Miracle-dz/UniFAR-FTUs huggingface dataset:
Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea

Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼106 cell ml-1) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22°C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 µg C L-1 d-1 ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.
Origin of evolutionary bifurcation in an enzyme

Evolution can lead to significantly distinct outcomes depending on the mutational path taken. Evolutionary bifurcation, in which two mutational trajectories segregate, becoming non-interchangeable over time, is the basis of diversification in all kingdoms of life. Here, we present a detailed molecular description of a bifurcation event that rapidly led to the emergence of two distinct enzymes from a common ancestor. When initiated from two starting points that differed by a single amino acid, the laboratory evolution of a phosphotriesterase (PTE) toward arylester hydrolysis resulted in different genetic and phenotypic outcomes. One trajectory led to a >35,000-fold increase in activity via the reorganization of its active site to achieve exquisite enzyme-substrate complementarity. The second trajectory gave rise to an evolved variant with a ∼500-fold increase in activity, but exhibiting an alternative substrate binding mode resulting from the destabilization of an active site loop. While initial mutations tend to dictate mutational accessibility, we rather observed the gradual divergence and specialisation of each trajectory, following the emergence of distinct molecular interaction networks. Intramolecular epistasis underlay pathway bifurcation by promoting unique synergistic interactions within each trajectory, while restricting the fixation of mutation across pathways. Our results illustrate how distinct molecular outcomes can radiate from a common protein ancestor and give rise to phenotypic diversity.
Exploring the activity and the essentiality of the putative Δ6-desaturase in the procyclic and bloodstream forms of Trypanosoma brucei

Trypanosomatids have been shown to possess an exclusive and finely regulated biosynthetic pathway for de novo synthesis of fatty acids (FAs) and particularly of polyunsaturated fatty acids (PUFAs). The key enzymes for the process of unsaturation are known as desaturases. In this work, we explored the biocatalytic activity of the putative Δ6-desaturase (Tb11.v5.0580) in the native organism T. brucei. Utilising fatty acid analysis via GC-MS, we were able to elucidate via genetic manipulation of the level of expression of Δ6-desaturases in both procyclic (PCF) and bloodstream (BSF) forms of T. brucei and via supplementation of the media with various levels of FA sources, that docosahexaenoic acid (22:6) and/or docosapentaenoic acid (22:5), and arachidonic acid (20:4) and/or docosatetraenoic acid (22:4) are the products and the substrates respectively of this Δ6-desaturases. Interestingly, we were able to observe, via lipidomic analysis with ESI-MS/MS, an increase in inositol-phosphoryl ceramide (IPC) in response to the overexpression of Δ6-desaturases in low-fat media, both in PCF and rather surprisingly in BSF. The formation of IPC is normally only observed in the stumpy and procyclic forms of T. brucei. Therefore, the expression levels of Δ6-desaturases, which varies between BSF and PCF, might be involved in the cascade(s) of metabolic events that cause these remodelling of the lipid pools and ultimately morphological changes, which are key to the transition between these life-cycle stages. Author summary Trypanosoma brucei is a unicellular parasite that causes human and animal African trypanosomiasis. These parasites have the special ability to make their own pool of fat molecules by assembling and modifying the fatty acid building blocks that they take up from the human and animal hosts and from the insect vector. In this study, we investigated the unknown activity of a desaturase enzyme. By modulating its activity, we showed that it can make different levels of high-value long chain polyunsaturated fatty acids (LC-PUFAs) often known as omega-6 and omega-3. If we increase or reduce the fat sources available from the outer environment, the cells respond by making more or less LC-PUFAs and by forming different type of lipids and sphingolipids for their cellular membranes. We highlighted that by tuning the level of activity of the desaturase and varying the type and amounts of fat sources available to the cells, T. brucei can alter their morphology. This is key for the parasites to adapt to the various environments and the nutrients therein that are often constantly changing within the host, allowing the shift between different life-stages during the complex life cycle from the insect vector to the host and back.
Mating preferences act independently on individual elements of visual signals in Heliconius butterflies

Mating cues are often comprised of several elements, which can act independently, or in concert to attract a suitable partner. Individual elements may also function in other contexts, such as predator defence or camouflage. In Heliconius butterflies, wing patterns comprise several individual colour pattern elements, which advertise the butterflies’ toxicity to predators. These wing patterns are also mating cues, and males predominantly court females that possess the same wing pattern as their own. However, it is not known whether male preference is based on the full wing pattern or only individual pattern elements. We compared preferences of male H. erato lativitta between female models with the full wing pattern and those with some pattern elements removed. We found no differences in preference between the full wing pattern model and a model with pattern elements removed, indicating that the complete composition of all elements is not essential to the mating signal. Wing pattern preferences also contribute to pre-mating isolation between two other Heliconius taxa, H. erato cyrbia and H. himera, therefore, we next compared preferences for the same models in these species. H. erato cyrbia and H. himera strongly differed in preferences for the models, potentially providing a mechanism for how pre-mating isolation acts between these species. These findings suggest that contrasting levels of selective constraint act on elements across the wing pattern.
Deep learning-based method to identify disease-resistance proteins in Oryza sativa and relative species

Rice (Oryza sativa) is a significant agricultural crop consumed by more than half of the global population. Its demand is expected to increase due to rising consumption and a growing global population. Moreover, the rice plant is frequently exposed to disease-causing pathogens, such as bacteria, fungi, viruses, and nematodes. Thus, cultivating disease-resistant varieties is an efficient way of disease control compared to pesticide applications. However, the rice plant has a well-defined defense system to prevent the onset of disease, including Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). The defense system is controlled by various disease-resistance proteins, such as resistance (R) proteins and pathogen recognition receptors (PRRs). Therefore, the identification of disease-resistance proteins not only reduces the amount of pesticides used in rice fields but also increases their yield. Though some resistant proteins have been characterized, their rapid identification, precise diagnosis, and appropriate management are still lacking. However, few methods based on sequence-similarity and de novo prediction, such as Machine Learning (ML), usually have low prediction power. In this study, we built a state-of-the-art classifier based on Deep Learning (DL) for the early detection of disease-resistance proteins in rice and related species. We compared the DL-based Multi-layer Perceptron (MLP) model with the five well-established ML-based methods using a protein dataset of rice and its related species. The DL-based MLP model outperformed all of the five classifiers on 10-fold cross-validation. The accuracy, Area Under Receiving Operating Characteristic (ROC) curve (AUC), F1-score, precision, and recall were superior in the DL-based MLP model. In conclusion, the MLP model is an effective DL model for predicting disease-resistance proteins with high scores in performance metrics. This study will provide insight to the breeders in developing disease-resistant rice varieties and assist in transforming traditional rice farming practices into a new age of smart rice farming.
Candida auris undergoes adhesin-dependent and -independent cellular aggregation

Candida auris is a fungal pathogen of humans responsible for nosocomial infections with high mortality rates. High levels of resistance to antifungal drugs and environmental persistence mean these infections are difficult to treat and eradicate from a healthcare setting. Understanding the life cycle and the genetics of this fungus underpinning clinically relevant traits, such as antifungal resistance and virulence, is of the utmost importance to develop novel treatments and therapies. Epidemiological and genomic studies have identified five geographical clades (I-V), which display phenotypic and genomic differences. Aggregation of cells, a phenotype primarily of clade III strains, has been linked to reduced virulence in mouse and Galleria mellonella infection models. The aggregation phenotype has thus been associated with conferring an advantage for (skin) colonisation rather than for systemic infection. However, strains with different clade affiliations were compared to infer the effects of different morphologies on virulence. This makes it difficult to distinguish morphology-dependent causes from clade-specific or even strain-specific genetic factors. Here, we identify two different types of aggregation: one induced by antifungal treatment which is a result of a cell separation defect; and a second which is controlled by growth conditions and only occurs in strains with the ability to aggregate. The latter aggregation type depends on an ALS-family adhesin which is differentially expressed during aggregation in an aggregative C. auris strain. Finally, we demonstrate that macrophages cannot clear aggregates, suggesting that aggregation might after all provide a benefit during systemic infection and could facilitate long-term persistence in the host. Author Summary Candida auris is a single-celled fungus, a yeast, that can cause severe infections in hospital patients. This fungus is difficult to treat because it is resistant to many antifungal drugs. Therefore, to understand the processes that enhance the virulence of this yeast with a view to developing new treatments. Previous studies have found that C. auris can form aggregates, or clumps of cells, which may play a role in how the fungus infects people. In this study, we identified two different types of aggregation in C. auris, one triggered by antifungal treatment, and another controlled by growth conditions. This discovery allowed us to study aggregate formation in the same genetic background. In doing so, we found that a certain protein, an ALS-family adhesin, is involved in the aggregation process. Surprisingly, we also discovered that aggregates may promote infection by making it harder for the immune system to clear the yeast. This new understanding could help researchers develop better ways to fight C. auris infections.
Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C

The SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a “pincer-like” conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5-nucleosome complex suggests that promoter proximal, histone H2B ubiquitinylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.
Acoustic Wave Equation Modeling in Cylindrical Coordinates with Convolutional PML

The finite difference modelling of wave equation are generally performed in Cartesian coordinates which is relatively easy to implement, but when dealing 3D axisymmetric media, even for simple layered medium, the simulation can be very time-consuming. Fortunately, for 3D (approximate) axisymmetric model, a more economical approach is to solve the wave equation in cylindrical coordinates, which can reduce the computation time to nearly as short as that of the 2D calculations. In this paper, the unsplit convolutional PML absorbing boundary is first implemented in 3D acoustic wave equation modelling in cylindrical coordinates. Numerical simulation results show that it's an accurate and efficient algorithm and exhibits good performance for absorbing artificial reflection. Thus our algorithm can be a tantalizing choice to efficiently simulate axisymmetric models.
Bdellovibrio’s Prey-Independent Growth is Fuelled by Amino Acids as a Carbon Source

Identifying the nutritional requirements and growth conditions of microorganisms is crucial for determining their applicability in industry and understanding their role in clinical ecology. Predatory bacteria such as Bdellovibrio bacteriovorus have emerged as promising tools for combating infections by human bacterial pathogens due to their natural killing features. Bdellovibrio’s lifecycle occurs inside prey cells, using the cytoplasm as a source of nutrients and energy. However, this lifecycle supposes a challenge when determining the specific uptake of metabolites from the prey to complete the growth inside cells, a process that has not been completely elucidated. Here, following a model-based approach we illuminate the ability of Bdellovibrio bacteriovorus to replicate DNA, increase biomass, and generate adenosine triphosphate (ATP) in an amino acid-based rich media in the absence of prey, keeping intact its predatory capacity. In this culture, we determined the main carbon sources used and their preference, being glutamate, serine, aspartate, isoleucine, and threonine. This study offers new insights into the role of predatory bacteria in natural environments and establishes the basis for developing new Bdellovibrio applications using appropriate metabolic and physiological methodologies.
Dynamic Protein Phosphorylation in Streptococcus pyogenes during Growth, Stationary Phase, and Starvation

Background Phosphorylation of proteins at serine, threonine, and tyrosine residues plays an important role in physiological processes of bacteria such as cell cycle, metabolism, virulence, dormancy, sporulation, and stationary phase functions. Streptococcus pyogenes possesses a single known transmembrane serine/threonine kinase belonging to the class of penicillin-binding protein and serine/threonine-associated (PASTA) kinases. To gain initial insights into the targets and dynamics of protein phosphorylation in S. pyogenes serotype M49 strain 591, we performed a proteomics and phosphoproteomics workflow using cultures from different growth conditions, stationary phase and starvation. Results The quantitative analysis of dynamic phosphorylation, which included a subset of 463 out of 815 identified phosphorylation sites, revealed two main types of phosphorylation events, distinguished by the growth phase in which they predominantly occur and their preference for either threonine or serine. A small group of phosphorylation events occurred almost exclusively at threonine residues of proteins related to the cell cycle and was enhanced in growing cells. Many of these phosphorylation sites are highly conserved targets of PASTA kinases in streptococci. The majority of phosphorylation events occurred during stationary phase or starvation, preferentially at serine residues. These phosphorylations may be important for regulatory processes in stationary phase or for persister cell formation, but their function and the kinases responsible for their formation need to be elucidated in further analyses. Moreover, our data indicate that the vast majority of proteins can be phosphorylated, but identification of their phosphopeptides depends on the sensitivity of the proteomic methods used. Conclusions PASTA kinase-dependent cell cycle regulation processes found in related bacteria are conserved in S. pyogenes, but account for only a small part of all phosphorylation events. Most phosphorylation events take place during stationary growth phase and starvation. This phenomenon has also been described for some other bacteria and may therefore be a general feature of bacterial protein phosphorylation.
Evaluation of Phage and Antibiotic Combinations for Staphylococcus aureus Biofilm Eradication: Insights from the Wax Worm Model

Background Galleria mellonella, an advantageous model organism, to investigate the therapeutic potential of bacteriophages. Employing the Galleria mellonella (waxworm) model, this study involved infecting the larvae with pathogenic Staphylococcus aureus, followed by combination treatment with staph phages; vB_Sau_Saa90 and vB_Sau_Saa165 at the concentrations of 107 and 109 PFU/mL and oxacillin, at 100 mg/kg. The treatment modalities were executed in three distinct orders: pre-phage treatment, simultaneous treatment, and post-phage treatment. Each treatment was administered at 90 min intervals. The health state index of the waxworms was monitored throughout the study. Results Among the three treatment orders, both pre-phage treatment and post-antibiotic treatment exhibited the significant outcomes. The survival percentages ranged from 40% to 50%, 30% to 50%, and 50% to 70% across strong, moderate, and weak biofilm conditions. Notably, the phages vB_Sau_Saa90 and vB_Sau_Saa165 displayed remarkable effectiveness in combination with antibiotics. This successful synergy showcased the potential of combinatorial treatment in effectively addressing biofilm-related infections. Conclusions This study holds considerable significance as it underscores the suitability of G. mellonella as a model organism for exploring bacteriophage-based therapeutic approaches. The study’s findings shed light on the efficacy of combining bacteriophages and antibiotics to target S. aureus biofilm cells. The observed results in the waxworm model highlight a promising avenue for managing biofilm infections. However, the need for further validation through larger animal models is emphasized, as this could potentially pave the way for novel treatment strategies with broader clinical implications.
Longitudinal trajectories of the neural encoding mechanisms of speech-sound features during the first year of life

Infants quickly recognize the sounds of their mother language, perceiving the spectrotemporal acoustic features of speech. However, the underlying neural machinery remains unclear. We used an auditory evoked potential termed frequency-following response (FFR) to unravel the neural encoding maturation for two speech sound characteristics: voice pitch and temporal fine structure. The FFR was elicited by a two-vowel stimulus (/oa/) in a sample of 41 healthy-term neonates, tested at birth and retested at the ages of six and twelve months. Results revealed a reduction in neural phase-locking time to the stimulus envelope from birth to six months, remaining stable thereafter. While neural encoding of voice pitch remained consistent, temporal fine structure encoding matured rapidly from birth to six months, without further improvement from this age onwards. Results highlight the critical importance of the first six months in the maturation of neural encoding mechanisms, crucial for phoneme discrimination during early language acquisition.
Increased FAN1 expression by mRNA-LNP attenuates CAG repeat expansion in Huntington patients’ iPSC-derived astrocytes

Expansion of repeat sequences within the human genome can lead to disease pathogenesis, such as Huntington’s Disease, primarily affecting the nervous system. Genome-wide association studies (GWAS) of age-at-onset in Huntington’s disease (HD) patients demonstrated DNA mismatch repair (MMR) genes are modifiers of somatic expansion and may be potential therapeutic targets for repeat expansion (RE) disorders. FAN1, a Fanconi anemia-associated nuclease, has been reported as an influencer of repeat expansion in the RE mouse models. Here, we show the first demonstration that FAN1 knock-out in HD patient-derived fibroblasts and results in increased CAG repeat length. We also develop a robust novel cell-based platform using stem cell technology to produce the HD patients’ iPSC-derived astrocytes (iAstro). This platform is a disease-relevant system and has a significantly wider assay window, making it more suitable to assess the effect of gene modulation on CAG repeats. A substantial and exponential increase in repeat instability was exhibited in this HD patient’s iPSC-derived astrocytes platform. Over-expression of FAN1 protein via FAN1 plasmid transfection in this platform reduced CAG repeat instability, suggesting that upregulation of FAN1 protein may have a potential protective effect in CAG repeat expansion for a therapeutic setting. We leveraged the mRNA-LNP modality to enhance FAN1 protein expression and revealed that codon-optimized FAN1 mRNA-LNP robustly prevented increased CAG repeat in HD patients’ iPSC-derived astrocytes platform. The data from these cell-based platforms highlight that FAN1 plays a protective role in attenuating expanded somatic HTT CAG repeats and shed light on new therapeutic directions against repeat expansion disorders.