Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of Multi-Strain Probiotics Combined with Gardeniae fructus on Intestinal Microbiota, Metabolites, and Morphology in Broilers

This study was conducted to investigate the effects of a multi-strain probiotic combined with Gardeniae fructus on the growth performance, intestinal microbiota composition and metabolites, and intestinal morphology of broiler chickens. The dietary treatments included the basal diet without any antimicrobials (C), the basal diet supplemented with 10 ppm avilamycin (A), the basal diet supplemented with 0.1% multi-strain probiotics powder containing Lactobacillus acidophilus LAP5, L. fermentum P2, L. casei L21, and Pediococcus acidophilus LS (1×107 CFU/g) (P), and the basal diet supplemented with a mixture of 0.1% multi-strain probiotics and 0.05% herbal medicine G. fructus (PH). The results showed no significant differences in growth performance across all groups. A denaturing gradient gel electrophoresis analysis indicated that the groups PH, P, and A exhibited an increase in the similarity coefficients of their intestinal microbial populations. The real-time polymerase chain reaction (PCR) analysis showed that the relative concentrations of Firmicutes and Lactobacillus in the cecum and Bifidobacterium spp. in the ileum were higher in the groups PH, P, and A than in group C, and the diet supplemented with multi-strain probiotics combined with G. fructus decreased the concentrations of cecal Escherichia spp. and Clostridium perfringens. The broilers fed with multi-strain probiotics combined with G. fructus showed a significant increase (P<0.05) in the cecal short-chain fatty acids (total SCFA, acetic acid, and butyric acid) compared to the other groups. The treatment with antibiotics, multi-strain probiotics, or multi-strain probiotics combined with G. fructus increased the villus height/crypt depth ratio in the ileum of broilers. In conclusion, the supplementation of multi-strain probiotics combined with G. fructus was beneficial to the intestinal microflora composition, metabolites, and morphology in broilers.
Association of ectomycorrhizal trees with high carbon‐to‐nitrogen ratio soils across temperate forests is driven by smaller nitrogen not larger carbon stocks

The distribution of mycorrhizal associations across biomes parallels a distinct gradient of soil carbon (C) and nitrogen (N) stocks, raising the question of how mycorrhizal traits relate to ecosystem properties. Arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) hosts and fungi employ contrasting strategies for N acquisition, which may manifest in differences in soil C and N pools and/or soil C:N. However, cross‐biome comparisons are confounded with climatic and edaphic gradients as well as phylogenetic and functional trait distributions of component plant species. Here, we test emerging hypotheses that soil C, N and C:N are related to the dominance of EM trees within a temperate forest region where AM and EM trees largely coexist but vary in local abundance. To determine the importance of mycorrhizal type on soil C and N, we analysed data from c. 1,000 forest inventory plots in the eastern United States. For each plot, we quantified the dominance of trees with different mycorrhizal associations and accounted for potentially confounding variables including phylogeny (angiosperm or gymnosperm), leaf N, soil clay content and climate. We used hierarchical Bayesian models to determine how these variables explained the patterns of soil C and N in the forest floor and mineral soil layers. Increasing EM dominance was associated with higher C:N across all soil layers. This relationship remained even after accounting for tree phylogeny, leaf N content, soil clay content, temperature and precipitation, which were all important for explaining soil C:N. However, this mycorrhizal pattern of soil C:N was not related to increases in soil C content; rather, increasing EM dominance was associated with reductions in soil N. Synthesis. Our findings are consistent with the proposition that mycorrhizal associations are related to terrestrial ecosystem properties. The mycorrhizal effect on soil C:N may result from differences in how arbuscular mycorrhizal and ectomycorrhizal plants interact with their fungal symbionts, decomposers and organic matter, to sustain differential cycling of C and N. Alternatively, these patterns could arise from differential success of the two mycorrhizal types in contrasting soil conditions; both processes may occur simultaneously, leading to a self‐reinforcing positive feedback.
High Arctic plants show independent responses to pollination and experimental warming

Arctic plants will experience both higher temperatures and changes to their pollination regime under future climate change scenarios. However, reproductive responses to pollination, warming, and a pollination–warming interaction likely vary with seasonal timing in phenology, and may be more pronounced in early-flowering plants than later-flowering plants. To test these hypotheses, we applied hand pollination and exclusion treatments to three Arctic plant species (early-flowering Salix arctica Pall., mid-season flowering Dryas integrifolia Vahl, and late-flowering Papaver radicatum Rottb.) inside and outside of open-top chambers (OTCs), to determine how pollination and warming may interact. We found that OTCs did not significantly reduce visitation by insects, nor did they reduce seed production in wind-pollinated S. arctica. Flower production and seed germination rates for D. integrifolia matched the predictions for warmth- and pollen-limited plants. Reproduction in P. radicatum did not respond strongly to either warming or pollination. Overall, we found that High Arctic plant reproduction is affected independently by pollination and OTC warming, indicating that plant responses to ongoing increases in temperature will not be strongly altered by changes in insect pollination.
Time-dependent mnemonic vulnerability induced by new-learning

Reactivation renders consolidated memory labile again, and the ensuing temporary reconsolidation process is highly susceptible to mnemonic modification. Here, we show that memories in such an unstable state could be reprogrammed by sheer behavioral means, bypassing the need for pharmacological intervention. In two experiments using a “face-location associationc” paradigm in which participants experienced a “Learning – New-learning – Final-test” programme, we demonstrate that reactivated memory traces were robustly hampered when the new learning was strategically administered within a critical 20-minute time window. Using fMRI, we further advance our theoretical understanding that this lability can be mechanistically explained by the differential activation in the hippocampal-amygdala memory system implicated by the new-learning whereas the mnemonic intrusion caused by newly learned memories is efficaciously reconciled by the left inferior frontal gyrus. Our findings provide important implications for educational and clinical practices in devising effective strategies for memory integration.
The probiotic effectiveness in experimental colitis is correlated with gut microbiome and host genetic features

Current evidence to support extensive use of probiotics in inflammatory bowel disease is limited and factors contribute to the inconsistent effectiveness of clinical probiotic therapy are not completely known. Here, as a proof-of-concept, we utilized Bifidobacterium longum JDM 301, a widely used commercial probiotic strain in China, to study potential factors that may influence the beneficial effect of probiotics in experimental colitis. We found that the probiotic therapeutic effect was varied across individual mouse even with the same genetic background and consuming the same type of food. The different probiotic efficacy was highly correlated with different microbiome features in each mouse. Consumption of a diet rich in fat can change the host sensitivity to mucosal injury-induced colitis but did not change the host responsiveness to probiotic therapy. Finally, the host genetic factor TLR2 was required for a therapeutic effect of B. longum JDM 301. Together, our results suggest that personalized microbiome and genetic features may modify the probiotic therapeutic effect.
The forms and meanings of baby birth, cultural discourse in manggarai language

espanolEste estudio describe las formas y significados del nacimiento del bebe, el discurso cultural en el idioma Manggarai en Indonesia. Los metodos de recopilacion de datos fueron la observacion, la entrevista, la discusion grupal focalizada y un estudio documental. Los datos se analizaron cualitativamente mediante el uso de un metodo inductivo. Los resultados del estudio muestran que las formas y significados del discurso cultural del nacimiento del bebe en el lenguaje Manggarai son especificos de la cultura Manggarai, ya que reflejan las conceptualizaciones de la gente Manggarai sobre el diferente estatus de una mujer y un hombre en el sistema social de Manggarai. tu, clan patrilineal-genealogico, basado en diferencias sexuales EnglishThis study describes the forms and meanings of baby birth,cultural discourse in Manggarai languagein Indonesia. The methodsof collecting data were observation, interview, focused-group discussion, and a documentary study. Data were analyzed qualitatively by using inductive method.The resultsof the study show that the forms and meanings of baby birth cultural discourse in the Manggarai languageare specific to Manggarai culture as they reflect the conceptualisations of Manggarai people on the different status of a female and male in the Manggarai social system of wa’u, patrilinealgenealogic clan, based on sexual differences.
Early detection of clinical mastitis from electrical conductivity data in an automatic milking system

Mastitis adversely affects profit and animal welfare in the Australian dairy industry. Electrical conductivity (EC) is increasingly used to detect mastitis, but with variable results. The aim of the present study was to develop and evaluate a range of indexes and algorithms created from quarter-level EC data for the early detection of clinical mastitis at four different time windows (7 days, 14 days, 21 days, 27 days). Historical longitudinal data collected (4-week period) for 33 infected and 139 healthy quarters was used to compare the sensitivity (Se; target >80%), specificity (Sp; target >99%), accuracy (target >90%) and timing of ‘alert’ by three different approaches. These approaches involved the use of EC thresholds (range 7.5– 10 mS/cm), testing of over 250 indexes (created ad hoc), and a statistical process-control method. The indexes were developed by combining factors (and levels within each factor), such as conditional rolling average increase, percentage of variation, mean absolute deviation, mean error %; infected to non-infected ratio, all relative to the rolling average (3–9 data points) of either the affected quarter or the average of the four quarters. Using EC thresholds resulted in Se, Sp and accuracy ranging between 47% and 92%, 39% and 92% and 51% and 82% respectively (threshold 7.5 mS/cm performed best). The six highest performing indexes achieved Se, Sp and accuracy ranging between 68% and 84%, 60% and 85% and 56% and 81% respectively. The statistical process-control approach did not generate accurate predictions for early detection of clinical mastitis on the basis of EC data. Improved Sp was achieved when the time window before treatment was reduced regardless of the test approach. We concluded that EC alone cannot provide the accuracy required to detect infected quarters. Incorporating other information (e.g. milk yield, milk flow, number of incomplete milking) may increase accuracy of detection and ability to determine early onset of mastitis.
Rapid production and characterization of antimicrobial colicins using Escherichia coli-based cell-free protein synthesis

Abstract Colicins are antimicrobial proteins produced by Escherichia coli, which, upon secretion from the host, kill non-host E. coli strains by forming pores in the inner membrane and degrading internal cellular components such as DNA and RNA. Due to their unique cell-killing activities, colicins are considered viable alternatives to conventional antibiotics. Recombinant production of colicins requires co-production of immunity proteins to protect host cells; otherwise, the colicins are lethal to the host. In this study, we used cell-free protein synthesis (CFPS) to produce active colicins without the need for protein purification and co-production of immunity proteins. Cell-free synthesized colicins were active in killing model E. coli cells with different modes of cytotoxicity. Pore-forming colicins E1 and nuclease colicin E2 killed actively growing cells in a nutrient-rich medium, but the cytotoxicity of colicin Ia was low compared to E1 and E2. Moreover, colicin E1 effectively killed cells in a nutrient-free solution, while the activity of E2 was decreased compared to nutrient-rich conditions. Both colicins E1 and E2 decreased the level of persister cells (metabolically dormant cell populations that are insensitive to antibiotics) by up to six orders of magnitude compared to that of the rifampin pretreated persister cells. This study finds that colicins can eradicate non-growing cells including persisters, and that CFPS is a promising platform for rapid production and characterization of toxic proteins.
ITS-based diversity of Colletotrichum from India

Rapid and precise species identification of plant pathogens such as Colletotrichum is essential for their effective control. Colletotrichum species have been traditionally identified based on conidial morphology and host-specificity. Recently, extra emphasis has been placed on DNA sequence comparison for rapid and accurate identification. In this study, we have analyzed the suitability of using internal transcribed spacer (ITS)/ 5.8S rRNA gene, which is the universal fungal barcode marker towards accurate identification of Colletotrichum species. We have sequenced 207 isolates of Colletotrichum and compared their ITS/ 5.8S rRNA gene-sequence data with that of the 183 reference sequences available for the 143 accepted Colletotrichum type strains. The results of phylogenetic analysis based on ITS/ 5.8S rRNA gene-sequence dataset along with sequencecomparison hints at the nomenclatural ambiguity of many isolates, which were initially diagnosed based on morphological characters. A local-BLAST analysis of the 588 GenBank sequences from India shows that 79% of the sequences were erroneously named and 97% of the 159 isolates procured from Indian culture collection centres were found to be misidentified. Mycologists need to work on identification of a potential secondary barcode for this genus as ITS/ 5.8S rRNA is found to be ineffective in accurate identification of Colletotrichum. Researchers should also follow a polyphasic approach for species identification, which would definitely not be rapid; nevertheless would be more reliable and accurate.
Effects of trophic stimulation on the maturation of neuromuscular junction

The neuromuscular junctions (NMJs) undergo maturation process after the initiation of nerve-muscle interaction. The morphological changes of NMJs during the process were meticulously studied. At the presynaptic side, SV clusters formed before the establishment of NMJ was enhanced at the nerve-muscle contact site. At the postsynaptic side, small puncta of nerve-induced AChR clusters consolidated into large patches. In addition, the apposition of preand postsynaptic specializations was also strengthened during the maturation process. Interestingly, chronic application of brain-derived neurotrophic factors (BDNF) or elevation of intracellular cyclic AMP (cAMP) level caused inhibitory effects on the NMJ maturation process. The density of nerve-induced AChR clusters as well as the apposition of SV and AChR clusters were significantly suppressed. However, the inhibitory effects of BDNF and cAMP were strongly reversed by TrkB and PKA inhibitors. It turns out that the TrkB signaling activated by BDNF plays an important role in the process through the mediation of PKA. FRET measurement of cAMP level in spinal cord neurons revealed that TrkB activation by BDNF raises intracellular cAMP level through the mediation of the MAPK pathway, which in turn leads to PKA activation. In addition, the PI3k-Akt pathway downstream of TrkB was also found to inhibit NMJ development. When the Akt activity was increased by PTEN inhibition, NMJ formation was compromised. This 2 process was partially rescued by rapamycin, which means that the target of rapamycin (TOR) mediates the inhibitory effects of the PI3k-Akt pathway on NMJ formation. As a result, the downstream effector molecules of PKA and TOR may together regulate the inhibitory effects of TrkB signaling on NMJ development. These results suggest that the TrkB signaling, though essential for neuronal survival and growth, needs to be turned down for NMJ formation and maturation.
Isolation and Characterization of the Corazonin Receptor and Possible Physiological Roles of Corazonin in the Kissing Bug, Rhodnius prolixus

Neuropeptides control many physiological and endocrinological processes in animals, acting as neuroactive chemicals within the central and peripheral nervous systems. Corazonin (CRZ) is one such neuropeptide that has a variety of physiological roles associated with control of heartbeat, ecdysis behaviour initiation, and cuticle colouration. These physiological effects are mediated by the CRZ receptor (CRZR) which is a G protein-coupled receptor. In order to understand the role of the CRZsignalling pathway in Rhodnius prolixus, the cDNA sequence encoding the Rhopr-CRZR has been isolated and cloned. The specificity of the Rhopr-CRZR was examined using CHOK1-aeq cells. Spatial expression pattern using quantitative PCR revealed receptor expression in the central nervous system, dorsal vessel, abdominal dorsal epidermis, and prothoracic glands. Receptor knockdown using dsRNA showed that CRZ maintains a higher heartbeat frequency in intact insects. Preliminary results using the knockdown have yet to show any effect on ecdysis or cuticle colouration.
Pax Romana: ‘refuge abandonment’ and spread of fearless behavior in a reconciling world

Intense human persecution of wildlife in the past selected for shy individuals that survived in suboptimal refuge habitats. It appears that this long‐term conflict is coming to an end in southern Europe, where direct persecution of wildlife has dramatically decreased due to human abandonment of the rural world and an increase in respectful attitudes toward wildlife. We provide a number of empirical examples of ongoing ‘refuge abandonment’ and the expansion of fearless behavior among southern European wildlife, including island and mainland case studies as well as predator and prey examples. We predict that many ecological refugees will increasingly abandon their historical refuges (of which many currently coincide with protected areas), and that the frequency of fearless behaviors will increase via cultural habituation and natural selection in populations of mammals and birds that were formerly persecuted. We also suggest that this has been a nonlinear process, which began considerably earlier than it became evident, with a long latent inertial regime, and a relatively rapid transition to a state of refuge abandonment and occupation of new, more anthropogenic habitats. The process of refuge abandonment and expansion of fearless behaviors will bring a new paradigm regarding human–wildlife relationships. It will also force changes in policies to protect high‐quality sites that are currently unoccupied and unprotected. Refuge abandonment may form a completely new research agenda and should be taken into account when studying patterns of wildlife dispersal or dynamics of spatially structured populations, among other relevant topics.
The effects of undercarboxylated osteocalcin on oxidative versus glycolytic skeletal muscle

The regulation of glucose uptake and mass in skeletal muscle are essential for the maintenance of functional capacity, general health, and quality of life. Skeletal muscle can be categorised into two major types, glycolytic and oxidative muscles. The regulation of muscle glucose uptake varies between the two muscle types, dependent on specific conditions, such as whether or not insulin is present, and whether the muscle is at rest or following exercise. Furthermore, muscle atrophy in response to disuse, disease or aging also occurs in a muscle type-specific manner. However, the exact mechanisms underlying these muscle type specificities still remain unclear. Emerging evidence indicates that undercarboxylated osteocalcin (ucOC), a hormone secreted from bone, may play a role in the regulation of muscle glucose uptake and muscle mass. The signalling pathways underlying the ucOC effect on muscle are not clear, but may include G protein-coupled receptor, class C, group 6, member A (GPRC6A) as the receptor, along with the activation of protein kinase B (Akt), extracellular signal-regulated kinases (ERK), 5' adenosine monophosphate-activated protein kinase (AMPK), protein kinase C (PKC), Akt substrate of 160kD (AS160), mammalian target of rapamycin complex 1 (mTORC1), and/or the class O of forkhead box transcription factors (FOXOs). It is also not clear whether the effect of ucOC on muscle glucose uptake and the loss of ucOC signalling during muscle atrophy are muscle type-specific, contributing to the muscle type specificities in glucose uptake regulation and muscle wasting, respectively. Therefore, this PhD thesis aimed to explore the link between ucOC and muscle glucose uptake (under various conditions) and muscle mass in glycolytic and oxidative muscles, as well as investigate the underlying mechanisms. The thesis contains four separate but related studies, all of which have been published in top journals in the area of bone and mineral research.
An issue of life or death: using eDNA to detect viable individuals in wilderness restoration

Analysis of aquatic environmental DNA (eDNA) is a promising tool for monitoring invasive species, but application of this method is hindered by the inability to distinguish whether sources are alive or dead. We analyzed how the detection of eDNA from dead and live model organisms (Carassius auratus) differs depending on collection method and applied the resulting method in the field. We sampled 15 microcosms containing dead or live fish through time using different filter membrane types and pore sizes at varying depths. We detected DNA from dead individuals only at the bottom of the water column. We found that as pore size increased, the quantity of DNA captured decreased for both treatments, the quantity of DNA from dead individuals decreased over time, and dead individuals were associated with less DNA than their live counterparts. We then sampled restoration sites across National Parks where nonnative fish were being removed to create habitat for endangered frogs (Rana sierrae and Rana muscosa). We sampled completed restoration sites (sites containing only dead fish; n = 21) and active restoration sites (sites containing dead and live fish; n = 9) with 1.2-µm polycarbonate track etch filters. Our field sampling accurately indicated the status of each site, except 1 probable false positive (low-level) and 1 false negative at a low-density site. Our results highlight that eDNA collection methods can be tailored to maximize the utility of eDNA techniques in aquatic habitat conservation. We recommend using eDNA techniques that maximize eDNA detection, sampling from water surfaces to avoid detection of dead individuals, and inferring presence of live individuals through the coupling of presence-only and quantification-based detections.