Miracle-dz/UniFAR-FTUs huggingface dataset:
Transkingdom Analysis of the Female Reproductive Tract Reveals Bacteriophages form Communities

The female reproductive tract (FRT) microbiome plays an important role in maintaining vaginal health. Viruses play a key role in regulating other microbial ecosystems, but little is known about how the FRT viruses (virome), particularly bacteriophages, impacts FRT health and dysbiosis. We hypothesize that bacterial vaginosis is associated with alterations in the FRT virome, and these changes correlate with bacteriome shifts. We conducted a retrospective, longitudinal analysis of vaginal swabs collected from 54 bacterial vaginosis (BV)-positive and 46 BV-negative South African women. Bacteriome analysis revealed samples clustered into five distinct bacterial community groups (CG). Bacterial alpha diversity was significantly associated with BV. Virome analysis on a subset of baseline samples showed FRT bacteriophages clustering into novel viral state types (VSTs), a viral community clustering system based on virome composition and abundance. Distinct BV bacteriophage signatures included increased alpha diversity along with Bacillus, Burkholderia and Escherichia bacteriophages. Discriminate bacteriophage-bacteria transkingdom associations were also identified between Bacillus and Burkholderia viruses and BV-associated bacteria, providing key insight for future studies elucidating transkingdom interactions driving BV-associated microbiome perturbations. In this cohort, bacteriophage-bacterial associations suggest complex interactions which may play a role in the establishment and maintenance of BV.
Rapid carbon accumulation at a saltmarsh restored by managed realignment far exceeds carbon emitted in site construction

Increasing attention is being paid to the carbon sequestration and storage services provided by coastal blue carbon ecosystems such as saltmarshes. Sites restored by managed realignment, where existing sea walls are breached to reinstate tidal inundation to the land behind, have considerable potential to accumulate carbon through deposition of sediment brought in by the tide and burial of vegetation in the site. While this potential has been recognised, it is not yet a common motivating factor for saltmarsh restoration, partly due to uncertainties about the rate of carbon accumulation and how this balances against the greenhouse gases emitted during site construction. We use a combination of field measurements over four years and remote sensing to quantify carbon accumulation at a large managed realignment site, Steart Marshes, UK. Sediment accumulated rapidly at Steart Marshes (mean of 75 mm yr-1) and had a high carbon content (4.4% total carbon, 2.2% total organic carbon), resulting in carbon accumulation of 36.6 t ha-1 yr-1 total carbon (19.4 t ha- 1 yr-1 total organic carbon). This rate of carbon accumulation is an order of magnitude higher than reported in many other restored saltmarshes, and is higher although more similar to values previously reported from another hypertidal system (Bay of Fundy, Canada). The estimated carbon emissions associated with the construction of the site were ∼2-4% of the observed carbon accumulation during the study period, supporting the view that managed realignment projects in such settings are likely to have significant carbon accumulation benefits. We outline further considerations that are needed to move towards a full carbon budget for saltmarsh restoration.
Characterisation of a highly diverged mitochondrial ATP synthase peripheral stalk subunit b in Trypanosoma brucei

The mitochondrial F1Fo ATP synthase of Trypanosoma brucei has been studied in detail. Whereas its F1 moiety is relatively highly conserved in structure and composition, the same is not the case for the Fo part and the peripheral stalk. A core subunit of the latter, the normally conserved subunit b, could not be identified in trypanosomes suggesting that it might be absent. Here we have identified a 17 kDa mitochondrial protein of the inner membrane that is essential for normal growth, efficient oxidative phosphorylation and membrane potential maintenance. Pulldown experiments and native PAGE analysis indicate that the protein is associated with the F1Fo ATP synthase. Its ablation reduces the levels of Fo subunits, but not those of F1, and disturbs the cell cycle. HHpred analysis showed that the protein has structural similarities to subunit b of other species, indicating that the Fo part of the trypanosomal ATP synthase does contain a highly diverged subunit b. Thus, the Fo part of the trypanosomal ATPase synthase may be more widely conserved than initially thought.
A Novel Mice Model of Catecholaminergic Polymorphic Ventricular Tachycardia Generated by CRISPR/Cas9

Catecholaminergic polymorphic ventricular tachycardia (CPVT) has been considered as one of the most important causes of children’s sudden cardiac death. Mutations in the genes for RyR2 and CASQ2, two mainly subtypes of CPVT, have been identified. However, the mutation in the gene of TECRL was rarely reported, which could be another genetic cause of CPVT. We evaluated myocardial contractility, electrophysiology, calcium handling in Tecrl knockout (Tecrl KO) mice and human induced pluripotent stem cell-derived cardiomyocytes. Immediately after epinephrine plus caffeine injection, Tecrl KO mice showed much more multiple premature ventricular beats and ventricular tachycardia. The Tecrl KO mice demonstrate CPVT phenotypes. Mechanistically, intracellular calcium amplitude was reduced, while time to baseline of 50 was increased in acute isolated cardiomyocytes. RyR2 protein levels decreased significantly upon cycloheximide treatment in TECRL deficiency cardiomyocytes. Overexpression of TECRL and KN93 can partially reverse cardiomyocytes calcium dysfunction, and this is p-CaMKII/CaMKII dependent. Therefore, a new CPVT mouse model was constructed. We propose a previously unrecognized mechanism of TECRL and provide support for the therapeutic targeting of TECRL in treating CPVT.
Linking intrinsic scales of ecological processes to characteristic scales of biodiversity and functioning patterns

Ecology is a science of scale, which guides our description of both ecological processes and patterns, but we lack a systematic understanding of how process scale and pattern scale are connected. Recent calls for a synthesis between population ecology, community ecology, and ecosystem ecology motivate the integration of phenomena at multiple levels of organization. Furthermore, many studies leave out the scaling of a critical process: species interactions, which may be non-local through movement or foraging and must be distinguished from dispersal scales. Here, we use simulations to explore the consequences of three different process scales (species interactions, dispersal, and the environment) on emergent patterns of biodiversity, ecosystem functioning, and their relationship, in a spatially-explicit landscape and stable equilibrium setting. A major result of our study is that the spatial scales of dispersal and species interactions have opposite effects: a larger dispersal scale homogenizes spatial biomass patterns, while a larger interaction scale amplifies their heterogeneity. Interestingly, the specific scale at which dispersal and interaction scales begin to influence landscape patterns depends on the scale of environmental heterogeneity – in other words, the scale of one process allows important scales to emerge in other processes. This interplay between process scales, i.e., a situation where no single process dominates, can only occur when the environment is heterogeneous and the scale of dispersal small. Finally, contrary to our expectations, we observe that the spatial scale of ecological processes is more clearly reflected in landscape patterns (i.e., distribution of local outcomes) than in global patterns such as Species-Area Relationships or large-scale biodiversity-functioning relationships. Overall we conclude that long-range interactions often act differently and even in opposite ways to dispersal, and that the landscape patterns that emerge from the interplay of long-ranged interactions, dispersal and environmental heterogeneity are not well captured by often-used metrics like the Species-Area Relationship.
Aged human iPSC-RPE organoid cultures display hallmarks of drusen formation

Age-related macular degeneration (AMD) is among the most common causes of irreversible vision loss. Disease progression is strongly associated with age-related pathological changes of retinal pigment epithelial (RPE) cells, such as accumulation of intracellular lipid-containing cell debris, extracellular lipid-rich deposits (drusen) and collagen-rich basal laminar deposits. Current AMD models provide a limited understanding of the complex pathomechanisms, revealing the lack of adequate physiological human AMD models. In this study, we developed an in vitro model applicable for the exploration of AMD pathomechanisms and risk factors for AMD progression and drusen formation. Advanced 3D culturing technologies allow long-term cultivation of hiPSC-derived RPE organoids (RPEorg) for up to 360 days, which is the time frame necessary for the development of an AMD-like phenotype. Aged RPEorg exhibit hallmarks of AMD and age-related alterations such as increased autofluorescence, accumulation of lipid droplets, calcification, and the formation of extracellular clusters of the drusen-associated proteins such as apolipoprotein E (APOE) and tissue inhibitor of metalloproteinases 3 (TIMP3). Electron microscopy further reveals drusen-like extracellular deposits mimicking the signs of late drusen formation and AMD progression. In summary, our results demonstrate that hiPSC-derived 3D RPEorg provide a promising model to study age-associated RPE pathology and drusen formation. We show here that RPEorg are applicable for disease modelling studies and early stages of drug development and provide the opportunity to uncover inter-individual genetic and epigenetic factors that alter the course of the disease.
Drosophila Tachykininergic Neurons Modulate the Activity of Two Groups of Receptor-Expressing Neurons to Regulate Aggressive Tone

Neuropeptides influence animal behaviors through complex molecular and cellular mechanisms, the physiological and behavioral effects of which are difficult to predict solely from synaptic connectivity. Many neuropeptides can activate multiple receptors, whose ligand affinity and downstream signaling cascades are often different from one another. Although we know that the diverse pharmacological characteristics of neuropeptide receptors form the basis of unique neuromodulatory effects on distinct downstream cells, it remains unclear exactly how different receptors shape the downstream activity patterns triggered by a single neuronal neuropeptide source. Here, we uncovered two separate downstream targets that are differentially modulated by tachykinin, an aggression-promoting neuropeptide in Drosophila. Tachykinin from a single male-specific neuronal type recruits two separate downstream groups of neurons. One downstream group, synaptically connected to the tachykinergic neurons, expresses the receptor TkR86C and is necessary for aggression. Here, tachykinin supports cholinergic excitatory synaptic transmission between the tachykinergic and TkR86C downstream neurons. The other downstream group expresses the TkR99D receptor and is recruited primarily when tachykinin is overexpressed in the source neurons. Differential activity patterns in the two groups of downstream neurons correlate with levels of male aggression triggered by the tachykininergic neurons. These findings highlight how the amount of neuropeptide released from a small number of neurons can reshape the activity patterns of multiple downstream neuronal populations. Our results lay the foundation for further investigations into the neurophysiological mechanism by which a neuropeptide controls complex behaviors. SIGNIFICANCE STATEMENT Neuropeptides control a variety of innate behaviors, including social behaviors, in both animals and humans. Unlike fast-acting neurotransmitters, neuropeptides can elicit distinct physiological responses in different downstream neurons. How such diverse physiological effects coordinate complex social interactions remains unknown. This study uncovers the first in vivo example of a neuropeptisde from a single neuronal source eliciting distinct physiological responses in multiple downstream neurons that express different neuropeptide receptors. Understanding the unique motif of neuropeptidergic modulation, which may not be easily predicted from a synaptic connectivity map, can help elucidate how neuropeptides orchestrate complex behaviors by modulating multiple target neurons simultaneously.
Phylogenetic profiling and cellular analyses of ARL16 reveal roles in traffic of IFT140 and INPP5E

The ARF family of regulatory GTPases is ancient, with 16 members predicted to have been present in the last eukaryotic common ancestor. Our phylogenetic profiling of paralogs in diverse species identified four family members whose presence correlates with that of a cilium/flagellum: ARL3, ARL6, ARL13, and ARL16. No prior evidence links ARL16 to cilia or other cell functions, despite its presence throughout eukaryotes. Deletion of ARL16 in MEFs results in decreased ciliogenesis yet increased ciliary length. We also found Arl16 KO in MEFs to alter ciliary protein content, including loss of ARL13B, ARL3, INPP5E, and the IFT-A core component IFT140. Instead, both INPP5E and IFT140 accumulate at the Golgi in Arl16 KO lines, while other IFT proteins do not, suggesting a specific defect in traffic from Golgi to cilia. We propose that ARL16 regulates a Golgi-cilia traffic pathway and is required specifically in the export of IFT140 and INPP5E from the Golgi. Summary Phylogenetic analyses of ARF family GTPases predict that ARL16 is linked to cilia. This was confirmed using MEFs deleted for ARL16, resulting in defects in Golgi to cilium traffic, with accumulation of IFT140 and INPP5E at Golgi.
A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy

Many SARS-CoV-2 variants have mutations at key sites targeted by antibodies. However, it is unknown if antibodies elicited by infection with these variants target the same or different regions of the viral spike as antibodies elicited by earlier viral isolates. Here we compare the specificities of polyclonal antibodies produced by humans infected with early 2020 isolates versus the B.1. 351 variant of concern (also known as Beta or 20H/501Y.V2), which contains mutations in multiple key spike epitopes. The serum neutralizing activity of antibodies elicited by infection with both early 2020 viruses and B.1. 351 is heavily focused on the spike receptor-binding domain (RBD). However, within the RBD, B.1. 351-elicited antibodies are more focused on the “class 3” epitope spanning sites 443 to 452, and neutralization by these antibodies is notably less affected by mutations at residue 484. Our results show that SARS-CoV-2 variants can elicit polyclonal antibodies with different immunodominance hierarchies.
Dynamic instability of dendrite tips generates the highly branched morphologies of sensory neurons

The highly ramified arbors of neuronal dendrites provide the substrate for the high connectivity and computational power of the brain. Altered dendritic morphology is associated with neuronal diseases. Many molecules have been shown to play crucial roles in shaping and maintaining dendrite morphology. Yet, the underlying principles by which molecular interactions generate branched morphologies are not understood. To elucidate these principles, we visualized the growth of dendrites throughout larval development of Drosophila sensory neurons and discovered that the tips of dendrites undergo dynamic instability, transitioning rapidly and stochastically between growing, shrinking, and paused states. By incorporating these measured dynamics into a novel, agent-based computational model, we showed that the complex and highly variable dendritic morphologies of these cells are a consequence of the stochastic dynamics of their dendrite tips. These principles may generalize to branching of other neuronal cell-types, as well as to branching at the subcellular and tissue levels.
Individual alpha power predicts language comprehension

Alpha power attenuation during cognitive task performing has been suggested to reflect a process of release of inhibition, increase of excitability, and thereby benefit the improvement of performance. Here, we hypothesized that changes in individual alpha power during the execution of a complex language comprehension task may correlate with the individual performance in that task. We tested this using magnetoencephalography (MEG) recorded during comprehension of German sentences of different syntactic complexity. Results showed that neither the frequency nor the power of the spontaneous oscillatory activity at rest were associated with the individual performance. However, during the execution of a sentences processing task, the individual alpha power attenuation did correlate with individual language comprehension performance. Source reconstruction localized effects in temporal-parietal regions of both hemispheres. While the effect of increased task difficulty is localized in the right hemisphere, the difference in power attenuation between tasks of different complexity exhibiting a correlation with performance was localized in left temporal-parietal brain regions known to be associated with language processing. From our results, we conclude that in-task attenuation of individual alpha power is related to the essential mechanisms of the underlying cognitive processes, rather than merely to general phenomena like attention or vigilance. Highlights Comprehension of structurally complexed embedded sentences is correlated with individual alpha power attenuation during task but not with alpha power at rest. These effects were localized in temporal-parietal brain regions known to be associated with language processing. Data availability statement Anonymized raw data will be made available upon request via email to the corresponding author provided the requesting researchers sign a formal data sharing agreement and cite this paper as origin of the data.
Altered cardiolipin metabolism is associated with cardiac mitochondrial dysfunction in pulmonary vascular remodeled perinatal rat pups

Background Pulmonary vascular remodeling (PVR) in utero results in the development of heart failure (HF). The alterations that occur in cardiac lipid and mitochondrial bioenergetics during the development of in utero PVR was unknown. Methods PVR was induced in pups in utero by exposure of pregnant dams to indomethacin and hypoxia. Cardiac lipids, echocardiographic function and cardiomyocyte mitochondrial function were subsequently examined. Results Perinatal rat pups with PVR exhibited elevated left and right cardiac ventricular internal dimensions and reduced ejection fraction and fractional shortening compared to controls. Cardiac myocytes from these pups exhibited increased glycolytic capacity and glycolytic reserve compared to controls. However, respiration with glucose as substrate was unaltered. Fatty acid oxidation and ATP-insensitive respiration were increased in isolated cardiac myocytes from these pups compared to controls indicating mitochondrial dysfunction. Although abundance of mitochondrial respiratory complexes were unaltered, increased trilinoleoyl-lysocardiolipin levels in these pups was observed. A compensatory increase in both cardiolipin (CL) and phosphatidylethanolamine (PE) content were observed due to increased synthesis of these phospholipids. Conclusion Alterations in cardiac cardiolipin and phospholipid metabolism in PVR rat pups is associated with the mitochondrial bioenergetic and cardiac functional defects observed in their hearts. Impact statement - Phospholipid metabolism was examined in pulmonary vascular remodeling in perinatal rat pups. - Pulmonary vascular remodeling was induced in utero by treating pregnant dams with hypoxia and indomethacin at 19-21 days of gestation. - The offspring exhibited altered pulmonary arterial remodeling with subsequent cardiac hypertrophy, ventricular dysfunction, cardiac myocyte mitochondrial dysfunction with altered fatty acid utilization. - In addition, the offspring exhibited elevated cardiolipin, lysocardiolipin and phosphatidylethanolamine content which may potentially contribute to the cardiac mitochondrial dysfunction.
A reservoir of timescales in random neural network

The temporal activity of many biological systems, including neural circuits, exhibits fluctuations simultaneously varying over a large range of timescales. The mechanisms leading to this temporal heterogeneity are yet unknown. Here we show that random neural networks endowed with a distribution of self-couplings, representing functional neural clusters of different sizes, generate multiple timescales of activity spanning several orders of magnitude. When driven by a time-dependent broadband input, slow and fast neural clusters preferentially entrain slow and fast spectral components of the input, respectively, suggesting a potential mechanism for spectral demixing in cortical circuits.
Vaccine-induced, high magnitude HIV Env-specific antibodies with Fc-mediated effector functions are insufficient to protect infant rhesus macaques against oral SHIV infection

Improved access to antiretroviral therapy and antenatal care have significantly reduced in-utero and peri-partum mother-to-child HIV transmission. However, as breastmilk transmission of HIV still occurs at an unacceptable rate there remains a need to develop an effective vaccine for the pediatric population. Previously, we compared different HIV vaccine strategies, intervals, and adjuvants in infant rhesus macaques to optimize the induction of HIV envelope (Env)-specific antibodies with Fc-mediated effector function. Here, we tested the efficacy of an optimized vaccine regimen against oral SHIV acquisition in infant macaques. One group of 12 animals was immunized with 1086.c gp120 protein adjuvanted with 3M-052 in stable emulsion and Modified Vaccinia Ankara (MVA) virus vector expressing 1086.c HIV Env, while the control group (n=12) was immunized only with empty MVA. The first vaccine dose was given within 10 days of birth and booster doses were administered at weeks 6 and 12. The vaccine regimen induced Env-specific plasma IgG antibodies capable of antibody-dependent cellular cytotoxicity (ADCC) and phagocytosis (ADCP). Beginning at week 15, infants were exposed orally to escalating doses of heterologous SHIV-1157(QNE)Y173H once a week until infected. Despite the induction of strong Fc-mediated antibody responses, the vaccine regimen did not reduce the risk of infection, time to acquisition, or peak viremia compared to controls. Our results suggest that the non-neutralizing Env-specific antibodies with Fc effector function elicited by this vaccine regimen were insufficient for protection against heterologous oral SHIV infection shortly after the final immunization. IMPORTANCE Women of childbearing age are three times more likely to contract HIV infection than their male counterparts. Poor HIV testing rates coupled with low adherence to antiretroviral therapy (ART) result in a high risk of mother-to-infant HIV transmission, especially during the breastfeeding period. A preventative vaccine could curb pediatric HIV infections, reduce potential health sequalae, and prevent the need for lifelong ART in this population. The results of the current study imply that the HIV Env-specific IgG antibodies elicited by this candidate vaccine regimen, despite high magnitude of Fc-mediated effector function, but lack of neutralizing antibodies and polyfunctional T cell responses, were insufficient to protect infant rhesus macaques against oral virus acquisition.