Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequence of Lactobacillus reuteri PNW1, a Promising Probiotic Candidate

This study reports the whole-genome sequence of Lactobacillus reuteri PNW1 isolated from gastrointestinal tracts of weaned piglets of the indigenous South African Windsnyer pig breed. A total of 5.2 GB data comprising 8,209,104 paired-end reads were generated. ABSTRACT This study reports the whole-genome sequence of Lactobacillus reuteri PNW1 isolated from gastrointestinal tracts of weaned piglets of the indigenous South African Windsnyer pig breed. A total of 5.2 GB data comprising 8,209,104 paired-end reads were generated. The assembled genome is 2,430,215 bp long in 420 contigs with 39% G+C content.
Inhibition of LOXL2 Enhances the Radiosensitivity of Castration-Resistant Prostate Cancer Cells Associated with the Reversal of the EMT Process

Introduction Radiotherapy is the mainstay in the treatment of prostate cancer. However, significant radioresistance of castration-resistant prostate cancer (CRPC) cells constitutes a main obstacle in the treatment of this disease. By using bioinformatic data mining methods, LOXL2 was found to be upregulated in both androgen-independent prostate cancer cell lines and radioresistant tumor samples collected from patients with prostate cancer. We speculate that LOXL2 may play an important role in the radioresistance of CRPC cells. Methods The effect of LOXL2 knockdown on the radiosensitivity of androgen-independent prostate cancer cells lines was measured by the clonogenic assay and xenograft tumor experiments under in vitro and in vivo conditions, respectively. In studies on the mechanism, we focused on the EMT phenotype changes and cell apoptosis changes induced by LOXL2 knockdown in DU145 cells. The protein levels of three EMT biomarkers, namely, E-cadherin, vimentin, and N-cadherin, were measured by western blotting and immunohistochemical staining. Cell apoptosis after irradiation was measured by flow cytometry and caspase-3 activity assay. Salvage experiment was also conducted to confirm the possible role of EMT in the radiosensitization effect of LOXL2 knockdown in CRPC cells. Results LOXL2 knockdown in CRPC cells enhanced cellular radiosensitivity under both in vitro and in vivo conditions. A significant reversal of EMT was observed in LOXL2-silenced DU145 cells. Cell apoptosis after irradiation was significantly enhanced by LOXL2 knockdown in DU145 cells. Results from the salvage experiment confirmed the key role of EMT process reversal in the radiosensitization effect of LOXL2 knockdown in DU145 cells. Conclusions LOXL2 plays an important role in the development of cellular radioresistance in CRPC cells. Targeting LOXL2 may be a rational avenue to overcome radioresistance in CRPC cells. A LOXL2-targeting strategy for CRPC treatment warrants detailed investigation in the future.
Associations between antenatal prednisone exposure and long-term cortisol and cortisone concentrations in children born to women with rheumatoid arthritis: results from a nationwide prospective cohort study

Objectives To identify whether children with antenatal prednisone exposure have chronically elevated cortisol and cortisone concentrations, an altered body composition or higher blood pressure. In addition, to identify whether maternal rheumatoid arthritis disease (RA) activity is associated with these alterations. Methods In this prospective study, 56 children (mean age=10.0 years) with and 61 children (mean age=9.6 years) without antenatal prednisone exposure, born to women with RA, were included. Hair cortisol and cortisone were analysed using liquid chromatography–tandem mass spectrometry. Linear regression models were built to analyse differences between the two groups, corrected for relevant covariates. Hair cortisol concentrations were also compared between the study population and an age-matched healthy reference group(n=150 children, mean age=9.8 years). Results Hair cortisol and cortisone concentrations were similar in children with and without antenatal prednisone exposure (median cortisol 1.14 pg/mg (IQR 0.67–1.75) and 1.15 pg/mg (IQR 0.65–2.21) and median cortisone 6.76 pg/mg (IQR 5.42–8.86) and 7.40 pg/mg (IQR 5.39–10.73), respectively). Antenatal prednisone exposure and maternal RA disease activity were also not associated with body composition or blood pressure. Hair cortisol concentrations were not different in children born to mothers with RA compared with children from the reference group. Conclusion This, in its kind, large and unique long-term prospective study demonstrates that low-dose antenatal prednisone exposure and maternal RA disease activity are not associated with negative consequences in prepubertal childhood. The findings of this study are reassuring and support the assumption that low-dose maternal prednisone use during pregnancy is safe for the offspring, at least until the age of approximately 10 years.
Integrative taxonomic reassessment of Odontophrynus populations in Argentina and phylogenetic relationships within Odontophrynidae (Anura)

Amphibians are the most vulnerable vertebrates to biodiversity loss mediated by habitat destruction, climate change and diseases. Informed conservation management requires improving the taxonomy of anurans to assess reliably the species’ geographic range. The genus Odontophrynus that is geographically refined to Argentina, Bolivia, Brazil, Uruguay and Paraguay includes currently 12 nominal species with many populations of uncertain taxonomic assignment and subsequently unclear geographic ranges. In this study, we applied integrative taxonomic methods combining molecular (mitochondrial 16S gene), allozyme, morphological and bioacoustic data to delimit species of the genus Odontophrynus sampled from throughout Argentina where most species occur. The combined evidence demonstrates one case of cryptic diversity and another of overestimation of species richness. The populations referred to as O. americanus comprise at least three species. In contrast, O. achalensis and O. barrioi represent junior synonyms of the phenotypically plastic species O. occidentalis. We conclude that each of the four species occurring in Argentina inhabits medium to large areas. The Red List classification is currently “Least Concern”. We also propose a phylogenetic hypothesis for the genus and associated genera Macrogenioglottus and Proceratophrys (Odontophrynidae).
The relationship between embb306 and embb406 mutations and ethambutol resistant in Mycobacterium tuberculosis isolated from patiens in west of Iran

Background: Mutations in embB gene have been reported in ethambutol (EMB) resistance Mycobacterium tuberculosis (M. tuberculosis) isolates. The aim of this study was survey on embB 306 and 406 EMB resistant M. tuberculosis isolated from patients in West of Iran (2014-2015). Methods: Fifty strains of M. tuberculosis from patients with pulmonary tuberculosis (TB) were considered. Drug susceptibility using proportional method was performed. Polymerase chain reaction (PCR) -DNA sequencing was applied for mutation in embB 306 and 406 codon detection. Data were analyzed in SPSS 16 software using descriptive statistics and Fisher's exact test (p<0.05). Results: In this study 7 (14%) M. tuberculosis isolates were resistant to EMB. 6 (85.71%) and 1 (14.28%) resistant isolates had embB 306 and 304 codon mutations, respectively. Between embB306 mutations and resistance to EMB and MDR isolates had a significant relationship (p<0.001). Conclusion: The data indicated that embB 306 mutations have effect on EMB resistant. Detection of EMB resistant and these mutations prominent for antibiotic prescription
Alternative reproductive strategies in black-winged territorial males of Paraphlebia zoe (Odonata, Thaumatoneuridae)

Alternative reproductive strategies are commonly associated with male dimorphism. In Paraphlebia zoe, a species of damselfly whose males are dimorphic in wing coloration, black-and-white-winged (BW) males defend territories, while hyaline-winged (HW) males usually play the role of satellites. We found that several BW males can sometimes share a territory, and we hypothesized that within this morph there are two alternative tactics: submissive and dominant. We conducted an experiment to test whether dominant and submissive roles are plastic or stable and fixed on each individual. To this end, we manipulated black and white spots of BW males in four treatments: (i) painting over white and black spots without changing their size, (ii) erasing the white spot using black painting, (iii) increasing the black spot and moving the white spot maintaining its size and (iv) control males. Additionally, we investigated the correlation between some phenotypic variables (wing asymmetry, survival and recapture probabilities) and male behaviour (in terms of quality of the territory). We found that the two behavioural roles (submissive and dominant) were not affected by the manipulative experiments, therefore suggesting that they are stable and fixed. Additionally, we found a positive correlation between body size and survival in both sexes, and a positive effect of territory quality and lifespan on mating success. Moreover, the largest and youngest BW males were the most symmetrical. We conclude that Paraphlebia zoe holds high behavioural diversity, with two types of strategies in BW males, dominant and submissive. The occurrence of this intra-morph behavioural diversity might depend on demographic factors such as population density and/or the relative frequency of the different morphs.
Soil risk maps – Interpreting soils data for policy makers, agencies and industry

Surface runoff, erosion, compaction and the leaching of potential pollutants from land can degrade the soil resource and damage the water environment, reducing crop yields, causing loss of valuable nutrients and organic matter, together with increasing flood risk. Increasingly, it is recognized that scientific information must be translated into practical tools to change practices and protect the soil and water resource. Working alongside agencies in Scotland, we applied a suite of simple, transparent, rule‐based models to identify areas most at risk of exporting sediment and pollutants that may degrade water quality based on field‐scale (1:25,000) soil maps. The maps have been used by Scottish Environment Protection Agency, Scottish Water and Scottish Government to assess soil risks to waters from field to regional scale. The work brought scientists together with policy makers, agencies and the water industry to pool their knowledge to apply these practical tools for decision‐making. It highlights the need to apply existing knowledge to answer salient questions. All three examples described show that providing the right type of information, which is based on fundamental soils data, can directly influence the implementation of policies, investment and monitoring decisions and provide evidence in support of government. However, this requires both researchers and agency scientists to develop skills as knowledge brokers and to normalize the use of soil data in everyday agency settings.
Stress responses upon starvation and exposure to bacteria in the ant Formica exsecta

Organisms are simultaneously exposed to multiple stresses, which requires regulation of the resistance to each stress. Starvation is one of the most severe stresses organisms encounter, yet nutritional state is also one of the most crucial conditions on which other stress resistances depend. Concomitantly, organisms often deploy lower immune defenses when deprived of resources. This indicates that the investment into starvation resistance and immune defenses is likely to be subject to trade-offs. Here, we investigated the impact of starvation and oral exposure to bacteria on survival and gene expression in the ant Formica exsecta. Of the three bacteria used in this study, only Serratia marcescens increased the mortality of the ants, whereas exposure to Escherichia coli and Pseudomonas entomophila alleviated the effects of starvation. Both exposure to bacteria and starvation induced changes in gene expression, but in different directions depending on the species of bacteria used, as well as on the nutritional state of the ants.
An Approach to Enhance Dissolution Rate of Tamoxifen Citrate

We tested the solubility and dissolution of tamoxifen citrate to ascertain the optimal conditions for faster dissolution. Using the solvent evaporation method and hydrophilic carriers, we formulated tamoxifen citrate (TC) that contained solid dispersions (SDs). We increased the solubility and dissolution rate of TC with a solid dispersion system that consisted of polyethylene glycol (PEG-6000), beta-cyclodextrin (β-CD), and a combination of carriers. Physicochemical characteristics of solubility (mg/ml) were found to be 0.987±0.04 (water), 1.324±0.05 (6.8pH PBS), and 1.156±0.03 (7.4 pH PBS) for F5 formulation, percentage yield was between 98.74 ± 1.11% and 99.06 ± 0.58%, drug content was between 98.06±0.58 and 99.06±1.10, and dissolution studies binary complex showed a faster release of TC as compared to a single polymer and pure drug. Furthermore, thermal properties, physicochemical drug and polymer interaction, crystal properties, and morphology were determined using differential scanning calorimetry (DSC), infrared spectroscopy (FT-IR), X-ray differential studies, and scanning electron microscopy. We used the same proportion of carrier concentrations of the formulations to calculate the solubility of TC. Our results demonstrated that increased concentrations of β-C yielded an improved solubility of TC, which was two times higher than pure TC. The uniformity in drug content was 97.99 %. A quicker drug release occurred from the binary complex formulation as seen in the dissolution profile. FTIR demonstrated an absence in the physicochemical interaction between the drug and carriers. The drug was also found to be dispersed in the amorphous state as revealed by DSC and XRD. The drug concentration did not vary during various storage conditions. Our in vivo studies demonstrated that SD displayed significantly higher values of Cmax (p < 0.05) and AUC0-24 (p < 0.05) as compared to free TC. Furthermore, Tmax in SD was significantly lower (p < 0.05), as compared to free TC.
Kinesin-6 regulates cell-size-dependent spindle elongation velocity to keep mitosis duration constant in fission yeast

The length of the mitotic spindle scales with cell size in a wide range of organisms during embryonic development. Interestingly, in C. elegans embryos, this goes along with temporal regulation: larger cells speed up spindle assembly and elongation. We demonstrate that, similarly in fission yeast, spindle length and spindle dynamics adjust to cell size, which allows to keep mitosis duration constant. Since prolongation of mitosis was shown to affect cell viability, this may resemble a mechanism to regulate mitosis duration. We further reveal how the velocity of spindle elongation is regulated: coupled to cell size, the amount of kinesin-6 Klp9 molecules increases, resulting in an acceleration of spindle elongation in anaphase B. In addition, the number of Klp9 binding sites to microtubules increases overproportionally to Klp9 molecules, suggesting that molecular crowding inversely correlates to cell size and might have an impact on spindle elongation velocity control.
How the extracellular matrix shapes neural development

During development, both cells and tissues must acquire the correct shape to allow their proper function. This is especially relevant in the nervous system, where the shape of individual cell processes, such as the axons and dendrites, and the shape of entire tissues, such as the folding of the neocortex, are highly specialized. While many aspects of neural development have been uncovered, there are still several open questions concerning the mechanisms governing cell and tissue shape. In this review, we discuss the role of the extracellular matrix (ECM) in these processes. In particular, we consider how the ECM regulates cell shape, proliferation, differentiation and migration, and more recent work highlighting a key role of ECM in the morphogenesis of neural tissues.
SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers

Abstract Super-enhancers (SEs) are enriched with a cluster of mediator binding sites, which are major contributors to cell-type-specific gene expression. Currently, a large quantity of long non-coding RNAs has been found to be transcribed from or to interact with SEs, which constitute super-enhancer associated long non-coding RNAs (SE-lncRNAs). These SE-lncRNAs play essential roles in transcriptional regulation through controlling SEs activity to regulate a broad range of physiological and pathological processes, especially tumorigenesis. However, the pathological functions of SE-lncRNAs in tumorigenesis are still obscure. In this paper, we characterized 5056 SE-lncRNAs and their associated genes by analysing 102 SE data sets. Then, we analysed their expression profiles and prognostic information derived from 19 cancer types to identify cancer-related SE-lncRNAs and to explore their potential functions. In total, 436 significantly differentially expressed SE-lncRNAs and 2035 SE-lncRNAs with high prognostic values were identified. Additionally, 3935 significant correlations between SE-lncRNAs and their regulatory genes were further validated by calculating their correlation coefficients in each cancer type. Finally, the SELER database incorporating the aforementioned data was provided for users to explore their physiological and pathological functions to comprehensively understand the blocks of living systems.
Feeding value potential of mulberry (Morus alba) leaf meal to replace concentrate mix

The experiment was carried out to estimate the feeding value of mulberry (Morus alba) leaf meal by evaluating its chemical composition in vitro organic matter digestibility and in sacco dry matter (DM) degradability. This study aimed to assess the potential of mulberry foliage in supplementing the feed of ruminant animals during the dry season, when other feed resources are scarce and their quality generally fall short of animal requirements. Dry matter (DM), crude protein (CP), ash, ether extract (EE), crude fiber (CF), neutral detergent fiber (NDF), acid detergent fiber (ADF) and acid detergent lignin (ADL) contents of the different diets were determined. In vitro organic matter digestibility was determined by two-stage method. In sacco rumen degradability was measured using three rumen fistulated Boran-Holstein Friesian cross steers at 0, 6, 12, 24, 48, 72, and 96 h. The composition of mulberry leaf meal compares favorably with that of the concentrate mixture in most of the nutrients. The ash content of mulberry leaf meal was more than double that of the concentrate mixture. Similarly, the calcium value of mulberry leaf meal was more than threefold to that of calcium content of concentrate mixture. Mulberry leaf meal alone had the greatest values for slowly degradable fraction (b) than the diets with less proportion of mulberry, whereas mulberry leaf meal alone (T5) and 75 g concentrate mix + 259.7 g mulberry leaf (T4) had significantly (p>0.05) less soluble fraction (a), and effective degradability (ED) values as compared to the diets with less proportion of mulberry. In a nutshell, all treatment diets recorded more than 66% DM degradability at 24 h, which implied that they were all greatly degradable in the rumen. Key words: Chemical composition, degradability, digestibility, Morus alba.
Epigenetic Co-Deregulation of EZH2/TET1 is a Senescence-Countering, Actionable Vulnerability in Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC) cells lack the expression of ER, PR and HER2. Thus, TNBC patients cannot benefit from hormone receptor-targeted therapy as non-TNBC patients, but can only receive chemotherapy as the systemic treatment and have a worse overall outcome. More effective therapeutic targets and combination therapy strategies are urgently needed to improve the treatment effectiveness. Methods: We analyzed the expression levels of EZH2 and TET1 in TCGA and our own breast cancer patient cohort, and tested their correlation with patient survival. We used TNBC and non-TNBC cell lines and mouse xenograft tumor model to unveil novel EZH2 targets and investigated the effect of EZH2 inhibition or TET1 overexpression in cell proliferation and viability of TNBC cells. Results: In TNBC cells, EZH2 decreases TET1 expression by H3K27me3 epigenetic regulation and subsequently suppresses anti-tumor p53 signaling pathway. Patients with high EZH2 and low TET1 presented the poorest survival outcome. Experimentally, targeting EZH2 in TNBC cells with specific inhibitor GSK343 or shRNA genetic approach could induce cell cycle arrest and senescence by elevating TET1 expression and p53 pathway activation. Using mouse xenograft model, we have tested a novel therapy strategy to combine GSK343 and chemotherapy drug Adriamycin and could show drastic and robust inhibition of TNBC tumor growth by synergistic induction of senescence and apoptosis. Conclusions: We postulate that the well-controlled dynamic pathway EZH2-H3K27me3-TET1 is a novel epigenetic co-regulator module and provide evidence regarding how to exploit it as a novel therapeutic target via its pivotal role in senescence and apoptosis control. Of clinical and therapeutic significance, the present study opens a new avenue for TNBC treatment by targeting the EZH2-H3K27me3-TET1 pathway that can modulate the epigenetic landscape.
Integrated Analysis of LncRNA-mRNA Coexpression in the Extracellular Matrix of Developing Deciduous Teeth in Miniature Pigs

Miniature pigs, a valuable alternative model for understanding human tooth development, have deciduous teeth from all four tooth families that are replaced once by permanent molars. The extracellular matrix (ECM) supports cells and maintains the integrity of tooth germs during tooth development. However, details on the role of the ECM in tooth development are poorly understood. Here, we performed long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in the ECM components of deciduous tooth germs by RNA sequencing in miniature pigs. From the early cap to the late bell stages, we identified 4,562 and 3,238 differentially expressed genes (DEGs) from E40 to E50 and E50 to E60, respectively. In addition, a total of 1,464 differentially expressed lncRNAs from E40 to E50 and 969 differentially expressed lncRNAs from E50 to E60 were obtained. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEGs were enriched significantly for multiple signaling pathways, especially for the ECM pathway. We then outlined the detailed dynamic gene expression profiling of ECM components during deciduous molar development. Comparison of the cap and bell stages revealed that the structure and functions of the ECM dynamically changed. The ECM-related genes, including THBS1, COL4A5, COL4A6, COL1A1, CHAD, TNR, GP1BA, and ITGA3, were significantly changed, and some were shown to enrich during the bell stage development. Finally, we outlined the coexpression of lncRNAs and ECM properties during tooth development. We showed that the interplay of key lncRNAs could change ECM processes and influence the ECM establishment of tooth patterns to accomplish full tooth formation. These results might provide information to elucidate the regulation network of the lncRNA and ECM in tooth development.