Miracle-dz/UniFAR-FTUs huggingface dataset:
A computational screen for alternative genetic codes in over 250,000 genomes

The genetic code has been proposed to be a “frozen accident”, but the discovery of alternative genetic codes over the past four decades has shown that it can evolve to some degree. Since most examples were found anecdotally, it is difficult to draw general conclusions about the evolutionary trajectories of codon reassignment and why some codons are affected more frequently. To fill in the diversity of genetic codes, we developed Codetta, a computational method to predict the amino acid decoding of each codon from nucleotide sequence data. We surveyed the genetic code usage of over 250,000 bacterial and archaeal genome sequences in GenBank and discovered five new reassignments of arginine codons (AGG, CGA, and CGG), representing the first sense codon changes in bacteria. In a clade of uncultivated Bacilli, the reassignment of AGG to become the dominant methionine codon likely evolved by a change in the amino acid charging of an arginine tRNA. The reassignments of CGA and/or CGG were found in genomes with low GC content, an evolutionary force which likely helped drive these codons to low frequency and enable their reassignment.
Ultrashort treatment with telacebec alone and with companion drugs in immunocompetent and immunosuppressed mouse footpad models of Buruli ulcer

The antimicrobial treatment of Mycobacterium ulcerans infection, or Buruli ulcer (BU), has a long duration and is therefore burdensome and linked to indirect costs for affected patients. The new antimycobacterial drug telacebec (Q203) has previously shown promising treatment-shortening potential in mouse models of BU. In the present study, we investigated the potential of Q203 to reduce the treatment duration further. The first experiment investigated the possibility of cure by one, three or five doses of Q203 (2 mg/kg) with or without a companion drug (bedaquiline, BDQ, clofazimine, CFZ, or clarithromycin, CLR) in immunocompetent BALB/c mice. The second experiment assessed the effect of five doses of Q203 with or without BDQ or CFZ on Mycobacterium ulcerans infection of immunocompromised SCID-beige mice with the aim to evaluate the contribution of host immunity to treatment efficacy. In BALB/c mice, a treatment duration as short as 3 days was sufficient to prevent relapse in nearly all footpads and a single dose of Q203 with or without BDQ or CFZ prevented relapse in approximately 50% of footpads. Unlike in BALB/c mice, a small percentage of SCID-beige mouse footpads were culture-positive after a treatment duration of five days, highlighting an important role of host immunity for M. ulcerans clearance. Our results confirm the marked potency and prolonged bactericidal and sterilizing effects of Q203, even in immunocompromised SCID-beige mice.
Diversity and evolution of pigment types and the phycobilisome rod gene region of marine Synechococcus cyanobacteria

Synechococcus picocyanobacteria are ubiquitous and abundant photosynthetic organisms in the marine environment and contribute for an estimated 16% of the ocean net primary productivity. Their light-harvesting complexes, called phycobilisomes (PBS), are composed of a conserved allophycocyanin core from which radiates six to eight rods with variable phycobiliprotein and chromophore content. This variability allows Synechococcus to optimally exploit the wide variety of spectral niches existing in marine ecosystems. Seven distinct pigment types or subtypes have been identified so far in this taxon, based on the phycobiliprotein composition and/or the proportion of the different chromophores in PBS rods. Most genes involved in their biosynthesis and regulation are located in a dedicated genomic region called the PBS rod region. Here, we examined the variability of gene sequences and organization of this genomic region in a large set of sequenced isolates and natural populations of Synechococcus representative of all known pigment types. All regions start with a tRNA-PheGAA and some possess mobile elements including tyrosine recombinases, suggesting that their genomic plasticity relies on a tycheposon-like mechanism. Comparison of the phylogenies obtained for PBS and core genes revealed that the evolutionary history of PBS rod genes differs from the rest of the genome and is characterized by the co-existence of different alleles and frequent allelic exchange. We propose a scenario for the evolution of the different pigment types and highlight the importance of population-scale mechanisms in maintaining a wide diversity of pigment types in different Synechococcus lineages despite multiple speciation events.
Mechanistic target of rapamycin complex 1 (mTORC1) activity occurs predominantly in the periphery of human skeletal muscle fibers, in close proximity to focal adhesion complexes, following anabolic stimuli

Following anabolic stimuli (e.g. mechanical loading and/or amino acid provision) the mechanistic target of rapamycin complex 1 (mTORC1), a master regulator of protein synthesis, translocates toward the cell periphery. However, it is unknown if mTORC1 activity occurs prior to or following this translocation. We therefore aimed to determine the cellular location of mTORC1 activity in human skeletal muscle following anabolic stimuli. Fourteen young, healthy males either ingested a protein-carbohydrate beverage (0.25g/kg protein, 0.75g/kg carbohydrate) alone (n=7, 23±5yrs, 76.8±3.6kg, 13.6±3.8%BF, FED) or following a whole-body resistance exercise bout (n=7, 22±2yrs, 78.1±3.6kg, 12.2±4.9%BF, EXFED). Vastus lateralis muscle biopsies were obtained at rest (PRE) and 120 and 300min following anabolic stimuli. The spatial regulation of mTORC1 activity was assessed through immunofluorescent staining of p-RPS6Ser240/244, an mTORC1-specific phosphorylation event. p-RPS6Ser240/244 measured by immunofluorescent staining or immunoblot was positively correlated (r=0.76, p<0.001). Peripheral staining intensity of p-RPS6Ser240/244 increased above PRE in both FED and EXFED at 120min (~54% and ~138% respectively, p<0.05) but was greater in EXFED at both post-stimuli time points (p<0.05). The peripheral-central ratio of p-RPS6240/244 staining was displayed a similar pattern, suggesting mTORC1 activity occurs predominantly in the periphery of fibers. Moreover, p-RPS6Ser240/244 intensity within paxillin-positive regions, a marker of focal adhesion complexes, was elevated at 120min irrespective of stimulus (p=0.006) before returning to PRE at 300min. These data confirm that mTORC1 activity occurs in the region of human muscle fibers to which mTORC1 translocates following anabolic stimuli and identifies focal adhesion complexes as a potential site of mTORC1 activation in vivo.
Climatic niche conservatism shapes the ecological assembly of Hawaiian arthropod communities

Spatial variation in climatic conditions along elevation gradients provides an important backdrop by which communities assemble and diversify. Lowland habitats tend to be connected through time, whereas highlands can be continuously or periodically isolated, conditions that have been hypothesized to promote high levels of species endemism. This tendency is expected to be accentuated among taxa that show niche conservatism within a given climatic envelope. While species distribution modeling approaches have allowed extensive exploration of niche conservatism among target taxa, a broad understanding of the phenomenon requires sampling of entire communities. Species-rich groups such as arthropods are ideal case studies for understanding ecological and biodiversity dynamics along elevational gradients given their important functional role in many ecosystems, but community-level studies have been limited due to their tremendous diversity. Here, we develop a novel semi-quantitative metabarcoding approach that combines specimen counts and size-sorting to characterize arthropod community-level diversity patterns along two elevational gradients across two volcanoes on the island of Hawai‘i. We find that arthropod communities between the two transects become increasingly distinct compositionally at higher elevations. Resistance surface approaches suggest that climatic differences between sampling localities are an important driver in shaping beta-diversity patterns, though the relative importance of climate varies across taxonomic groups. Nevertheless, the climatic niche position of OTUs between transects was highly correlated, suggesting that climatic filters shape the colonization between adjacent volcanoes. Taken together, our results highlight climatic niche conservatism as an important factor shaping ecological assembly along elevational gradients and suggest topographic complexity as an important driver of diversification.
The functional properties of synapses made by regenerated axons across spinal cord lesion sites

While the anatomical properties of regenerated axons across spinal cord lesion sites have been studied extensively, little is known of how the functional properties of regenerated synapses compare to those in unlesioned animals. This comparison has been performed here in the lamprey, a model system for spinal injury research, in which functional locomotor recovery after spinal cord lesions is associated with axonal regeneration across the lesion site. Regenerated synapses below the lesion site did not differ to synapses from unlesioned axons with respect to the amplitude and duration of single excitatory postsynaptic potentials (EPSPs). They also showed the same activity-dependent depression over spike trains. However, regenerated synapses did differ to unlesioned synapses as the estimated number of synaptic vesicles was greater and there was evidence for an increased postsynaptic quantal amplitude. For axons above the lesion site, the amplitude and duration of single synaptic inputs also did not differ significantly to unlesioned animals. However, in this case there was evidence of a reduction in release probability and inputs facilitated rather that depressed over spike trains. Synaptic inputs from single regenerated axons below the lesion site thus do not increase in amplitude to compensate for the reduced number of descending axons after functional recovery. However, the postsynaptic input is maintained at the unlesioned level using different synaptic properties. Conversely, the facilitation from the same initial amplitude above the lesion site will make the synaptic input over spike trains functionally stronger. This may help to increase propriospinal activity across the lesion site to compensate for the lesion-induced reduction in supraspinal inputs.
Extensive protein dosage compensation in aneuploid human cancers

Aneuploidy is a hallmark of human cancers, but the effects of aneuploidy on protein expression remain poorly understood. To uncover how chromosome copy number changes influence the cancer proteome, we have conducted an analysis of hundreds of human cancer cell lines with matched copy number, RNA expression, and protein expression data. We found that a majority of proteins exhibit dosage compensation and fail to change by the degree expected based on chromosome copy number alone. We uncovered a variety of gene groups that were recurrently buffered upon both chromosome gain and loss, including protein complex subunits and cell cycle genes. Several genetic and biophysical factors were predictive of protein buffering, highlighting complex post-translational regulatory mechanisms that maintain appropriate gene product dosage. Finally, we established that chromosomal aneuploidy has an unexpectedly moderate effect on the expression of oncogenes and tumor suppressors, demonstrating that these key cancer drivers can be subject to dosage compensation as well. In total, our comprehensive analysis of aneuploidy and dosage compensation across cancers will help identify the key driver genes encoded on altered chromosomes and will shed light on the overall consequences of aneuploidy during tumor development.
Concealed identity information detection with pupillometry in rapid serial visual presentation

The concealed information test (CIT) relies on bodily reactions to stimuli that are hidden in mind. However, people can use countermeasures, such as purposely focusing on irrelevant things, to confound the CIT. A new method designed to prevent countermeasures uses rapid serial visual presentation (RSVP) to present stimuli on the fringe of awareness. Previous studies that used RSVP in combination with electroencephalography (EEG) showed that participants exhibit a clear reaction to their real first name, even when they try to prevent such a reaction (i.e., when their name is concealed information). Since EEG is not easily applicable outside the laboratory, we investigated here whether pupil size, which is easier to measure, can also be used to detect concealed identity information. In our first study, participants adopted a fake name, and searched for this name in an RSVP task, while their pupil sizes were recorded. Apart from this fake name, their real name and a control name also appeared in the task. We found pupil dilation in response to the task-irrelevant real name, as compared to control names. However, while most participants showed this effect qualitatively, it was not statistically significant for most participants individually. In a second study, we preregistered the proof-of-concept methodology and replicated the original findings. Taken together, our results show that the current RSVP task with pupillometry can detect concealed identity information at a group level. Further development of the method is needed to create a valid and reliable concealed identity information detector at the individual level.
A multiscale approach for computing gated ligand binding from molecular dynamics and Brownian dynamics simulations

We develop an approach to characterise the effects of gating by a multi-conformation protein consisting of macrostate conformations that are either accessible or inaccessible to ligand binding. We first construct a Markov state model of the apo-protein from atomistic molecular dynamics simulations from which we identify macrostates and their conformations, compute their relative macrostate populations and interchange kinetics, and structurally characterise them in terms of ligand accessibility. We insert the calculated first-order rate constants for conformational transitions into a multi-state gating theory from which we derive a gating factor γ that quantifies the degree of conformational gating. Applied to HIV-1 protease, our approach yields a kinetic network of three accessible (semi-open, open and wide-open) and two inaccessible (closed and a newly identified, ‘parted’) macrostate conformations. The ‘parted’ conformation sterically partitions the active site, suggesting a possible role in product release. We find that the binding kinetics of drugs and drug-like inhibitors to HIV-1 protease falls in the slow gating regime. However, because γ=0.75, conformational gating only modestly slows ligand binding. Brownian dynamics simulations of the diffusional association of eight inhibitors to the protease - that have a wide range of experimental association constants (~104 - 1010 M−1s−1) - yields gated rate constants in the range ~0.5-5.7 × 108 M−1s−1. This indicates that, whereas the association rate of some inhibitors could be described by the model, for many inhibitors either subsequent conformational transitions or alternate binding mechanisms may be rate-limiting. For systems known to be modulated by conformational gating, the approach could be scaled computationally efficiently to screen association kinetics for a large number of ligands. Graphical TOC Entry
Crisscross multilayering of cell sheets

Simple hydrostatic skeletons such as the Hydra’s consist of two stacked layers of cells perpendicularly oriented. Although this crisscross architecture can be recapitulated in vitro, little is known on the formation of such multilayers starting from a monolayer. In the present article, we show that bilayering of myoblasts results from the organization and activity of the cells originally in the monolayer which can be described as a contractile active nematic. As expected, most of the +1/2 topological defects that are associated with this nematic order self-propel. However, a subpopulation of these defects remains immobile. Perpendicular bilayering occurs exclusively at these motionless defects. Indeed, cells located at the head of these defects converge toward the (immobile) core and accumulate there until they start migrating on top of the tail of the first layer while the tail cells migrate in the opposite direction under the head cells. Since the cells keep their initial orientations, the two stacked layers end up perpendicularly oriented. This concerted process leading to a bilayer is dependent on the apical secretion of Extra Cellular Matrix (ECM) by the cells. Indeed, we evidence the presence of ECM between the cell layers and at the apical surface of the topmost layer. ECM molecules are oriented in the direction of the cells that produce them, which may guide the migration of the subsequent cell layers on their apical side. Significance Statement Hydrostatic skeletons such as that of the Hydra consist of two stacked layers of cells perpendicularly oriented whose coordinated contraction allows for complex movements. Such crisscross organization is also observed with myoblasts in culture. Confluent monolayers organize in well-aligned domains between which topological defects position themselves. Although these singularities are generally self-propelled, a fraction of them remains motionless. Perpendicular bilayering occurs exclusively at these particular pinned defects. Cells first accumulate at the head of the defects until they split in two perpendicular layers migrating in an antiparallel way on top of each other. Such a concerted process is highly dependent on the precise organization of the cell-secreted Extra Cellular Matrix (ECM).
A Multi-omics Strategy Enabled by Sequential Metabolomics and Proteomics for Human Pluripotent Stem Cell-derived Cardiomyocytes

Human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) have shown immense promise for patient-specific disease modeling, cardiotoxicity screening, and regenerative therapy development. However, hPSC-CMs in culture have not recapitulated the structure or functional properties of adult CMs in vivo thus far. To gain global insight into hPSC-CM biology, we introduce a multi-omics strategy for analyzing the hPSC-CM metabolome and proteome from the same cell culture, creating multi-dimensional profiles of hPSC-CMs. Here we developed a sequential extraction to capture metabolites and proteins from hPSC-CM monolayer cultures, and analyzed these extracts using high resolution mass spectrometry (MS). Using this strategy, we identified an average of 205 metabolites/lipids and 4,008 protein groups from 106 cells with high reproducibility. We further integrated the proteome and metabolome measurements to create network profiles of molecular phenotypes for hPSC-CMs. Out of the 310 total pathways identified using metabolomics and proteomics data, 40 pathways were considered significantly overrepresented (FDR-corrected p ≤ 0.05). Highly populated pathways included those involved in protein synthesis (ribosome, spliceosome), ATP generation (oxidative phosphorylation), and cardiac muscle contraction. This multi-omics method achieves deep coverage of metabolites and proteins, creating a multidimensional view of the hPSC-CM phenotype. This strategy can be used to generate biological hypotheses and identify biomarker candidates to advance the understanding of hPSC-CM differentiation and maturation.
Opioid antagonism reduces wanting by strengthening frontostriatal connectivity

Goal-directed behavior depends on both motivational (“wanting”) and hedonic (“liking”) dimensions of rewards. Previous animal and human research linked wanting and liking to anatomically and neurochemically distinct brain mechanisms, but it remains unknown as to how the different brain regions and neurotransmitter systems interact in processing distinct reward dimensions. Here, we assessed how pharmacological manipulations of opioid and dopamine receptor activation modulate the neural processing of wanting and liking in humans in a randomized, placebo-controlled, double-blind clinical trial. Blocking opioid receptor activation with naltrexone selectively reduced wanting of rewards, which on a neural level was reflected by stronger coupling between dorsolateral prefrontal cortex and the striatum under naltrexone compared with placebo. Our findings thus provide insights into how opioid receptors mediate frontostriatal gating of specifically motivational, not hedonic, aspects of rewards.
Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense

To enhance the genomics and genetics of azalea, the whole-genome sequences of two species of Rhododendron were determined and analyzed in this study: Rhododendron ripense, the cytoplasmic donor and ancestral species of large-flowered and evergreen azalea cultivars, respectively; and Rhododendron kiyosumense, a native of Chiba prefecture (Japan) seldomly bred and cultivated. A chromosome-level genome sequence assembly of R. ripense was constructed by single-molecule real-time (SMRT) sequencing and genetic mapping, while the genome sequence of R. kiyosumense was assembled using the single-tube long fragment read (stLFR) sequencing technology. The R. ripense genome assembly contained 319 contigs (506.7 Mb; N50 length: 2.5 Mb) and was assigned to the genetic map to establish 13 pseudomolecule sequences. On the other hand, the genome of R. kiyosumense was assembled into 32,308 contigs (601.9 Mb; N50 length: 245.7 kb). A total of 34,606 genes were predicted in the R. ripense genome, while 35,785 flower and 48,041 leaf transcript isoforms were identified in R. kiyosumense through Iso-Seq analysis. Overall, the genome sequence information generated in this study enhances our understanding of genome evolution in the Ericales and reveals the phylogenetic relationship of closely-related species. This information will also facilitate the development of phenotypically attractive azalea cultivars.
Unigems: plasmids and parts to facilitate teaching on assembly, gene expression control and logic in E. coli

Synthetic biology is as an excellent vehicle for education, as it enables creative combination of engineering and molecular biology approaches for quantitative characterisations of the assembled constructs. However, there is a limited number of resources available for such applications in the educational context, where straightforward setup, easily measurable phenotypes and extensibility are of particular importance. To expand the availability of education-friendly resources to teach synthetic biology and genetic engineering, we developed Unigems, a set of 10 plasmids that enable out-of-the-box investigations of principles of gene expression control, as well as more complex designs a biological logic gate. The system uses a common high-copy plasmid backbone and a common set of primers to enable Gibson-assembly of PCR-generated or synthesised parts into a target vector. It currently has two reporter genes with either two constitutive (high- or low-level) or two inducible (lactose- or arabinose-) promoters, as well as a single-plasmid implementation of an AND logic gate. The Unigems system has already been employed in undergraduate teaching settings, during outreach events and for training of iGEM teams. All plasmids have been deposited in Addgene.