Miracle-dz/UniFAR-FTUs huggingface dataset:
Seven-CpG DNA Methylation Age Determined by Single Nucleotide Primer Extension and Illumina’s Infinium MethylationEPIC Array Provide Highly Comparable Results

DNA methylation age (DNAm age, epigenetic clock) is a novel and promising biomarker of aging. It is calculated from the methylation fraction of specific cytosine phosphate guanine sites (CpG sites) of genomic DNA. Several groups have proposed epigenetic clock algorithms and these differ mostly regarding the number and location of the CpG sites considered and the method used to assess the methylation status. Most epigenetic clocks are based on a large number of CpGs, e.g. as measured by DNAm microarrays. We have recently evaluated an epigenetic clock based on the methylation fraction of seven CpGs that were determined by methylation-sensitive single nucleotide primer extension (MS-SNuPE). This method is more cost-effective when compared to array-based technologies as only a few CpGs need to be examined. However, there is only little data on the correspondence in epigenetic age estimation using the 7-CpG clock and other algorithms. To bridge this gap, in this study we measured the 7-CpG DNAm age using two methods, via MS-SNuPE and via the MethylationEPIC array, in a sample of 1,058 participants of the Berlin Aging Study II (BASE-II), assessed as part of the GendAge study. On average, participants were 75.6 years old (SD: 3.7, age range: 64.9 – 90.0, 52.6% female). Agreement between methods was assessed by Bland-Altman plots. DNAm age was highly correlated between methods (Pearson’s r=0.9) and Bland-Altman plots showed a difference of 3.1 years. DNAm age by the 7-CpG formula was 71.2 years (SD: 6.9 years, SNuPE) and 68.1 years (SD: 6.4 years, EPIC array). The mean of difference in methylation fraction between methods for the seven individual CpG sites was between 0.7 and 13 percent. To allow direct conversion between methods we developed an adjustment formula with a randomly selected training set of 529 participants using linear regression. After conversion of the Illumina data in a second and independent validation set, the adjusted DNAm age was 71.44 years (SD: 6.1 years, n=529). In summary, we found the results of DNAm clocks to be highly comparable. Furthermore, we developed an adjustment formula that allows for direct conversion of estimates between methods and enables one singular clock to be used in studies that employ either the Illumina or the SNuPE method.
Band gap opening of graphene by forming a graphene/PtSe2 van der Waals heterojunction

Opening a band gap and finding a suitable substrate for graphene are two challenges for constructing graphene based nano-electronic devices. Recently, a new two-dimensional layered crystal PtSe2 with novel electronic properties has been efficiently synthesized by direct “selenization”. In this work, we demonstrate that PtSe2 can be used as a suitable substrate for graphene by forming a graphene/PtSe2 van der Waals (vdW) heterojunction. Hybrid density functional calculations show that PtSe2 as a substrate could introduce a sizeable gap of 0.264 eV into graphene, which is sufficiently large enough for overcoming the thermal excitation of electrons at room temperature. The underlying mechanism for the band gap opening of graphene is that the PtSe2 substrate can produce inhomogeneous electrostatic potential to break the symmetry of the A and B sub-lattices of graphene. By applying a vertical strain to the graphene/PtSe2 vdW heterojunction, the electronic properties of the heterojunction can be effectively tuned. As the vertical strain increases, the band gap monotonously increases and can reach as large as 0.781 eV. The tunable band gap, together with the high carrier mobility of both graphene and PtSe2, suggests the great potential of the PtSe2/graphene heterojunction in high performance field effect transistors.
Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation

Because of the continuous rise of foodborne illnesses caused by the consumption of raw fruits and vegetables, effective post-harvest anti-microbial strategies are needed. This study evaluated the dose × time effects on the anti-microbial action of ozone (O3) gas against the Gram-negative Escherichia coli O157:H7 and Gram-positive Listeria monocytogenes, which are common contaminants in fresh produce. The study on non-host tomato environment correlated the dose × time aspects of xenobiosis by examining the correlation between bacterial survival in terms of log-reduction and defense responses at the level of gene expression. In E. coli, low (1 μg O3/g of fruit) and moderate (2 μg O3/g of fruit) doses caused insignificant reduction in survival, while high dose (3 μg/g of fruit) caused significant reduction in survival in a time-dependent manner. In L. monocytogenes, moderate dose caused significant reduction even with short-duration exposure. Distinct responses to O3 xenobiosis between E. coli and L. monocytogenes are likely related to differences in membrane and cytoplasmic structure and components. Transcriptome profiling by RNA-Seq showed that primary defenses in E. coli were attenuated after exposure to a low dose, while the responses at moderate dose were characterized by massive upregulation of pathogenesis and stress-related genes, which implied the activation of defense responses. More genes were downregulated during the first hour at high dose, with a large number of such genes getting significantly upregulated after 2 hr and 3 hr. This trend suggests that prolonged exposure led to potential adaptation. In contrast, massive downregulation of genes was observed in L. monocytogenes regardless of dose and exposure duration, implying a mechanism of defense distinct from that of E. coli. The nature of bacterial responses revealed by this study should guide the selection of xenobiotic agents for eliminating bacterial contamination on fresh produce without overlooking the potential risks of adaptation.
Cross-species incompatibility between a DNA satellite and the Drosophila Spartan homolog poisons germline genome integrity

Satellite DNA spans megabases of eukaryotic sequence and evolves rapidly. Paradoxically, satellite-rich genomic regions mediate strictly conserved, essential processes like chromosome segregation and nuclear structure. A leading resolution to this paradox posits that satellite DNA and satellite-associated chromosomal proteins coevolve to preserve these essential functions. We experimentally test this model of intra-genomic coevolution by conducting the first evolution-guided manipulation of both chromosomal protein and DNA satellite. The 359bp satellite spans an 11Mb array in D. melanogaster that is absent from its sister species, D. simulans. This species-specific DNA satellite colocalizes with the adaptively evolving, ovary-enriched protein, Maternal Haploid (MH)–the Drosophila homolog of Spartan. To determine if MH and 359 coevolve, we swapped the D. simulans version of MH (“MH[sim]”) into D. melanogaster. MH[sim] triggers ovarian cell death, reduced ovary size, and loss of mature eggs. Surprisingly, the D. melanogaster mh null mutant has no such ovary phenotypes, suggesting that MH[sim] is toxic in a D. melanogaster background. Using both cell biology and genetics, we discovered that MH[sim] poisons oogenesis through a DNA damage pathway. Remarkably, deleting the D. melanogaster-specific 359 satellite array completely restores mh[sim] germline genome integrity and fertility, consistent with a history of coevolution between these two fast-evolving loci. Germline genome integrity and fertility are also restored by overexpressing Topoisomerase II (Top2), suggesting that MH[sim] interferes with Top2-mediated processing of 359. The observed 359-MH[sim] cross-species incompatibility supports a model under which ostensibly inert repetitive DNA and essential chromosomal proteins must coevolve to preserve germline genome integrity.
Phase-locking patterns underlying effective communication in exact firing rate models of neural networks

Macroscopic oscillations in the brain have been observed to be involved in many cognitive tasks but their role is not completely understood. One of the suggested functions of the oscillations is to dynamically modulate communication between neural circuits. The Communication Through Coherence (CTC) theory establishes that oscillations reflect rhythmic changes in excitability of the neuronal populations. Thus, populations need to be properly phase-locked so that input volleys arrive at the peaks of excitability of the receiving population to communicate effectively. Here, we present a modeling study to explore synchronization between neuronal circuits connected with unidirectional projections. We consider an Excitatory-Inhibitory (E-I) network of quadratic integrate-and-fire neurons modeling a Pyramidal-Interneuronal Network Gamma (PING) rhythm. The network receives an external periodic input from either one or two sources, simulating the inputs from other oscillating neural groups. We use recently developed mean-field models which provide an exact description of the macroscopic activity of the spiking network. This low-dimensional mean field model allows us to use tools from bifurcation theory to identify the phase-locked states between the input and the target population as a function of the amplitude, frequency and coherence of the inputs. We identify the conditions for optimal phaselocking and selective communication. We find that inputs with high coherence can entrain the network for a wider range of frequencies. Besides, faster oscillatory inputs than the intrinsic network gamma cycle show more effective communication than inputs with similar frequency. Our analysis further shows that the entrainment of the network by inputs with higher frequency is more robust to distractors, thus giving them an advantage to entrain the network. Finally, we show that pulsatile inputs can switch between attended inputs in selective attention. Author summary Oscillations are ubiquitous in the brain and are involved in several cognitive tasks but their role is not completely understood. The Communication Through Coherence theory proposes that background oscillations in the brain regulate the information flow between neural populations. The oscillators that are properly phase-locked so that inputs arrive at the peaks of excitability of the receiving population communicate effectively. In this paper, we study the emerging phase-locking patterns of a network generating PING oscillations under external periodic forcing, simulating the oscillatory input from other neural groups. We identify the conditions for optimal phase-locking and selective communication. Namely, we find that inputs with higher frequency and coherence have an adavantage to entrain the network and we quantify how robust are to distractors. Furthermore, we show how selective attention can be implemented by means of phase locking and we show that pulsatile inputs can switch between attended inputs.
Autophagy coordinates chondrocyte development and early joint formation in zebrafish

Autophagy is a catabolic process responsible for the removal of waste and damaged cellular components by lysosomal degradation. It plays a key role in fundamental cell processes, including ER stress mitigation, control of cell metabolism, and cell differentiation and proliferation, all of which are essential for cartilage cell (chondrocyte) development and survival, and for the formation of cartilage. Correspondingly, autophagy dysregulation has been implicated in several skeletal disorders such as osteoarthritis and osteoporosis. To test the requirement for autophagy during skeletal development in zebrafish, we generated an atg13 CRISPR knockout zebrafish line. This line showed a complete loss of atg13 expression, and restricted autophagic activity in vivo. In the absence of autophagy, chondrocyte maturation was accelerated, with chondrocytes exhibiting signs of premature hypertrophy. Focussing on the jaw element, autophagy disruption affected joint articulation causing restricted mouth opening. This gross behavioural phenotype corresponded with a failure to thrive, and death in homozygote atg13 nulls within 17 days. Taken together, our results are consistent with autophagy contributing to the timely regulation of chondrocyte maturation and for extracellular matrix formation.
Effects of land-use and landscape drivers in the species richness and distribution of carnivores in Faragosa-Fura Landscape of Southern Rift Valley, Ethiopia

Understanding the species richness and distribution of carnivores across anthropogenic land-use types in an area is an essential first step for biodiversity conservation and human-carnivore coexistence. However, quantitative data on carnivore species coexisting with humans in different land-use types remain largely missing. Thus, this paper investigated the effect of anthropogenic land-use and landscape drivers on carnivore species richness and distribution in the Faragosa-Fura Landscape, Gamo Zone, southern Ethiopia. To collect data, we employed the line transect method using three complementary field surveys techniques: sign survey, camera-trapping, and opportunistic sighting survey during wet and dry seasons in 2020 and 2021. We stratified the study landscape into five land-use types-forest, wetland, grassland, agricultural land, and settlement. The result proved the occurrence of 12 carnivore species belonging to six families, including vulnerable Felidae species - Panthera pardus. Family Felidae and Herpestidae were composed of a greater number of species, while Hyaenidae and Mustelidae were each represented by single species. Out of identified species, only two species (Panthera pardus and Crocuta crocuta) were large-sized, while the rest were medium and small-sized carnivores. Overall, the mean richness of the study area was 5.73±0.284(SE). The species richness was highest in the wetland (n = 12, mean = 7.67±0.494(SE)) and lowest in the settlement (n = 5, mean = 4.25±0.479(SE)). The regression analysis showed that most of the carnivores displayed a strong negative relationship with agriculture, roads, and settlement while displayed a strong positive relationship with wetland and forest. In general, out of 32 species recorded in Ethiopia, this study quantified 12 carnivore species that signify the area is an important area for wildlife conservation in Ethiopia. Further, the study concluded that the wetland is the most important habitat, particularly for larger-sized and habitat specialists while anthropogenic land-uses types adversely affecting species richness. Thus, a generic paradigm to reconcile land management and biodiversity conservation is highly important.
Learning from the path not taken: Sensory prediction errors are sufficient for implicit adaptation of withheld movements

Current theories of motor control emphasize forward models as a critical component of the brain’s motor execution and learning networks. These internal models are thought to predict the consequences of movement before sensory feedback from these movements can reach the brain, allowing for smooth, continuous online motor performance and for the computation of prediction errors that drive implicit motor learning. Taking this framework to its logical extreme, we tested the hypothesis that movements are not necessary for the generation of predictions, the computation of prediction errors, and implicit motor adaptation. Human participants were cued to move a computer mouse to a visually displayed target and were subsequently cued to withhold those movements on a subset of trials. Visual errors displayed on both trials with and without movements to the target induced single-trial learning. Furthermore, learning on trials without movements persisted when accompanying movement trials were never paired with errors and when movement and sensory feedback trajectories were decoupled. These data provide compelling evidence supporting an internal model framework in which forward models generate sensory predictions independent of the generation of movements.The brain can learn to update movements that are not performed, representing a mechanism for learning based only on movement planning and sensory expectation.Supports a fundamental role for prediction in adaptation.Provides further support for the role of forward models in predictive motor control.
Autophagy cargo receptors are secreted via extracellular vesicles and particles in response to endolysosomal inhibition or impaired autophagosome maturation

The endosome-lysosome (endolysosome) system plays central roles in both autophagic degradation and secretory pathways, including the exocytic release of extracellular vesicles and particles (EVPs). Although previous work has revealed important interconnections between autophagy and EVP-mediated secretion, our molecular understanding of these secretory events during endolysosome inhibition remains incomplete. Here, we delineate a secretory autophagy pathway upregulated in response to endolysosomal inhibition that mediates the EVP-associated extracellular release of autophagic cargo receptors, including p62/SQSTM1. This extracellular secretion is highly regulated and critically dependent on multiple ATGs required for the progressive steps of early autophagosome formation as well as Rab27a-dependent exocytosis. Furthermore, the disruption of autophagosome maturation, either due to genetic inhibition of the autophagosome-to-autolyosome fusion machinery or blockade via the SARS-CoV2 viral protein ORF3a, is sufficient to induce robust EVP-associated secretion of autophagy cargo receptors. Finally, we demonstrate that this ATG-dependent, EVP-mediated secretion pathway buffers against the intracellular accumulation of autophagy cargo receptors when classical autophagic degradation is impaired. Based on these results, we propose that secretory autophagy via EVPs functions as an alternate route to clear sequestered material and maintain proteostasis in response to endolysosomal dysfunction or impaired autophagosome maturation.
Humanoid robots are perceived as an evolutionary threat

Studying how we perceive humanoid robots will provide insights for a deeper understanding of human-robot interaction. Our ideas about humanoid robots are mainly informed by science fiction, and humanoid robots are generally described as an evolutionary threat in science fiction that has not been tested. The preparedness model has emphasized that the fear module is automatically activated by evolutionary threats, and its underlying neural circuit is centered on the amygdala. We hypothesized that if humanoid robots are perceived as an evolutionary threat even though humanoid robots are manmade, modern objects, we would expect to observe a monocular advantage for humanoid robots and an amygdala response to unconsciously presented humanoid robots that were previously only evident in evolutionary threats. Here, we observed a monocular advantage for the perception of humanoid robots the same as an evolutionary threat (i.e., snakes). Our neuroimaging analysis indicated that unconscious presentation of humanoid robot vs. human images led to significant amygdala activation. Despite a positive humanoid robot-related association had been established by associative learning (as evidenced by results of successfully weakening the negative implicit attitude to humanoid robots and enhancing functional connectivity between the amygdala and hippocampus), the amygdala could still automatically and quickly detect humanoid robots. Our results reveal that processing of information about humanoid robots displays automaticity with regard to recruitment of visual pathway and amygdala activation. Our findings that humans apparently perceive humanoid robots as an evolutionary threat may help inform redefinition of human-robot interaction and robot ethics.
Maternal γδ T cells shape offspring pulmonary type-2 immunity in a microbiota-dependent manner

Immune system development is greatly influenced by vertically transferred cues. However, beyond antibody-producing B cells, little is known about the role of other cell subsets of the maternal immune system in regulating offspring immunity. We reasoned γδ T cells to be attractive candidates based on their tissue distribution pattern: abundant in the skin, mammary glands and female reproductive tract. Here we found that mice born from γδ T cell-deficient (TCRδ-/-) dams display, early after birth, a pulmonary milieu selectively enriched in type-2 cytokines such as IL-33, IL-4, IL-5, and IL-13, and type-2-polarized immune cells, when compared to the progeny of γδ T cell-sufficient dams. In addition, upon helminth infection, mice born from TCRδ-/- dams sustained an increased type-2 inflammatory response. Critically, this was independent of the genotype of the pups. Despite similar levels of circulating antibodies in mothers and progeny, the intestinal microbiota in the offspring of TCRδ-/- and TCRδ+/- dams harbored distinct bacterial communities acquired during birth and fostering. These differences were accompanied by changes in the intestinal short-chain fatty acids (SCFA) profile. Importantly, antibiotic treatment abrogated the differences observed in the pulmonary milieu, and exogenous SCFA supplementation suppressed first-breath- and infection-induced inflammation. In summary, maternal γδ T cells control the establishment of a neonatal gut–lung axis by conditioning the postnatal microbial colonization of the off-spring and bacterial-derived metabolite availability; ultimately impacting on the development of pulmonary type-2 immunity in the offspring.
wnt16 exerts pleiotropic effects on bone and lean mass in zebrafish

Osteoporosis, a disease of bone fragility, and sarcopenia, a condition of reduced muscle mass and strength, commonly occur in the same individual--a condition termed osteosarcopenia. Genetic variants at the CPED1-WNT16 locus have pleiotropic effects on human bone mineral density (BMD) and lean tissue mass. However, our current understanding of Wnt16 and its influence on bone fails to explain effects on lean mass at this locus. In this study, we sought to better understand the biological mechanism underlying pleiotropy at the CPED1-WNT16 locus on BMD and lean mass. Using single cell analysis, microCT imaging, and genetic approaches in zebrafish, we show that wnt16 exerts dual influence on muscle and bone, and provide evidence that this occurs through a function in somite development, a period in which precursors for both of these tissues are specified. We show that mutations in wnt16 alter vertebral size and lean mass during axial skeletogenesis. We show that wnt16+ cells transcriptionally resemble cells within the amniote dermomyotome, and provide evidence they function as myogenic precursors during embryonic development. We also provide evidence that WNT16 is a gene of major effect on lean mass at the CPED-WNT16 locus. Our studies support the potential for wnt16 to exert pleiotropic effects on bone and lean mass through a function in myogenic precursors.