Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of the microbiota dynamics associated with Moniliophthora roreri, causal agent of cocoa frosty pod rot disease, reveals new viral species

Introduction Theobroma cacao, the cocoa tree, is a target for pathogens, such as fungi from the genera Phytophthora, Moniliophthora, Colletotrichum, Ceratocystis, among others. Some cacao pathogens are restricted to specific regions of the world, such as the Cacao swollen shoot virus (CSSV) in West African countries, while others are expanding geographically, such as Moniliophthora roreri in the Americas. M. roreri is one of the most threatening cacao pathogens since it directly attacks the cacao pods driving a significant reduction in production, and therefore economic losses. Despite its importance, the knowledge about the microenvironment of this pathogen and the cocoa pods is still poorly characterized. Methods Herein we performed RNA sequencing of spores in differential stages of culture in a medium supplemented with cacao pod extract and mycelium collected of the susceptible variety ICT 7121 naturally infected by the pathogen to evaluate the diversity and transcriptional activity of microorganisms associated with the in vitro sporulation of M. roreri. Results Our data revealed a great variety of fungi and bacteria associated with M. roreri, with an exceptional diversity of individuals from the genus Trichoderma sp. Interestingly, the dynamics of microorganisms from different kingdoms varied proportionally, suggesting they are somehow affected by M. roreri culture time. We also identified three sequences similar to viral genomes from the Narnaviridae family, posteriorly confirmed by phylogenetic analysis as members of the genus Narnavirus. Screening of M. roreri public datasets indicated the virus sequences circulating in samples from Ecuador, suggesting a wide spread of these elements. Of note, we did not identify traces of the viral sequences in the M. roreri genome or DNA sequencing, restricting the possibility of these sequences representing endogenized elements. Discussion To the best of our knowledge, this is the first report of viruses infecting the fungus of the genus Moniliophthora and only the third description of viruses that are able to parasite elements from the Marasmiaceae family.
Recent advances in constructed wetlands methane reduction: Mechanisms and methods

Constructed wetlands (CWs) are artificial systems that use natural processes to treat wastewater containing organic pollutants. This approach has been widely applied in both developing and developed countries worldwide, providing a cost-effective method for industrial wastewater treatment and the improvement of environmental water quality. However, due to the large organic carbon inputs, CWs is produced in varying amounts of CH4 and have the potential to become an important contributor to global climate change. Subsequently, research on the mitigation of CH4 emissions by CWs is key to achieving sustainable, low-carbon dependency wastewater treatment systems. This review evaluates the current research on CH4 emissions from CWs through bibliometric analysis, summarizing the reported mechanisms of CH4 generation, transfer and oxidation in CWs. Furthermore, the important environmental factors driving CH4 generation in CW systems are summarized, including: temperature, water table position, oxidation reduction potential, and the effects of CW characteristics such as wetland type, plant species composition, substrate type, CW-coupled microbial fuel cell, oxygen supply, available carbon source, and salinity. This review provides guidance and novel perspectives for sustainable and effective CW management, as well as for future studies on CH4 reduction in CWs.
Transcriptome-based analysis of key pathways relating to yield formation stage of foxtail millet under different drought stress conditions

Although foxtail millet, as small Panicoid crop, is of drought resilient, drought stress has a significant effect on panicle of foxtail millet at the yield formation stage. In this study, the changes of panicle morphology, photosynthesis, antioxidant protective enzyme system, reactive oxygen species (ROS) system, and osmotic regulatory substance and RNA-seq of functional leaves under light drought stress (LD), heavy drought stress (HD), light drought control (LDCK) and heavy drought control (HDCK) were studied to get a snap-shot of specific panicle morphological changes, physiological responses and related molecular mechanisms. The results showed that the length and weight of panicle had decreased, but with increased empty abortive rate, and then yield dropped off 14.9% and 36.9%, respectively. The photosynthesis of millet was significantly decreased, like net photosynthesis rate, stomatal conductance and transpiration rate, especially under HD treatment with reluctant recovery from rehydration. Under LD and HD treatment, the peroxidase (POD) was increased by 34% and 14% and the same as H2O2 by 34.7% and 17.2% compared with LDCK and HDCK. The ability to produce and inhibit O2- free radicals under LD treatment was higher than HD. The content of soluble sugar was higher under LD treatment but the proline was higher under HD treatment. Through RNA-seq analysis, there were 2,393 and 3,078 different genes expressed under LD and HD treatment. According to the correlation analysis between weighted gene coexpression network analysis (WGCNA) and physiological traits, the co-expression network of several modules with high correlation was constructed, and some hub genes of millet in response to drought stress were found. The expression changes relating to carbon fixation, sucrose and starch synthesis, lignin synthesis, gibberellin synthesis, and proline synthesis of millet were specifically analyzed. These findings provide a full perspective on how drought affects the yield formation of foxtail millet by constructing one work model thereby providing theoretical foundation for hub genes exploration and drought resistance breeding of foxtail millet.
Socioeconomic status and problem behaviors in young Chinese children: A moderated mediation model of parenting styles and only children

Introduction This study tested a moderated mediation model of child number (CN) and parenting styles (PS) in the relationships between family socioeconomic status (SES) and young children’s problem behaviors (PB). Methods A sample of 1,101 children (Mage = 4.90 years, SD = 1.07) and their parents participated in this study. Parents reported on PS, SES, and children’s PB. Results and Discussion The results show SES was positively related to authoritative parenting and negatively related to authoritarian parenting; problem behaviors were negatively related to authoritative parenting and positively related to authoritarian parenting; authoritative parenting and authoritarian parenting mediated the relationship between SES and PB; and singleton moderated the relationship between SES and PB. The combination of only children and low levels of SES could lead to high PB levels, while the combination of non-only children and high levels of SES could lead to high PB levels. At the same SES, only children had higher PB levels than non-only children.
The Pathway from Perceived Peer Support to Achievement via School Motivation in Girls and Boys: A Moderated-Mediation Analysis

Abstract While it is well established that positive peer relationships lead to positive outcomes, little is known about the mediating role of school motivation on the association between perceived peer support and school achievement among middle grades students. Even less is known about the effect of gender on this mediation. The current study examined whether school motivation mediates the association between perceived peer support and achievement. In addition, the gender effect on the mediation was examined using multigroup structural equation modeling. A total of 501 middle grades students (259 girls and 242 boys, aged 10–14 years) completed the self-report questionnaires assessing their perceived peer support, school motivation, and achievement. All models showed good model-data fit and indicated that school motivation fully mediates the associations between perceived peer support and school achievement in both genders. Also, the findings suggested that the association between school motivation and achievement was moderated by gender. The findings were discussed, and implications were shared for enhancing school achievement of middle grade students.
The formation of an expanding memory representation in the hippocampus

How episodic memories are stored within brains is poorly understood. While certain memory-retaining neurons have been potentially identified1–3, it is unclear if they retain learned information4,5. Further, there is considerable evidence that neuronal activity is unstable and may require additional mechanisms to support robust memory6–11. To examine these issues, we recorded the activity of a hippocampal CA1 neuronal population for 7 days as mice learned cued reward locations. These data and modelling results suggest that two place cell (PC) pools, distinguished by place field (PF) stability, are formed each day (transient: ~1.5 days; sustained: ~2 weeks)8. Notably, the proportions of these pools changed across the week as unstable transient PCs were progressively replaced by sustained PCs, markedly enhancing the stability of the total representation. This growing stable representation contained behaviorally relevant information and sustained PCs became active immediately at the start of each session. Finally, the initial formation of sustained PCs was associated with a higher rate and efficacy of behavioral timescale synaptic plasticity (BTSP) and these PCs showed elevated and more reliable activity. It, therefore, appears that BTSP stabilizes particularly informative PCs, incorporating them into an expanding and readily retrievable representation that displays hallmarks of a long-lasting memory.
The source of microbial transmission influences niche colonization and microbiome development

Early life microbial colonizers shape and support the immature vertebrate immune system. Microbial colonization relies on the vertical route via parental provisioning and the horizontal route via environmental contribution. Vertical transmission is mostly a maternal trait making it hard to determine the source of microbial colonization in order to gain insight in the establishment of the microbial community during crucial development stages. The evolution of unique male pregnancy in pipefishes and seahorses enables the disentanglement of both horizontal and vertical transmission, but also facilitates the differentiation of maternal vs. paternal provisioning ranging from egg development, to male pregnancy and early juvenile development. Using 16s rRNA amplicon sequencing and source-tracker analyses, we revealed how the distinct origins of transmission (maternal, paternal & horizontal) shaped the juvenile internal and external microbiome establishment in the broad-nosed pipefish Syngnathus typhle. Paternal provisioning mainly shaped the juvenile external microbiome, whereas maternal microbes were the main source of the internal juvenile microbiome, later developing into the gut microbiome. This suggests that stability of niche microbiomes may vary depending on the route and time point of colonization, the strength of environmental influences (i.e., horizontal transmission), and potentially the homeostatic function of the niche microbiome.
Analysis of Nucleotide Variations in Human G-Quadruplex Forming Regions Associated with Disease States

While the role of G4 G quadruplex structures has been identified in cancers and metabolic disorders, single nucleotide variations (SNVs) and their effect on G4s in disease contexts have not been extensively studied. The COSMIC and CLINVAR databases were used to detect SNVs present in G4s to identify sequence level changes and their effect on alteration of G4 secondary structure. 37,515 G4 SNVs in the COSMIC database and 2,115 in CLINVAR were identified. Of those, 7,236 COSMIC (19.3%) and 416 (18%) of the CLINVAR variants result in G4 loss, while 2,728 (COSMIC) and 112 (CLINVAR) SNVs gain a G4 structure. The gene ontology term “GnRH (Gonadotropin-releasing hormone) secretion” is enriched in 21 genes in this pathway that have a G4 destabilizing SNV. Analysis of mutational patterns in the G4 structure show a higher selective pressure (3-fold) in the coding region on the template strand compared to the non-template strand. At the same time, an equal proportion of SNVs were observed among intronic, promoter and enhancer regions across strands. Using GO and pathway enrichment, genes with SNVs for G4 forming propensity in the coding region are enriched for Regulation of Ras protein signal transduction and Src homology 3 (SH3) domain binding.
Localist versus distributed representation of sounds in the auditory cortex controlled by distinct inhibitory neuronal subtypes

Cortical circuits contain multiple types of inhibitory neurons which shape how information is processed within neuronal networks. Here, we asked whether somatostatin-expressing (SST) and vasoactive intestinal peptide-expressing (VIP) inhibitory neurons may have distinct effects on population neuronal responses to noise bursts of varying intensities. We optogenetically stimulated SST or VIP neurons while simultaneously measuring the calcium responses of populations of hundreds of neurons in the auditory cortex of male and female awake, head-fixed mice to sounds. Upon SST neuronal activation, noise bursts representations became more discrete for different intensity levels, relying on cell identity rather than strength. In contrast, upon VIP neuronal activation, noise bursts of different intensity level activated overlapping neuronal populations, albeit at different response strengths. At the single-cell level, SST and VIP neuronal activation differentially activated the response-level curves of monotonic and nonmonotonic neurons. SST neuronal activation effects were consistent with a shift of the neuronal population responses toward a more localist code with different cells responding to sounds of different intensity. By contrast, VIP neuronal activation shifted responses towards a more distributed code, in which sounds of different intensity level are encoded in the relative response of similar populations of cells. These results delineate how distinct inhibitory neurons in the auditory cortex dynamically control cortical population codes. Different inhibitory neuronal populations may be recruited under different behavioral demands, depending on whether categorical or invariant representations are advantageous for the task. SIGNIFICANCE Information about sounds is represented in the auditory cortex by neuronal population activity that has a characteristic sparse structure. Cortical neuronal populations comprise multiple types of excitatory and inhibitory neurons. Here, we find that activating different types of inhibitory neurons differentially controls population neuronal representations, with one type of inhibitory neurons increasing the differences in the identity of the cells recruited to represent the different sounds, and another inhibitory neuron type changing the relative activity level of overlapping neuronal populations. Such transformations may be beneficial for different types of auditory behaviors, suggesting that these different types of inhibitory neurons may be recruited under different behavioral constraints in optimizing neuronal representations of sounds.
Dopamine Increases Accuracy and Lengthens Deliberation Time in Explicit Motor Skill Learning

Although animal research implicates a central role for dopamine in motor skill learning, a direct causal link has yet to be established in neurotypical humans. Here, we tested if a pharmacological manipulation of dopamine alters motor learning, using a paradigm which engaged explicit, goal-directed strategies. Participants (27 females, 11 males, aged 18-29 years) first consumed either 100mg of Levodopa (n=19), a dopamine precursor that increases dopamine availability, or placebo (n=19). Then, during training, participants learnt the explicit strategy of aiming away from presented targets by instructed angles of varying sizes. Targets shifted mid-movement by the instructed aiming angle. Task success was thus contingent upon aiming accuracy. The effect of the dopamine manipulations on skill learning was assessed during training, and at an overnight follow-up. Increasing dopamine availability improved aiming accuracy and lengthened reaction times, particularly for larger, more difficult aiming angles, both at training, and at follow-up. Results support the proposal that dopamine is important in decisions to engage instrumental motivation to optimise performance, particularly when learning to execute goal-directed strategies in motor skill learning.
Genetic diversity and population structure of Epichloe fungal pathogens of plants in natural ecosystems

Understanding the population genetic processes driving the evolution of plant pathogens is of central interest to plant pathologists and evolutionary biologists alike. However, most studies focus on host-pathogen associations in agricultural systems of high genetic and environmental homogeneity and less is known about the genetic structure of pathogen populations infecting wild plants in natural ecosystems. We performed parallel population sampling of two pathogenic Epichloe species occurring sympatrically on different host grasses in natural and seminatural grasslands in Europe: E. typhina infecting Dactylis glomerata and E. clarkii infecting Holcus lanatus. We sequenced 422 haploid isolates and generated genome-wide SNP datasets to investigate genetic diversity and population structure. In both species geographically separated populations formed genetically distinct groups, however population separation was less distinct in E. typhina compared to E. clarkii. The patterns of among population admixture also differed between species across the same geographic range: we found higher levels of population genetic differentiation and a stronger effect of isolation by distance in E. clarkii compared to E. typhina, consistent with lower levels of gene flow in the former. This pattern may be explained by the different dispersal abilities of the two pathogens and is expected to be influenced by the genetic structure of host populations. In addition, genetic diversity was higher in E. typhina populations compared to E. clarkii, indicative of higher effective population size in E. typhina. These results suggest that the effect of genetic drift and the efficacy of selection may differ in the two species. Our study provides evidence of how ecologically similar species occupying the same geographical space can experience different evolutionary contexts, which could influence local adaptation and coevolutionary dynamics of these fungal pathogens.
Interplay between PLEKHG3-regulated actin dynamics and lysosomal trafficking in cell motility

Lysosomes are highly dynamic organelles that regulate metabolic signaling pathways by recruiting cytosolic molecules to protein platforms on the lysosomal membrane. We performed a proximity-dependent labeling screen to identify novel proteins recruited to the LAMTOR complex, which regulates lysosome positioning and key signaling pathways such as mTORC1, AMPK, and MEK/ERK. We identified a network of proteins involved in actin remodelling, including Pleckstrin homology domain-containing family G member 3 (PLEKHG3), an actin-binding Rho guanine nucleotide exchange factor enriched in protrusions. We show that GFP-PLEKHG3 accumulates in focal adhesion sites, where it colocalizes with peripheral lysosomes. Peripheral accumulation of lysosomes concentrates PLEKHG3 below the plasma membrane, inhibits protrusion formation and limits cell motility. Thus, subcellular positioning of lysosomes impacts PLEKHG3 subcellular localization and the cell’s protrusion activity, shape, and motility. The results shed new light on the interplay between lysosomes and actin dynamics and provides insights into the mechanisms controlling cellular processes such as shape regulation and motility of the plasma membrane.
Temporal regulation of AgRP neurons mediates context-induced feeding

An environment can have a powerful influence over appetite and feeding behaviour. For example, an environmental context, which reliably predicts food, will increase the appetitive food drive to the same environment context. Interestingly, mice are required to be hungry to develop such a context-induced feeding (CIF) response, suggesting the neural circuits sensitive to hunger play an important role to associate an internal energy state with a particular environment context. Hunger-sensing Agouti related peptide (AgRP) neurons are activated by circulating signals of energy deficit and reset to a silenced state by gut feedback mechanisms following food consumption. We hypothesised that AgRP neurons are both necessary and sufficient to drive CIF in the absence of hunger. While fasting increased CIF, chemogenetic inhibition of AgRP neurons during context acquisition prevented this effect. Intriguingly, chemogenetic activation of AgRP neurons during context acquisition did not increase CIF, suggesting precise temporal firing properties may be required. Indeed, photostimulation of AgRP neurons, only during context exposure (ON-OFF in context), increased CIF. Moreover, AgRP photostimulation prior to context exposure, coupled with the termination of photostimulation in the context in the absence of food consumption, was sufficient to drive a subsequent CIF. Our results suggest that AgRP neurons regulate the acquisition of CIF when the temporal firing properties are matched to context exposure. These results further highlight that acute AgRP inhibition is a salient neural event underscoring the effect of hunger on associative learning.
Induction of Transmucosal Protection by Oral Vaccination with an Attenuated Chlamydia

Chlamydia muridarum has been used to study chlamydial pathogenesis because it induces mice to develop hydrosalpinx, a pathology observed in C. trachomatis-infected women. We identified a C. muridarum mutant that is no longer able to induce hydrosalpinx. ABSTRACT Chlamydia muridarum has been used to study chlamydial pathogenesis because it induces mice to develop hydrosalpinx, a pathology observed in C. trachomatis-infected women. We identified a C. muridarum mutant that is no longer able to induce hydrosalpinx. In the current study, we evaluated the mutant as an attenuated vaccine. Following an intravaginal immunization with the mutant, mice were protected from hydrosalpinx induced by wild-type C. muridarum. However, the mutant itself productively colonized the mouse genital tract and produced infectious organisms in vaginal swabs. Nevertheless, the mutant failed to produce infectious shedding in the rectal swabs following an oral inoculation. Importantly, mice orally inoculated with the mutant mounted transmucosal immunity against challenge infection of wild-type C. muridarum in the genital tract. The protection was detected as early as day 3 following the genital challenge infection and the orally immunized mice were protected from any significant pathology in the upper genital tract. However, the same orally immunized mice failed to prevent the colonization of wild-type C. muridarum in the gastrointestinal tract. The transmucosal immunity induced by the oral mutant was further validated in the airway. The orally vaccinated mice were protected from both lung infection and systemic toxicity caused by intranasally inoculated wild-type C. muridarum although the same mice still permitted the gastrointestinal colonization by the wild-type C. muridarum. These observations suggest that the mutant C. muridarum may be developed into an intracellular oral vaccine vector (or IntrOv) for selectively inducing transmucosal immunity in extra-gut tissues.