissler Stephen M. , Liau Brian B.
Published: April 2022

Cancer mutations in Polycomb Repressive Complex 2 (PRC2) drive aberrant epigenetic states. Although therapies inhibiting the PRC2 enzymatic component EZH2 are FDA-approved, oncogene-specific dependencies remain to be discovered. Here, we identify mutations that confer both resistance and drug addiction to PRC2 inhibitors in EZH2-mutant lymphoma, resulting in cancer cells that paradoxically depend on drug for survival. Drug addiction is mediated by hypermorphic mutations in the CXC domain of EZH2, which maintain H3K27me3 levels even in the presence of PRC2 inhibitors. Drug removal leads to overspreading of H3K27me3, surpassing a repressive methylation ceiling compatible with lymphoma cell survival. Activating EZH2 cancer mutations establish an epigenetic state precariously close to this ceiling, which we show can be breached by inhibition of SETD2, a PRC2 antagonist, to block lymphoma growth. More broadly, we highlight how approaches to identify drug addiction mutations can be leveraged to discover cancer vulnerabilities.
Molecular-Dynamics Simulation Methods for Macromolecular Crystallography
Authors: Wych David C. , Aoto Phillip C. , Vu Lily , Wolff Alexander M. , Mobley David L. , Fraser James S. , Taylor Susan S. , Wall Michael E.
Published: April 2022

To assess the potential benefits of molecular-dynamics (MD) simulations for macromolecular crystallography (MX), we performed room-temperature X-ray diffraction studies of the catalytic subunit of mouse protein kinase A (PKA-C). We then performed crystalline MD simulations of PKA-C, computed simulated electron densities from the water, protein, and ion components of the MD simulations, and carefully compared them to the initial crystal structure. The results led to the development of an MD-MX analysis procedure and several associated methods: 1)density comparisonto evaluate consistency between the MD and the initial crystal structure model; 2)water buildingto generate alternative solvent models; and 3)protein remodelingto improve the crystal structure where interpretation of density is unclear. This procedure produced a revised structure of PKA with a new ordered water model and a modified protein structure. The revisions yield new insights into PKA mechanisms, including: a sensitivity of the His294 conformation to protonation state, with potential consequences for regulation of substrate binding; a remodeling of the Lys217 side chain along with a bound phosphate; an alternative conformation for Lys213 associated with binding to the regulatory subunit; and an alternative conformation for catalytic base Asp166 and nearby waters, suggesting a mechanism of progression of the phosphotransfer reaction via changes in Mg2+coordination. Based on the benefits seen applying these methods to PKA, we recommend incorporating our MD-MX procedure into MX studies, to decide among ambiguous interpretations of electron density that occur, inevitably, as part of standard model refinement.
Climate change will redefine taxonomic, functional, and phylogenetic diversity patterns of Odonata in space and time
Authors: Cancellario Tommaso , Miranda Rafael , Baquero Enrique , Fontaneto Diego , Martínez Alejandro , Mammola Stefano
Published: April 2022

Climate change is rearranging the mosaic of biodiversity on our planet. These broad-scale species re-distributions will affect the structure of communities across multiple biodiversity facets (taxonomic, phylogenetic, and functional diversity). The current challenges to understand such effects involve focusing on organisms other than vertebrates and considering the signature of species redistribution on phylogenetic and functional diversity in addition to species composition. Using European dragonflies and damselflies (Odonata), we asked: i) how climate change will redefine taxonomic, phylogenetic, and functional diversity at continental scales; ii) which traits will mediate species’ response to global change; and iii) whether this response will be conserved across the phylogeny. First, we constructed stacked species distribution models for 107 species of Odonata under current and future climate conditions. Then, we quantified the temporal variation of taxonomic, functional and phylogenetic components, forecasting alpha and beta diversity changes through our geographical grid. Lastly, we used phylogenetic comparative models to test the influence of phylogeny and traits on range shifts. We observed broad latitudinal and altitudinal rearrangements in community composition driven by climate change. Given the high dispersal ability of Odonata, changes are predicted to be rapid, especially in areas experiencing faster climate change rates. According to our predictions, changes in species composition cascade to affect functional and phylogenetic diversity, determining broad turnovers in traits and evolutionary lineages. There was no clear phylogenetic signal in the range-shift response of European Odonata to climate change. According to our phylogenetic regression models, only body size and flight period can be partly correlated with observed range shifts. By considering all three primary facets of biodiversity, our results support the design of inclusive management and conservation strategies, accounting not only for the diversity of species, but also the services they provide and the phylogenetic heritage they carry in a targeted ecosystem.
Mechanism-based crosslinking probes capture E. coli ketosynthase FabB in conformationally-distinct catalytic states
Authors: Chen Aochiu , Mindrebo Jeffrey T. , Davis Tony D. , Kim Woojoo E. , Katsuyama Yohei , Jiang Ziran , Ohnishi Yasuo , Noel Joseph P. , Burkart Michael D.
Published: April 2022

Ketosynthases (KS) catalyse essential carbon-carbon bond forming reactions in fatty acid biosynthesis using a two-step, ping-pong reaction mechanism. In E. coli, there are two homodimeric elongating KSs, FabB and FabF, both of which possess overlapping substrate selectivity. However, FabB is essential for the biosynthesis of unsaturated fatty acids (UFAs) required for cell survival in the absence of exogenous UFAs. Additionally, FabB has reduced activity towards substrates longer than 14 carbons, whereas FabF efficiently catalyses the elongation of saturated C14 and unsaturated C16:1 acyl-acyl carrier protein (ACP) complexes. In this study, we solved two crosslinked crystal structures of FabB in complex with ACPs functionalized with long-chain fatty acid crosslinking probes that approximate catalytic steps. Both homodimeric structures possess asymmetric substrate binding pockets, suggestive of cooperative relationships between the two FabB monomers when engaged with C14 and C16 acyl chains. In addition, these structures capture an unusual rotamer of the active site gating residue, F392, potentially representative of the catalytic state prior to substrate release. These structures demonstrate the utility of mechanism-based crosslinking methods to capture and elucidate at near atomic resolution conformational transitions accompanying KS-mediated catalysis.

Synopsis

Crystal structures of KS-ACP crosslinked complex elucidate chain length preference and substrate processing mechanism of E. coli FabB.
Characterizing the extracellular matrix transcriptome of cervical, endometrial, and uterine cancers
Authors: Cook Carson J. , Miller Andrew E. , Barker Thomas H. , Di Yanming , Fogg Kaitlin C.
Published: April 2022

Increasingly, the matrisome, a set of proteins that form the core of the extracellular matrix (ECM) or are closely associated with it, has been demonstrated to play a key role in tumor progression. However, in the context of gynecological cancers, the matrisome has not been well characterized. A holistic, yet targeted, exploration of the tumor microenvironment is critical for better understanding the progression of gynecological cancers, identifying key biomarkers for cancer progression, establishing the role of gene expression in patient survival, and for assisting in the development of new targeted therapies. In this work, we explored the matrisome gene expression profiles of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), uterine corpus endometrial carcinoma (UCEC), and uterine carcinosarcoma (UCS) using publicly available RNA-seq data from The Cancer Genome Atlas (TCGA) and The Genotype-Tissue Expression (GTEx) portal. We hypothesized that the matrisomal expression patterns of CESC, UCEC, and UCS would be highly distinct with respect to genes which are differentially expressed and hold inferential significance with respect to tumor progression, patient survival, or both. Through a combination of statistical and machine learning analysis techniques, we identified sets of genes and gene networks which characterized each of the gynecological cancer cohorts. Our findings demonstrate that the matrisome is critical for characterizing gynecological cancers and transcriptomic mechanisms of cancer progression and outcome. Furthermore, while the goal of pan-cancer transcriptional analyses is often to highlight the shared attributes of these cancer types, we demonstrate that they are highly distinct diseases which require separate analysis, modeling, and treatment approaches. In future studies, matrisome genes and gene ontology terms that were identified as critical for predicting patient survival or cancer stage can be evaluated as potential drug targets and incorporated intoin vitromodels of disease.