bluuebunny/crossref_metadata_2025 huggingface dataset:
Alan Graham MacDiarmid. 14 April 1927—7 February 2007
Authors: Holmes FRS Andrew B. , Klein FRS Michael L. , Baughman Ray H.
Published: February 2023

Alan G. M
ac
Diarmid was an inorganic chemist by training who pioneered the field of synthetic metals. He grew up in a family that lived frugally, and he had to work in the Chemistry Department of the Victoria University of Wellington as a laboratory assistant before he could undertake part-time degree studies. He was awarded a Fulbright Scholarship to the University of Wisconsin, where he completed his first PhD with Norris Hall. The desire to receive a higher degree in the UK led to a Shell Scholarship to complete a second doctorate with Harry Emeléus FRS. After a sojourn at the University of St Andrews, Alan M
ac
Diarmid was appointed to an academic position at the University of Pennsylvania, where he remained essentially for his whole career. His early research was based on the properties of silicon hydrides, but he also became interested in poly(sulfur nitride). This led to a search in collaboration with Alan J. Heeger for intrinsically conducting non-metallic materials. A chance meeting with Hideki Shirakawa at the University of Tokyo led to M
ac
Diarmid being shown thin metallic-like films of poly(acetylene) made in Shirakawa's laboratory. Shirakawa travelled to Philadelphia to collaborate with M
ac
Diarmid and Heeger on the halogen ‘doping’ of poly(acetylene), which led to the discovery that the doped material was an excellent conductor. Thus, the field of synthetic metals was born. This paradigm-shifting work in which a polymer was shown to be a conductor led to the award of the 2000 Nobel Prize in Chemistry to these three individuals. M
ac
Diarmid went on to study in great detail the properties of polyaniline; the fact that it could be processed from solution and further modified by oxidative and protonic doping led to all sorts of potentially interesting opportunities in optoelectronics. From all this research, the modern field of organic electronic materials emerged as an important disruptive technology whose advancement depended on an entirely new branch of interdisciplinary science.
A highly active mineral-based ice nucleating agent supports
in situ
cell cryopreservation in a high throughput format
Authors: Daily Martin I. , Whale Thomas F. , Kilbride Peter , Lamb Stephen , John Morris G. , Picton Helen M. , Murray Benjamin J.
Published: February 2023

Cryopreservation of biological matter in microlitre scale volumes of liquid would be useful for a range of applications. At present, it is challenging because small volumes of water tend to supercool, and deep supercooling is known to lead to poor post-thaw cell viability. Here, we show that a mineral ice nucleator can almost eliminate supercooling in 100 µl liquid volumes during cryopreservation. This strategy of eliminating supercooling greatly enhances cell viability relative to cryopreservation protocols with uncontrolled ice nucleation. Using infrared thermography, we demonstrate a direct relationship between the extent of supercooling and post-thaw cell viability. Using a mineral nucleator delivery system, we open the door to the routine cryopreservation of mammalian cells in multiwell plates for applications such as high throughput toxicology testing of pharmaceutical products and regenerative medicine.
Impact of phylogeny on structural contact inference from protein sequence data
Authors: Dietler Nicola , Lupo Umberto , Bitbol Anne-Florence
Published: February 2023

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ancestry, their sequences also feature phylogenetic correlations, which can impair contact inference. We investigate this effect by generating controlled synthetic data from a minimal model where the importance of contacts and of phylogeny can be tuned. We demonstrate that global inference methods, specifically Potts models, are more resilient to phylogenetic correlations than local methods, based on covariance or mutual information. This holds whether or not phylogenetic corrections are used, and may explain the success of global methods. We analyse the roles of selection strength and of phylogenetic relatedness. We show that sites that mutate early in the phylogeny yield false positive contacts. We consider natural data and realistic synthetic data, and our findings generalize to these cases. Our results highlight the impact of phylogeny on contact prediction from protein sequences and illustrate the interplay between the rich structure of biological data and inference.
Rapid change of friction causes the illusion of touching a receding surface
Authors: Monnoyer Jocelyn , Willemet Laurence , Wiertlewski Michaël
Published: February 2023

Shortly after touching an object, humans can tactually gauge the frictional resistance of a surface. The knowledge of surface friction is paramount to tactile perception and the motor control of grasp. While potent correlations between friction and participants’ perceptual response have been found, the causal link between the friction of the surface, its evolution and its perceptual experience has yet to be demonstrated. Here, we leverage new experimental apparatus able to modify friction in real time, to show that participants can perceive sudden changes in friction when they are pressing on a surface. Surprisingly, only a reduction of the friction coefficient leads to a robust perception. High-speed imaging data indicate that the sensation is caused by a release of a latent elastic strain over a 20 ms timeframe after the activation of the friction-reduction device. This rapid change of frictional properties during initial contact is interpreted as a normal displacement of the surface, which paves the way for haptic surfaces that can produce illusions of interacting with mechanical buttons.
On the gain of entrainment in the
n
-dimensional ribosome flow model
Authors: Ofir Ron , Kriecherbauer Thomas , Grüne Lars , Margaliot Michael
Published: February 2023

The ribosome flow model (RFM) is a phenomenological model for the flow of particles along a one-dimensional chain of
n
sites. It has been extensively used to study ribosome flow along the mRNA molecule during translation. When the transition rates along the chain are time-varying and jointly
T
-periodic the RFM entrains, i.e. every trajectory of the RFM converges to a unique
T
-periodic solution that depends on the transition rates, but not on the initial condition. In general, entrainment to periodic excitations like the 24 h solar day or the 50 Hz frequency of the electric grid is important in numerous natural and artificial systems. An interesting question, called the gain of entrainment (GOE) in the RFM, is whether proper coordination of the periodic translation rates along the mRNA can lead to a larger average protein production rate. Analysing the GOE in the RFM is non-trivial and partial results exist only for the RFM with dimensions
n
= 1, 2. We use a new approach to derive several results on the GOE in the general
n
-dimensional RFM. Perhaps surprisingly, we rigorously characterize several cases where there is no GOE, so to maximize the average production rate in these cases, the best choice is to use constant transition rates all along the chain.
JMM Profile: Salmonella enterica serovar Gallinarum, biovars Pullorum and Gallinarum
Authors: Wales Andrew , Lawes Joanna
Published: February 2023

Salmonella

serovar Gallinarum has two distinct biovars, Pullorum and Gallinarum. They are host-adapted avian pathogens that infect a number of wild and domesticated species but they pose a particular threat to farmed and backyard chickens and turkeys. Both biovars cause invasive and septicaemic disease, often resulting in high mortality. Pullorum is transmitted in eggs and typically affects birds soon after hatch. Gallinarum may cause disease in any age of bird, which often progresses through mature flocks. The establishment of clean breeding stock has resulted in freedom from the pathogens in many countries although even in these territories sporadic incursions still occur.
Multicentre surveillance of epidemiologically important pathogens causing nosocomial bloodstream infections and pneumonia trials in Brazilian adult intensive care units
Authors: Almeida Junior Elias Rodrigues de , Braga Iolanda Alves , Filho Paulo Pinto Gontijo , Ribas Rosineide Marques
Published: February 2023

Introduction. Healthcare-associated infections (HAIs) are the most recurrent adverse event in hospitals worldwide and represent an important public health problem.

Gap statement. There are a paucity of multicentric data describing severe HAIs such as bloodstream infection (BSI) and pneumonia in Brazil.

Aim. To provide an up-to-date picture of the extent and patterns of HAIs in adult intensive care units (ICUs), as well as to identify variables associated with the risk of development of severe infections.

Methodology. Point prevalence surveys were conducted using standardized protocols in 35 ICUs from Minas Gerais state, Brazil. Medical records of eligible inpatients at or before 8 am on the survey day were reviewed to identify HAIs present at the time of the survey. A matched-pairs case–control study was performed on a total of 66 pairs for BSI and 115 pairs for pneumonia according to the selection criteria developed.

Results. Overall, 171 patients (45.7%) had at least one HAI, with most (78.4%) acquired in the ICU. These patients presented a total of 240 infections; including 123 pneumonia (51.3%) and 66 BSI (27.5%), and 78.9 and 80.3 %, respectively, were acquired in the ICU. Their aetiology showed a predominance of Gram-negative bacteria versus Gram-positive bacteria (48.9 versus 43.3 %), with

Acinetobacter baumannii

(13.7%) and

Pseudomonas aeruginosa

(12.8%) being prominent. One striking observation from our data was the higher prevalence of

Staphylococcus aureus

(14.5%) and coagulase-negative staphylococci (10.2%) observed in the overall HAIs.

Conclusion. A high severe ICU-acquired HAI burden was found when compared with findings from other low- and middle-income countries. These data can be utilized for better planning of nosocomial infection surveillance programmes in our hospitals.
Robust biomarker discovery through multiplatform multiplex image analysis of breast cancer clinical cohorts
Authors: Eng Jennifer , Bucher Elmar , Hu Zhi , Sanders Melinda , Chakravarthy Bapsi , Gonzalez Paula , Pietenpol Jennifer A. , Gibbs Summer L. , Sears Rosalie C. , Chin Koei
Published: February 2023

Abstract

Spatial profiling of tissues promises to elucidate tumor-microenvironment interactions and enable development of spatial biomarkers to predict patient response to immunotherapy and other therapeutics. However, spatial biomarker discovery is often carried out on a single patient cohort or imaging technology, limiting statistical power and increasing the likelihood of technical artifacts. In order to analyze multiple patient cohorts profiled on different platforms, we developed methods for comparative data analysis from three disparate multiplex imaging technologies: 1) cyclic immunofluorescence data we generated from 102 breast cancer patients with clinical follow-up, in addition to publicly available 2) imaging mass cytometry and 3) multiplex ion-beam imaging data. We demonstrate similar single-cell phenotyping results across breast cancer patient cohorts imaged with these three technologies and identify cellular abundance and proximity-based biomarkers with prognostic value across platforms. In multiple platforms, we identified lymphocyte infiltration as independently associated with longer survival in triple negative and high-proliferation breast tumors. Then, a comparison of nine spatial analysis methods revealed robust spatial biomarkers. In estrogen receptor-positive disease, quiescent stromal cells close to tumor were more abundant in good prognosis tumors while tumor neighborhoods of mixed fibroblast phenotypes were enriched in poor prognosis tumors. In triple-negative breast cancer (TNBC), macrophage proximity to tumor and B cell proximity to T cells were greater in good prognosis tumors, while tumor neighborhoods of vimentin-positive fibroblasts were enriched in poor prognosis tumors. We also tested previously published spatial biomarkers in our ensemble cohort, reproducing the positive prognostic value of isolated lymphocytes and lymphocyte occupancy and failing to reproduce the prognostic value of tumor-immune mixing score in TNBC. In conclusion, we demonstrate assembly of larger clinical cohorts from diverse platforms to aid in prognostic spatial biomarker identification and validation.

Statement of significance

Our single-cell spatial analysis of multiple clinical cohorts uncovered novel biomarkers of patient outcome in breast cancer. Additionally, our data, software, and methods will help advance spatial characterization of the tumor microenvironment.
A novel preclinical secondary pharmacology resource illuminates target-adverse drug reaction associations of marketed drugs
Authors: Sutherland Jeffrey J , Yonchev Dimitar , Fekete Alexander , Urban Laszlo
Published: February 2023

In vitrosecondary pharmacology assays are an important tool for predicting clinical adverse drug reactions (ADRs) of investigational drugs. We created the Secondary Pharmacology Database (SPD) by testing 1958 drugs using 200 assays to validate target-ADR associations. Compared to public and subscription resources, 95% of all and 36% of active (AC50 < 1 µM) results were unique to SPD, with bias towards higher activity in public resources. Annotating drugs with free maximal plasma concentrations, we found 684 physiologically relevant novel off-target activities. Furthermore, 64% of putative ADRs linked to target activity in key literature reviews were not statistically significant in SPD. Systematic analysis of all target-ADR pairs identified several novel associations confirmed by publications. Finally, candidate mechanisms for known ADRs are proposed based on SPD off-target activities. Taken together, we present a unique freely-available resource for benchmarking ADR predictions, explaining novel phenotypic activity and investigating clinical properties of marketed drugs.
FHF2 phosphorylation and regulation of native myocardial NaV1.5 channels
Authors: Lesage Adrien , Lorenzini Maxime , Burel Sophie , Sarlandie Marine , Bibault Floriane , Maloney Dan , Silva Jonathan R. , Reid Townsend R. , Nerbonne Jeanne M. , Marionneau Céline
Published: February 2023

Phosphorylation of the cardiac NaV1.5 channel pore-forming subunit is extensive and critical in modulating channel expression and function, yet the regulation of NaV1.5 by phosphorylation of its accessory proteins remains elusive. Using a phosphoproteomic analysis of NaVchannel complexes purified from mouse left ventricles, we identified nine phosphorylation sites on Fibroblast growth factor Homologous Factor 2 (FHF2). To determine the roles of phosphosites in regulating NaV1.5, we developed two models from neonatal and adult mouse ventricular cardiomyocytes in which FHF2 expression is knockdown and rescued by WT, phosphosilent or phosphomimetic FHF2-VY. While the increased rates of closed-state and open-state inactivation of NaVchannels induced by the FHF2 knockdown are completely restored by the FHF2-VY isoform in adult cardiomyocytes, sole a partial rescue is obtained in neonatal cardiomyocytes. The FHF2 knockdown also shifts the voltage-dependence of activation towards hyperpolarized potentials in neonatal cardiomyocytes, which is not rescued by FHF2-VY. Parallel investigations showed that the FHF2-VY isoform is predominant in adult cardiomyocytes, while expression of FHF2-VY and FHF2-A is comparable in neonatal cardiomyocytes. Similar to WT FHF2-VY, however, each FHF2-VY phosphomutant restores the NaVchannel inactivation properties in both models, preventing identification of FHF2 phosphosite roles. FHF2 knockdown also increases the late Na+current in adult cardiomyocytes, which is restored similarly by WT and phosphosilent FHF2-VY. Together, our results demonstrate that ventricular FHF2 is highly phosphorylated, implicate differential roles for FHF2 in regulating neonatal and adult mouse ventricular NaV1.5, and suggest that the regulation of NaV1.5 by FHF2 phosphorylation is highly complex.

eTOC Summary

Lesageet al. identify the phosphorylation sites of FHF2 from mouse left ventricular NaV1.5 channel complexes. While no roles for FHF2 phosphosites could be recognized yet, the findings demonstrate differential FHF2-dependent regulation of neonatal and adult mouse ventricular NaV1.5 channels.
CATE: A fast and scalable CUDA implementation to conduct highly parallelized evolutionary tests on large scale genomic data
Authors: Perera Deshan , Reisenhofer Elsa , Hussein Said , Higgins Eve , Huber Christian D. , Long Quan
Published: February 2023

Statistical tests for molecular evolution provide quantifiable insights into the selection pressures that govern a genome’s evolution. Increasing sample sizes used for analysis leads to higher statistical power. However, this requires more computational nodes or longer computational time. CATE (CUDA Accelerated Testing of Evolution) is a computational solution to this problem comprised of two main innovations. The first is a file organization system coupled with a novel search algorithm and the second is a large-scale parallelization of algorithms using both GPU and CPU. CATE is capable of conducting evolutionary tests such as Tajima’s D, Fu and Li’s, and Fay and Wu’s test statistics, McDonald–Kreitman Neutrality Index, Fixation Index, and Extended Haplotype Homozygosity. CATE is magnitudes faster than standard tools with benchmarks estimating it being on average over 180 times faster. For instance, CATE processes all 54,849 human genes for all 22 autosomal chromosomes across the five super populations present in the 1000 Genomes Project in less than thirty minutes while counterpart software took 3.62 days. This proven framework has the potential to be adapted for GPU-accelerated large-scale parallel analyses of many evolutionary and genomic analyses.
A Chromosome-Level Genome Assembly for the Rock Ptarmigan (Lagopus muta)
Authors: Squires Theodore E. , Rödin-Mörch Patrik , Formenti Giulio , Tracey Alan , Abueg Linelle , Brajuka Nadolina , Jarvis Erich , Halapi Eva C. , Melsted Páll , Höglund Jacob , Magnússon Kristinn Pétur
Published: February 2023

The Rock Ptarmigan (Lagopus muta) is a cold-adapted, largely sedentary, game bird with a Holarctic distribution. The species represents an important example of an organism likely to be affected by ongoing climatic shifts across a disparate range. We provide here a high-quality reference genome and mitogenome for the Rock Ptarmigan assembled from PacBio HiFi and Hi-C sequencing of a female bird from Iceland. The total size of the genome is 1.03 Gb with a scaffold N50 of 71.23 Mb and a contig N50 of 17.91 Mb. The final scaffolds represent all 40 predicted chromosomes, and the mitochondria with a BUSCO score of 98.6%. Gene annotation resulted in 16,078 protein-coding genes out of a total 19,831 predicted (81.08% excluding pseudogenes). The genome included 21.07% repeat sequences, and the average length of genes, exons, and introns were, 33605, 394, and 4265 bp respectively. The availability of a new reference-quality genome will contribute to understanding the Rock Ptarmigan’s unique evolutionary history, vulnerability to climate change, and demographic trajectories around the globe and serve as a reference genome for the species in the family Tetraonidae (order Galliformes).
Computational biology predicts metabolic engineering targets for increased production of 102 valuable chemicals in yeast
Authors: Domenzain Iván , Lu Yao , Shi Junling , Lu Hongzhong , Nielsen Jens
Published: February 2023

Development of efficient cell factories that can compete with traditional chemical production processes is complex and generally driven by case-specific strategies, based on the product and microbial host of interest. Despite major advancements in the field of metabolic modelling in recent years, prediction of genetic modifications for increased production remains challenging. Here we present a computational pipeline that leverages the concept of protein limitations in metabolism for prediction of optimal combinations of gene engineering targets for enhanced chemical bioproduction. We used our pipeline for prediction of engineering targets for 102 different chemicals usingSaccharomyces cerevisiaeas a host. Furthermore, we identified sets of gene targets predicted for groups of multiple chemicals, suggesting the possibility of rational model-driven design of platform strains for diversified chemical production.

One sentence summary

Novel strain design algorithm ecFactory on top of enzyme-constrained models provides unprecedented chances for rational strain design and development.
Characterization and Validation of a Middle-Down Hydrophobic Interaction Chromatography Method to Monitor Methionine Oxidation in IgG1
Authors: Khalil Somar , Patel Nisha , Bevillard-Kumar Francoise , Chéry Cyrille , Burkitt William , O’Hara John , Gervais Annick
Published: February 2023

Post-translational modifications (PTMs) of therapeutic monoclonal antibodies (mAbs) can impact the efficacy of a drug. Methionine oxidation can alter the overall hydrophobicity of an antibody, thereby inducing conformational changes and affecting its biological activity. To ensure high quality, safety, and efficacy of mAbs, routine monitoring of PTMs such as methionine (Met) oxidation is essential. Met oxidation in the fragment crystallizable (Fc) region of immunoglobulin-G1 (IgG1) is a critical quality attribute because it impacts not only the interaction with the neonatal Fc receptor and protein A but also the half-life of mAbs in serum circulation. Although bottom-up mass spectrometry provides high site specificity, it may have limited application in quality control workflows, and its complicated sample preparation could result in procedure-induced oxidation. In this study, we describe the development and characterization of a rapid and robust middle-down hydrophobic interaction chromatography method for monitoring Met oxidation in the Fc region of IgG1. Additionally, we assessed a comprehensive method validation package and demonstrated the specificity, linearity, precision, and accuracy of the new method within a range of 3.8–37.7%. The relative quantitative data provided by this method may be used in a regulated workflow to support process and formulation development as well as in the later stages of drug development and batch release and stability studies.
Hypothesis-free phenotype prediction within a genetics-first framework
Authors: Lu Chang , Zaucha Jan , Gam Rihab , Fang Hai , Smithers Ben , Oates Matt E. , Bernabe-Rubio Miguel , Williams James , Thurlby Natalie , Pandurangan Arun Prasad , Tandon Himani , Shihab Hashem , Kalaivani Raju , Sung Minkyung , Sardar Adam , Tzovoras Bastian Greshake , Danovi Davide , Gough Julian
Published: February 2023

Cohort-wide sequencing studies have revealed that the largest category of variants is those deemed ‘rare’, even for the subset located in coding regions (99% of known coding variants are seen in less than 1% of the population1–3). Our understanding of how rare genetic variants influence disease and organism-level phenotypes has achieved limited progress, partly explained by the intrinsic difficulty in statistically evaluating the biological significance of rare events. Here we show that discoveries can instead be made through a knowledge-based approach using protein domains and ontologies (function and phenotype) that considers all coding variants regardless of allele frequency. We describe anab initio, genetics-first method making molecular knowledge-based interpretations for exome-wide non-synonymous variants for phenotypes at the organism and cellular level. By using this reverse approach, we identify plausible novel genetic causes for developmental disorders that have eluded other established methods and present novel molecular hypotheses for the causal genetics of 40 phenotypes generated from a direct-to-consumer genotype cohort. This system offers a chance to extract further discovery from genetic data after standard tools have been applied.
DeepD3, an Open Framework for Automated Quantification of Dendritic Spines
Authors: Fernholz Martin H P , Guggiana Nilo Drago A , Bonhoeffer Tobias , Kist Andreas M
Published: February 2023

Dendritic spines are the seat of most excitatory synapses in the brain, and a cellular structure considered central to learning, memory, and activity-dependent plasticity. The quantification of dendritic spines from light microscopy data is usually performed by humans in a painstaking and error-prone process. We found that human-to-human variability is substantial (inter-rater reliability 82.2±6.4%), raising concerns about the reproducibility of experiments and the validity of using human-annotated ‘ground truth’ as an evaluation method for computational approaches of spine identification. To address this, we present DeepD3, an open deep learning-based framework to robustly quantify dendritic spines in microscopy data in a fully automated fashion. DeepD3’s neural networks have been trained on data from different sources and experimental conditions, annotated and segmented by multiple experts and they offer precise quantification of dendrites and dendritic spines. Importantly, these networks were validated in a number of datasets on varying acquisition modalities, species, anatomical locations and fluorescent indicators. The entire DeepD3 open framework, including the fully segmented training data, a benchmark that multiple experts have annotated, and the DeepD3 model zoo is fully available, addressing the lack of openly available datasets of dendritic spines while offering a ready-to-use, flexible, transparent, and reproducible spine quantification method.
Exploring the role of task success in implicit motor adaptation
Authors: Al-Fawakhiri Naser , Ma Ambri , Taylor Jordan A. , Kim Olivia A.
Published: February 2023

While implicit motor adaptation is driven by sensory-prediction errors (SPEs), recent work has shown that task success modulates this process. Task success has typically been defined as hitting a target, which signifies the goal of the movement. Visuomotor adaptation tasks are uniquely situated to experimentally manipulate task success independently from SPE by changing the target size or the location of the target. These two, distinct manipulations may influence implicit motor adaptation in different ways, so, over four experiments, we sought to probe the efficacy of each manipulation. We found that changes in target size which caused the target to fully envelop the cursor only affected implicit adaptation for a narrow range of SPE sizes, while jumping the target to overlap with the cursor more reliably and robustly affected implicit adaptation. Taken together, our data indicate that, while task success exerts a small effect on implicit adaptation, these effects are susceptible to methodological variations. Future investigations of the effect of task success on implicit adaptation could benefit from employing target jump manipulations instead of target size manipulations.
The effectiveness of selection in a species affects the direction of amino acid frequency evolution
Authors: McShea Hanon , Weibel Catherine , Wehbi Sawsan , Goodman Peter , James Jennifer E. , Wheeler Andrew L. , Masel Joanna
Published: February 2023

Nearly neutral theory predicts that species with higher effective population size (Ne) are better able to purge slightly deleterious mutations. We compare evolution in high-Nevs. low-Nevertebrates to reveal which amino acid frequencies are subject to subtle selective preferences. We take three complementary approaches, two measuring flux and one measuring outcomes. First, we fit non-stationary substitution models of amino acid flux using maximum likelihood, comparing the high-Neclade of rodents and lagomorphs to its low-Nesister clade of primates and colugos. Second, we compare evolutionary outcomes across a wider range of vertebrates, via correlations between amino acid frequencies andNe. Third, we dissect the details of flux in human, chimpanzee, mouse, and rat, as scored by parsimony – this also enables comparison to a historical paper. All three methods agree on which amino acids are preferred under more effective selection. Preferred amino acids tend to be smaller, less costly to synthesize, and to promote intrinsic structural disorder. Parsimony-induced bias in the historical study produces an apparent reduction in structural disorder, perhaps driven by slightly deleterious substitutions. Within highly exchangeable pairs of amino acids, arginine is strongly preferred over lysine, and valine over isoleucine, consistent with more effective selection preferring a marginally larger free energy of folding. These two preferences match differences between thermophiles and mesophilic relatives. These results reveal the biophysical consequences of mutation-selection-drift balance, and demonstrate the utility of nearly neutral theory for understanding protein evolution.

Significance statement

According to the nearly neutral theory of molecular evolution, selection is less able to distinguish between similar alleles in species with lower population size. We identify which amino acids are subject to such weak preferences – these tend to be smaller, to be less costly to make, to promote structural disorder of proteins, and to be enriched in thermophiles relative to mesophiles. The latter agrees with theories of marginal protein stability under mutation-selection-drift balance.
EntomonVR: a New Virtual Reality Game for Learning Insect Morphology
Authors: Saqalaksari Mikaeel Pasandideh , Talebi Ali Asghar , van de Kamp Thomas , Haghighi Sajjad Reyhani , Zimmermann Dominique , Richter Adrian
Published: February 2023

In recent years, the study of insect morphology has benefited greatly from the emergence of new digital imaging and analysis technologies such as X-ray micro-computed tomography (μ-CT), digital 3D reconstruction, and animation. Through interactive gaming and virtual reality, the external morphology of insects can be studied by a broad audience of both entomologists and non-specialists. EntomonVR is a serious game designed to investigate the external morphology of insects with adequate quality for the virtual reality platform. We discuss the advantages of virtual reality, introduce the EntomonVR new educational game, and conclude about future perspectives, validations, and cost-effectiveness. For game assessment, we have tested this game on 25 participants with an entomological background and improved the game based on their feedback. This study demonstrates the efficacy of virtual reality technology for an experimental learning environment in teaching the morphology of insects and the crucial needs for advancing an efficient and interactive educational program.
CAM evolution is associated with gene family expansion in an explosive bromeliad radiation
Authors: Crego Clara Groot , Hess Jaqueline , Yardeni Gil , de La Harpe Marylaure , Priemer Clara , Beclin Francesca , Saadain Sarah , Cauz-Santos Luiz A. , Temsch Eva M. , Weiss-Schneeweiss Hanna , Barfuss Michael H.J. , Till Walter , Weckwerth Wolfram , Heyduk Karolina , Lexer Christian , Paun Ovidiu , Leroy Thibault
Published: February 2023

1.

The subgenusTillandsia(Bromeliaceae) belongs to one of the fastest radiating clades in the plant kingdom and is characterised by the repeated evolution of Crassulacean Acid Metabolism (CAM). Despite its complex genetic basis, this water-conserving trait has evolved independently across many plant families and is regarded as a key innovation trait and driver of ecological diversification in Bromeliaceae. By producing high-quality genome assemblies of aTillandsiaspecies pair displaying divergent photosynthetic phenotypes, and combining genome-wide investigations of synteny, TE dynamics, sequence evolution, gene family evolution and temporal differential expression, we were able to pinpoint the genomic drivers of CAM evolution inTillandsia. Several large-scale rearrangements associated with karyotype changes between the two genomes and a highly dynamic TE landscape shaped the genomes ofTillandsia. However, our analyses show that rewiring of photosynthetic metabolism is mainly obtained through regulatory evolution rather than coding sequence evolution, as CAM-related genes are differentially expressed across a 24-hour cycle between the two species, but are no candidates of positive selection. Gene orthology analyses reveal that CAM-related gene families manifesting differential expression underwent accelerated gene family expansion in the constitutive CAM species, further supporting the view of gene family evolution as a driver of CAM evolution.
Effective Rapid Blood Perfusion inXenopus
Authors: Jonas-Closs Rachael A , Peshkin Leonid
Published: February 2023

Xenopushas been a powerful model organism for understanding vertebrate development and disease for over a hundred years. Here we define a rapid blood perfusion protocol inXenopusaimed at a consistent and drastic reduction of blood across tissues. Perfusion is done by inserting a needle directly into the ventricle and pumping heparin in PBS through the vascular system. The whole procedure should take about 10 minutes per frog. Blood is dominated by a few highly abundant proteins and cell types which create numerous issues by masking most other molecules and cell types of interest. Reproducible characterization of adultXenopustissues with quantitative proteomics and single cell transcriptomics will gain from applying this protocol prior to organ dissections defined in companion papers. The procedure is aimed at standardization of practice across the animals of different gender, age andXenopusspecies, specificallyX.laevisandX.tropicalis.

An effective rapid blood perfusion protocol to prepare tissue samples for transcriptomics and proteomics studies.
Deficient mitochondrial respiration impairs sirtuin activity in dorsal root ganglia in Friedreich Ataxia mouse and cell models
Authors: Sanz-Alcázar Arabela , Britti Elena , Delaspre Fabien , Medina-Carbonero Marta , Pazos-Gil Maria , Tamarit Jordi , Ros Joaquim , Cabiscol Elisa
Published: February 2023

Friedreich ataxia (FA) is a rare, recessive neuro-cardiodegenerative disease caused by deficiency of the mitochondrial protein frataxin. Mitochondrial dysfunction, a reduction in the activity of iron-sulfur enzymes, iron accumulation, and increased oxidative stress have been described. However, the mechanisms causing such cellular disturbances in mammals are not completely understood. Dorsal root ganglion (DRG) sensory neurons are among the cellular types most affected in the early stages of this disease. We have previously demonstrated that frataxin depletion in primary cultures of DRG neurons results in calcium dysregulation, neurite degeneration and apoptotic cell death. However, its effect on mitochondrial function remains to be elucidated. In the present study, we found that in primary cultures of DRG neurons as well as in DRGs from the FXNI151Fmouse model, frataxin deficiency resulted in lower activity and levels of the electron transport complexes, mainly complexes I and II. As a consequence, the NAD+/NADH ratio was reduced and SirT3, a mitochondrial NAD+-dependent deacetylase, was impaired. We identified alpha tubulin as the major acetylated protein from DRG homogenates whose levels were increased in FXNI151Fmice compared to WT mice. Mitochondrial superoxide dismutase (SOD2), a SirT3 substrate, displayed increased acetylation in frataxin-deficient DRG neurons. Since SOD2 acetylation inactivates the enzyme, and higher levels of mitochondrial superoxide anion were detected, oxidative stress markers were analyzed. Elevated levels of hydroxynonenal bound to proteins and mitochondrial Fe2+accumulation were detected when frataxin decreased. Honokiol, a SirT3 activator, restores mitochondrial respiration. Altogether, these results provide the molecular bases to understand mitochondria dysfunction in sensory neurons which have greater susceptibility to frataxin deficiency compared to other tissues.
Imaging Architecture of Granulomas Induced byMycobacterium tuberculosisInfections with Single-Molecule FISH
Authors: Kumar Ranjeet , Kolloli Afsal , Subbian Selvakumar , Kaushal Deepak , Shi Lanbo , Tyagi Sanjay
Published: February 2023

Granulomas are an important hallmark ofMycobacterium tuberculosis(Mtb) infection. They are organized and dynamic structures created by an assembly of immune cells around the sites of infection in the lungs to locally restrict the bacterial growth and the host’s inflammatory responses. The cellular architecture of granulomas is traditionally studied by immunofluorescence labeling of phenotypic surface markers. However, very few antibodies are available for model animals used in tuberculosis research, such as non-human primates and rabbits; secreted immunological markers such as cytokines cannot be imagedin situusing antibodies; and traditional phenotypic surface markers do not provide sufficient resolution for the detection of many subtypes and differentiation states of immune cells. Using single-molecule fluorescentin situhybridization (smFISH) and its derivatives, amplified smFISH (ampFISH) and iterative smFISH, we developed a platform for imaging mRNAs encoding immune markers in rabbit and macaque tuberculosis granulomas. Multiplexed imaging for several mRNA and protein markers was followed by quantitative measurement of expression of these markers in single cellsin situ. A quantitative analysis of combinatorial expressions of these markers allowed us to classify the cells into several subtypes and chart their distributions within granulomas. For one mRNA target, HIF-1α, we were able to image its mRNA and protein in the same cells, demonstrating the specificity of probes. This method paves the way for defining granular differentiation states and cell subtypes from transcriptomic data, identifying key mRNA markers for these cell subtypes, and then locating the cells in the spatial context of granulomas.
Automated Workflows using Quantitative Colour Pattern Analysis (QCPA): A Guide to Batch Processing and Downstream Data Analysis
Authors: van den Berg Cedric P. , Condon Nicholas D. , Conradsen Cara , White Thomas E. , Cheney Karen L.
Published: February 2023

Animal and plant colouration presents a striking dimension of phenotypic variation, the study of which has driven general advances in ecology, evolution, and animal behaviour. Quantitative Colour Pattern Analysis (QCPA) is a dynamic framework for analysing colour patterns through the eyes of non-human observers. However, its extensive array of user-defined image processing and analysis tools means image analysis is often time-consuming. This hinders the full use of analytical power provided by QCPA and its application to large datasets. Here, we offer a robust and comprehensive batch script, allowing users to automate many QCPA workflows. We further provide a set of useful R scripts for downstream data extraction and analysis. These scripts will empower users to exploit the full analytical power of QCPA and facilitate the development of customised semi-automated workflows. Such quantitatively scaled workflows are crucial for exploring colour pattern space and developing ever-richer frameworks for analysing organismal colouration accounting for the visual perception in animals other than humans. These advances will, in turn, facilitate testing hypotheses on the function and evolution of vision and signals at quantitative and qualitative scales, which are otherwise computationally unfeasible.
Construction of a 3D whole organism spatial atlas by joint modeling of multiple slices
Authors: Wang Gefei , Zhao Jia , Yan Yan , Wang Yang , Wu Angela Ruohao , Yang Can
Published: February 2023

Spatial transcriptomics (ST) technologies are revolutionizing the way that researchers explore the spatial architecture of tissues. Currently, ST data analysis is often restricted to 2D space within a single tissue slice, limiting our capacity to understand biological processes that take place in 3D space. Here, we present STitch3D, a unified computational framework that integrates multiple 2D tissue slices to reconstruct 3D cellular structures from the tissue level to the whole organism level. By jointly modeling multiple 2D tissue slices and integrating them with cell-type-specific expression profiles derived from single-cell RNA-sequencing data, STitch3D simultaneously identifies 3D spatial regions with coherent gene expression levels and reveals 3D distributions of cell types. STitch3D distinguishes biological variation among slices from batch effects, and effectively borrows shared information across slices to assemble powerful 3D models of tissues. Through comprehensive experiments using diverse datasets, we demonstrate the performance of STitch3D in building comprehensive 3D tissue architectures of the mouse brain, the human heart, and theDrosophilaembryo, which allow 3D analysis in the entire tissue region or even the whole organism. To gain deeper biological insights, the outputs of STitch3D can be used for downstream tasks, such as inference of spatial trajectories, identification of spatially variable genes enriched in tissue regions or subregions, denoising or imputation of spatial gene expressions, as well as generation of virtual tissue slices.
Bifurcation Left Main Stenting with or without intracoronary imaging: Outcomes From the EBC MAIN trial
Authors: Maznyczka Annette , Arunothayaraj Sandeep , Egred Mohaned , Banning Adrian , Brunel Philippe , Ferenc Miroslaw , Hovasse Thomas , Wlodarczak Adrian , Pan Manuel , Schmitz Thomas , Silvestri Marc , Erglis Andrejs , Kretov Evgeny , Lassen Jens Flensted , Chieffo Alaide , Lefevre Thierry , Burzotta Francesco , Cockburn James , Darremont Olivier , Stankovic Goran , Morice Marie-Claude , Louvard Yves , Hildick-Smith David ,   the EBC MAIN (European Bifurcation Club Left Main Coronary Stent study) investigators
Published: February 2023

Background

The impact of intracoronary imaging on outcomes, after provisional versus dual-stenting for bifurcation left main (LM) lesions, is unknown.

Objectives

We investigated the effect of intracoronary imaging in the EBC MAIN trial (European Bifurcation Club Left Main Coronary Stent study).

Methods

467 patients were randomised to dual-stenting or a stepwise provisional strategy. 455 patients were included. Intravascular ultrasound (IVUS) or optical coherence tomography (OCT) was undertaken at the operator’s discretion. The primary endpoint was death, myocardial infarction or target vessel revascularisation at 1-year.

Results

Intracoronary imaging was undertaken in 179 patients (39%; IVUS n=151, OCT n=28). As a result of IVUS findings, operators re-intervened in 42 procedures. The primary outcome did not differ with intracoronary imaging versus angiographic-guidance alone (17% vs. 16%; odds ratio (OR): 1.09 [95% confidence interval (CI): 0.66-1.82] p=0.738), nor for re-intervention based on IVUS versus none (14% vs.16%; OR: 0.86 [95% CI: 0.35-2.12] p=0.745). With angiographic-guidance only, primary outcome events were more frequent with dual versus provisional stenting (21% vs. 10%; OR: 2.24 [95% CI: 1.13-4.45] p=0.022). With intracoronary imaging, there were numerically fewer primary outcome events with dual versus provisional stenting (13% vs. 21%; OR: 0.54 [95% CI: 0.24-1.22] p=0.137).

Conclusions

In EBC MAIN, the primary outcome did not differ between patients who did or did not have intracoronary imaging. However, in patients without intracoronary imaging, outcomes were worse with a dual-stent than provisional strategy, and when intracoronary imaging was used, there was a trend toward better outcomes with the dual-stent than provisional strategy.

Condensed abstract

We investigated whether intracoronary imaging during LM bifurcation stenting was associated with less death, myocardial infarction and revascularisation at 1 year, for patients undergoing systematic dual versus stepwise provisional stenting. We included 455 patients from the EBC MAIN trial; 39% had intracoronary imaging. Overall, outcomes were similar between patients who did or did not have intracoronary imaging. In those with angiographic guidance only, outcomes were worse with dual versus provisional stenting (21% vs. 10%; OR: 2.24 [95% CI: 1.13-4.45] p=0.022). In those with intracoronary imaging, there was a trend toward better outcomes with dual versus provisional stenting (13% vs. 21%).
Deep learning permits imaging of multiple structures with the same fluorophores
Authors: Jin Luhong , Liu Jingfang , Zhang Heng , Zhu Yunqi , Yang Haixu , Wang Jianhang , Zhang Luhao , Xu Yingke , Kuang Cuifang , Liu Xu
Published: February 2023

Fluorescence microscopy is a powerful tool for life sciences, which employs fluorescent tags to label and observe cellular structures and their dynamics. However, due to the spectral overlap between different dyes, a limited number of structures can be separately labeled and imaged for live cell applications. Here we propose a novel double-structure network (DBSN) that consists of multiple connected models, which can extract six subcellular structures from three images with only two separate fluorescent labels. DBSN combines the intensity-balance models to compensate for uneven fluorescent labels for different structures and the structure-separation models to extract multiple different structures with the same fluorescent labels. Therefore, DBSN permits the imaging of multiple structures with only one fluorescent label. It significantly reduces photobleaching, breaks the bottleneck of the existing technologies, and would have vast applications in cell biology.
The Soil Food Web Ontology: aligning trophic groups, processes, resources, and dietary traits to support food-web research
Authors: Guillarme Nicolas Le , Hedde Mickael , Potapov Anton M. , Martínez-Muñoz Carlos A. , Berg Matty P. , Briones Maria J.I. , Calderón-Sanou Irene , Degrune Florine , Hohberg Karin , Martinez-Almoyna Camille , Pey Benjamin , Russell David J. , Thuiller Wilfried
Published: February 2023

Although soil ecology has benefited from recent advances in describing the functional and trophic traits of soil organisms, data reuse for large-scale soil food-web reconstructions still faces challenges. These obstacles include: (1) most data on the trophic interactions and feeding behaviour of soil organisms being scattered across disparate repositories, without well-established standard for describing and structuring trophic datasets; (2) the existence of various competing terms, rather than consensus, to delineate feeding-related concepts such as diets, trophic groups, feeding processes, resource types, leading to ambiguities that hinder meaningful data integration from different studies; (3) considerable divergence in the trophic classification of numerous soil organisms, or even the lack of such classifications, leading to discrepancies in the resolution of reconstructed food webs and complicating the reuse and comparison of food-web models within synthetic studies. To address these issues, we introduce the Soil Food Web Ontology, a novel formal conceptual framework designed to foster agreement on the trophic ecology of soil organisms. This ontology represents a collaborative and ongoing endeavour aimed at establishing consensus and formal definitions for the array of concepts relevant to soil trophic ecology. Its primary objective is to enhance the accessibility, interpretation, combination, reuse, and automated processing of trophic data. By harmonising the terminology and fundamental principles of soil trophic ecology, we anticipate that the Soil Food Web Ontology will improve knowledge management within the field. It will help soil ecologists to better harness existing information regarding the feeding behaviours of soil organisms, facilitate more robust trophic classifications, streamline the reconstruction of soil food webs, and ultimately render food-web research more inclusive, reusable and reproducible.