Miracle-dz/UniFAR-FTUs huggingface dataset:
Site‐dependent regulation of breeding success: Evidence for the buffer effect in the common guillemot, a colonially breeding seabird

Abstract Density‐dependent regulation can offer resilience to wild populations experiencing fluctuations in environmental conditions because, at lower population sizes, the average quality of habitats or resources is predicted to increase. Site‐dependent regulation is a mechanism whereby individuals breed at the highest quality, most successful, sites, leaving poorer quality, less successful sites vacant. As population size increases, higher quality sites become limiting but when populations decline, lower quality sites are vacated first, offering resilience. This process is known as the ‘buffer effect’. However, few studies have tested whether such regulation operates in populations experiencing changes in size and trend. We used data from a population of common guillemots Uria aalge, a colonially breeding seabird, to investigate the relationship between site occupancy probability, site quality and population size and trend. These data were collected at five sub‐colonies spanning a 38‐year period (1981–2018) comprising phases of population increase, decrease and recovery. We first tested whether site quality and population size in sub‐colonies explained which sites were occupied for breeding, and if this was robust to changes in sub‐colony trend. We then investigated whether disproportionate use of higher quality sites drove average site quality and breeding success across sub‐colony sizes and trends. Finally, we tested whether individuals consistently occupied higher quality sites during periods of decline and recovery. Higher quality sites were disproportionality used when sub‐colony size was smaller, resulting in higher average site quality and breeding success at lower population sizes. This relationship was unaffected by changes in sub‐colony trend. However, contrary to the predictions of the buffer effect, new sites were established at a similar rate to historically occupied sites during sub‐colony decline and recovery despite being of lower quality. Our results provide support for the buffer effect conferring resilience to populations, such that average breeding success was consistently higher at lower population size during all phases of population change. However, this process was tempered by the continued establishment of new, lower quality, sites which could act to slow population recovery after periods when colony size was low.
Development of ACE2 loaded decoy liposomes and their effect on SARS-CoV-2 for Covid-19 treatment

Abstract SARS-CoV-2 is a novel coronavirus with a positively oriented single-stranded RNA that first appeared in December 2019. In this study, Angiotensin Converting Enzyme 2 (ACE2) loaded decoy liposomes were developed and characterized. ACE2 protein was loaded onto a liposomal carrier system and its toxicity and effectiveness were evaluated in cell culture and in vitro virus neutralization studies. Liposomes were prepared with the film hydration method and adjusted for size with the dialysis membrane method or the ultrasonic homogenization method. All formulations showed high entrapment efficiency between 99.98–79.6%. Liposomes with two different particle sizes above 2 µm and below 500 nm were obtained with the dialysis membrane method and homogenization method. Two optimum formulations, M6-S90 with a PDI value of 0.383 ± 0.053 and particle size of 397.7 ± 28.25 nm which was produced by ultrasonic homogenization and M6-4 with a PDI 0.769 ± 0.205 and particle size of 2606 ± 1396.00 were chosen as optimum formulations for further studies. M6-S90 was stable and showed low toxicity on Calu3 lung epithelial cells. Pre-incubation of M6-S90 with with 3.1 × 105 PFU/mL of SARS-CoV-2 followed by incubation with Vero E6 cells resulted in a 4 log fold change reduction in cell death compared to virus alone. This suggests that MS6-S90 had good neutralization activity on SARS-CoV-2 whilst maintaining viability of the host cell. The novel ACE-2 loaded decoy liposomes described in this study can be further evaluated for the treatment of COVID-19.
The effect of testosterone and antioxidants nanoliposomes on gene expressions and sperm parameters in asthenospermic individuals

Abstract Background Antioxidants that used for the infertility treatment cannot have their complete effectiveness, because of their instability in the culture medium. Significance One of the most advances, in the drug delivery systems, is nanoliposomes-loaded, as biodegradable and bioavailable carriers. Hormonal and antioxidant agents encapsulating inside the nanoliposomes were used, to increase the effectiveness of antioxidants in the sperm culture medium. Materials Semen sample from 15 asthenospermia were divided into 10 equal parts. After preparation, the sperms were incubated with free form of drugs and nanocarriers contained resveratrol, catalase, resveratrol-catalase and testosterone for 45 min. All sperm parameters, sperm DNA and gene expressions were evaluated before and after freezing. Results Before freezing, all nanocarriers and free testosterone showed higher sperm motility compared to free drugs (p=.000). Free Testosterone and free resveratrol-catalase had higher DNA damage compared to nanocarriers (p=.000). Before freezing, the blank nanoliposome and testosterone nanoliposomes had the lowest HSP70 gene expression respectively (p = 0.005) (p = 0.001). After freezing, a significant reduction in sperm motility was observed in the free resveratrol-catalase group (p=.003). Also, a significant increase in sperm viability was observed in the free testosterone and nanoliposomes of blank and testosterone (p > 0.05). The least DNA fragmentation was related to catalase nanoliposomes (p=.000). All nanoliposomes, especially catalase, had the highest percentage of class I morphology compared to the control group (p=.000). Conclusions Nanoliposomes could improve the sperm parameters and DNA integrity before and after freezing, by increasing the effectiveness of antioxidants. So, it can be recommended in the ART lab.
Protein/Creatinine ratio versus 24-hours urine protein in preeclampsia.

OBJECTIVES Proteinuria is one of the diagnostic criteria of preeclampsia (PE). Measurement of 24-hour urine protein is the gold standard method for detection of proteinuria in PE. The 24-hour urine sampling is time-consuming, and inconvenient. To evaluate the accuracy of protein/creatinine (P/C) ratio in detection of significant proteinuria ( > 1 g/24-hours urine) in PE. MATERIAL AND METHODS One hundred and ten (110) preeclamptic women were included in this study and admitted for blood pressure monitoring, 24-hour urine collection, fetal well-being assessment and spot urine sample for measuring of P/C ratio. After thorough history and clinical examination, routine antenatal investigations were done for the women included in the study according to the hospital protocol, and to excluded pre-existing chronic renal disease. Twenty-four-hour urine collection started on the morning following hospital admission. Spot urine samples were obtained shortly before the 24-hour urine collection for measuring of P/C ratio. Collected data statistically analyzed to evaluate the accuracy of P/C ratio in detection of significant proteinuria in PE. RESULTS The P/C ratio of 1.35 ± 2.54 had 94.4% sensitivity, 94.9% specificity, 97.1% positive predictive value (PPV), 90.2% negative predictive value (NPV), and 94.5% overall accuracy in detection of significant proteinuria ( > 1 g/24-hour urine) in PE. CONCLUSIONS The P/C ratio of 1.35 ± 2.54 had 94.4% sensitivity, 94.9% specificity, 97.1% PPV, 90.2% NPV, and 94.5% overall accuracy in detection of significant proteinuria ( > 1 g/24-hour urine) in PE. This study suggests the use of P/C ratio as an alternative to 24-hour urine protein to detect significant proteinuria in PE.
CFTR interactome mapping using the mammalian membrane two‐hybrid high‐throughput screening system

Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a chloride and bicarbonate channel in secretory epithelia with a critical role in maintaining fluid homeostasis. Mutations in CFTR are associated with Cystic Fibrosis (CF), the most common lethal autosomal recessive disorder in Caucasians. While remarkable treatment advances have been made recently in the form of modulator drugs directly rescuing CFTR dysfunction, there is still considerable scope for improvement of therapeutic effectiveness. Here, we report the application of a high‐throughput screening variant of the Mammalian Membrane Two‐Hybrid (MaMTH‐HTS) to map the protein–protein interactions of wild‐type (wt) and mutant CFTR (F508del), in an effort to better understand CF cellular effects and identify new drug targets for patient‐specific treatments. Combined with functional validation in multiple disease models, we have uncovered candidate proteins with potential roles in CFTR function/CF pathophysiology, including Fibrinogen Like 2 (FGL2), which we demonstrate in patient‐derived intestinal organoids has a significant effect on CFTR functional expression.
Personality Organization and Depressive Symptoms Among Psychiatric Outpatients

Abstract Previous research has demonstrated relations between lower level of personality organization (PO) and multiple indices of mental health disturbances. The goal of this research was to examine whether experience of shame would mediate the relationship between PO and depressive symptoms in a sample of 321 Croatian psychiatric outpatients (64% female; mean age, 38.67 years). The total PO level exhibited positive associations with depressive symptoms and with all three subscales of shame (p < 0.01). Characterological, behavioral, and bodily shame showed significant mediating effects in the PO-depression relationship, while controlling for the influence of age and sex. PO level seems to be strongly related to depressive disturbances, with the experience of shame representing one of the underlying mechanisms of this relationship. Given that patients with personality disorders (i.e., low PO level) suffer from poorer treatment outcomes for major mental disorders, more emphasis should be placed on psychotherapeutic management of shame-proneness.
Plasmid-based CRISPR-Cas9 system efficacy for introducing targeted mutations in CD81 gene of MDA-MB-231 cell line.

INTRODUCTION Breast cancer has been represented a challenging issue worldwide as it is one of the major leading causes of death among women. CD81 gene, a member of the tetraspanin protein family, has been associated with the development of human cancers. Genome editing technologies, particularly the CRISPR-Cas9 system, have shown rapid progress in gene function studies. In this study, we aimed to evaluate the ability of the CRISPR-Cas9 plasmid-based system to modify specific regions of the CD81 gene in the MDA-MB-231 breast cancer cell line. MATERIALS AND METHODS Using bioinformatics database search, four different single guide RNAs (sgRNAs) to target exon 3 and exon 5 of the CD81 gene were designed. The intended sgRNAs sequences were cloned into the expression plasmid pSpCas9(BB)-2A-GFP (PX458) bearing sgRNA scaffold backbone, Cas9, and EGFP coding sequences, which was confirmed by colony PCR and sequencing. Transfection efficiency was determined by fluorescence microscopy and flow cytometry analysis. Gene editing efficiency was measured qualitatively and quantitatively using the T7E1 and TIDE software, respectively. RESULTS Our data show that expression constructs were successfully introduced into MDA-MB-231 cells with an acceptable transfection efficiency. Two sgRNAs that were afforded to introduce significant mutations in their target regions were detected by TIDE software (p-value < 0.05). To the best of our knowledge, CD81 gene editing in these cells has been investigated for the first time in this study using the CRISPR/Cas9 technique. CONCLUSIONS Taken together, our data show that the CRISPR-Cas9 system can change the genomic sequence in the target area of MDA-MB-231 cells. Along with previous studies, we propose forethought when using T7E1-based quantitative indel estimates, as comparing activities of multiple gRNAs with the T7E1 assay may lead to inaccurate conclusions. Instead, estimating non-homologous end-joining events (NHEJ) by Sanger sequencing and subsequent TIDE analysis is recommended.
Visualization of Aqueous Geochemical Data Using Python and WQChartPy

Graphical methods have been widely used for visualization, classification, and interpretation of aqueous geochemical data to obtain a better understanding of surface and subsurface hydrologic systems. This method note presents WQChartPy, an open‐source Python package developed to plot a total of 12 diagrams for analysis of aqueous geochemical data. WQChartPy can handle various data formats including Microsoft Excel, comma‐separated values (CSV), and general delimited text. The 12 diagrams include eight traditional diagrams (trilinear Piper, Durov, Stiff, Chernoff face, Schoeller, Gibbs, Chadha, and Gaillardet) and four recently proposed diagrams (rectangle Piper, color‐coded Piper, contour‐filled Piper, and HFE‐D) that have not been implemented in existing graphing software. The diagrams generated by WQChartPy can be saved as portable network graphics (PNG), scalable vector graphics (SVG), or portable document format (PDF) files for scientific publications. Jupyter and Google Colab notebooks are available online to illustrate how to use WQChartPy with example datasets. The geochemical diagrams can be generated with several lines of Python codes. Source codes of WQChartPy are publicly available at GitHub (https://github.com/jyangfsu/WQChartPy) and PyPI (https://pypi.org/project/wqchartpy/).
Human umbilical cord mesenchymal stem cells contribute to the reconstruction of bladder function after acute spinal cord injury via p38 mitogen-activated protein kinase/nuclear factor-kappa B pathway

ABSTRACT The association between spinal cord injury (SCI) and bladder symptoms has been intensively described. Human umbilical cord mesenchymal stem cell (hUC-MSC) treatment is beneficial to the recovery of bladder function after SCI, but its mechanism is unclear. We established an SCI model, and prepared hUC-MSCs in advance, followed by verification using flow cytometry. The Basso, Beattie and Bresnahan (BBB) score and urodynamic index were employed to evaluate motor function and bladder functions, respectively. Hematoxylin–eosin staining, luxol fast blue staining, and Masson’s trichrome staining were utilized to assess pathological changes. Real-time quantitative PCR and Western blot were used to determine the mRNA and protein expressions in bladder tissues. The immunophenotypes of the HUC-MSCs were CD90+ and CD105+, but CD34−, CD45− and HLA-DR−. Rats appeared severe motor dysfunction after SCI, but the BBB score was increased in hUC-MSCs after the second week. Pathologically, the improvement of the lesion area on the dorsal spinal cord, augmented anterior gray horn neuron cells of the spinal cord and lessened bladder tissue remodeling (fibrosis, collagen deposition) as well as modulated inflammation could be observed. Besides, SCI increased bladder weight, bladder capacity, urine volume and residual urine volume, and decreased urination efficiency. HUC-MSCs ameliorated SCI-induced pathological changes and bladder functions, the expressions of Collagen I, Collagen III, fibroblast growth factor 2 (FGF2), phospho-p38, transient receptor potential vanilloid 1, Toll-like receptor 4 and phospho-nuclear factor-kappa B (p-NF-κB). To sum up, HUC-MSCs contribute to the reconstruction of bladder function after SCI by repressing p38 MAPK/NF-κB pathway. Graphical abstract
Interaction Tolerance Detection Test for Understanding the Killing Efficacy of Directional Antibiotic Combinations

The killing efficacy of antibiotic combinations is rarely measured in the clinical setting. However, in cases where the treatment is required to kill the infecting organism and not merely arrest its growth, the information on the killing efficacy is important, especially when tolerant strains are implicated. ABSTRACT Combination treatments are commonly prescribed for enhancing drug efficacy, as well as for preventing the evolution of resistance. The interaction between drugs is typically evaluated near the MIC, using growth rate as a measure of treatment efficacy. However, for infections in which the killing activity of the treatment is important, measurements far above the MIC are needed. In this regime, the killing rate often becomes weakly concentration dependent, and a different metric is needed to characterize drug interactions. We evaluate the interaction metric on killing using an easy visual assay, the interaction tolerance detection test (iTDtest), that estimates the survival of bacteria under antibiotic combinations. We identify antibiotic combinations that enable the eradication of tolerant bacteria. Furthermore, the visualization of the antibiotic interactions reveals directional drug interactions and enables predicting high-order combination outcomes, therefore facilitating the determination of optimal treatments. IMPORTANCE The killing efficacy of antibiotic combinations is rarely measured in the clinical setting. However, in cases where the treatment is required to kill the infecting organism and not merely arrest its growth, the information on the killing efficacy is important, especially when tolerant strains are implicated. Here, we report on an easy method for the determination of the killing efficacy of antibiotic combinations which enabled to reveal combinations effective against tolerant bacteria. The results could be generally used to guide antimicrobial therapy in life-threatening infections.
Molecular Basis of Rhodomyrtone Resistance in Staphylococcus aureus

Antibiotic resistance is a growing public health problem, and alternative antibiotics are urgently needed. Rhodomyrtone (Rom), an antimicrobial compound originally isolated from Rhodomyrtus tomentosa, is active against multiple resistant Gram-positive pathogens. ABSTRACT Rhodomyrtone (Rom) is a plant-derived broad-spectrum antibiotic active against many Gram-positive pathogens. A single point mutation in the regulatory farR gene (farR*) confers resistance to Rom in Staphylococcus aureus (RomR). The mutation in farR* alters the activity of the regulator, FarR*, in such a way that not only its own gene, farR*, but also the divergently transcribed farE gene and genes controlled by the global regulator, agr, are highly upregulated. Here, we show that mainly the upregulation of the fatty acid efflux pump FarE causes the RomR phenotype, as farE deletion in either the parent or the RomR strain (RomR ΔfarE) yielded hypersensitivity to Rom. Comparative lipidome analysis of the supernatant (exolipidomics) and the pellet fraction revealed that the RomR strain excreted about 10 times more phospholipids (PGs) than the parent strain or the ΔfarE mutants. Since the PG content in the supernatant (2,244 ng/optical density [OD]) was more than 100-fold higher than that of fatty acids (FA), we assumed that PG interacts with Rom, thereby abrogating its antimicrobial activity. Indeed, by static and dynamic light scattering (SLS and DLS) and isothermal titration calorimetry (ITC) analyses, we could demonstrate that both PG and Rom were vesicular and reacted with each other in milliseconds to form a 1:1.49 [Rom-PG(32:0), where PG(32:0) is PG with C32:0 lipids] complex. The binding is entropically driven and hence hydrophobic and of low specificity in nature. Our results indicate that the cytoplasmic membrane is the actual target of Rom, which is also in agreement with Rom’s induced rapid collapse of the membrane potential and decreased membrane integrity. IMPORTANCE Antibiotic resistance is a growing public health problem, and alternative antibiotics are urgently needed. Rhodomyrtone (Rom), an antimicrobial compound originally isolated from Rhodomyrtus tomentosa, is active against multidrug-resistant Gram-positive pathogens. However, Rom-resistant (RomR) mutants occur with low frequency. In this study, we unraveled the underlying resistance mechanism, which is based on a point mutation in the farR regulator gene, causing overexpression of FarE, which most likely acts as a phospholipid (PG) efflux pump, as large amounts of PG were found in the supernatant and the pellet fraction. We show that PG can bind to Rom, thereby abrogating its antimicrobial activity. The direct interaction of Rom with PG suggests that Rom’s actual target is the cytoplasmic membrane. Antibiotics that interact with PG are rare. Since Rom can be chemically synthesized, it serves as a lead compound for synthesis of improved variants.
Signal Peptidase-Mediated Cleavage of the Anti-σ Factor RsiP at Site 1 Controls σP Activation and β-Lactam Resistance in Bacillus thuringiensis

β-Lactam antibiotics are important for the treatment of many bacterial infections. However, resistance mechanisms have become increasingly more prevalent. ABSTRACT In Bacillus thuringiensis, β-lactam antibiotic resistance is controlled by the extracytoplasmic function (ECF) σ factor σP. σP activity is inhibited by the anti-σ factor RsiP. In the presence of β-lactam antibiotics, RsiP is degraded and σP is activated. Previous work found that RsiP degradation requires cleavage of RsiP at site 1 by an unknown protease, followed by cleavage at site 2 by the site 2 protease RasP. The penicillin-binding protein PbpP acts as a sensor for β-lactams. PbpP initiates σP activation and is required for site 1 cleavage of RsiP but is not the site 1 protease. Here, we describe the identification of a signal peptidase, SipP, which cleaves RsiP at a site 1 signal peptidase cleavage site and is required for σP activation. Finally, many B. anthracis strains are sensitive to β-lactams yet encode the σP-RsiP signal transduction system. We identified a naturally occurring mutation in the signal peptidase cleavage site of B. anthracis RsiP that renders it resistant to SipP cleavage. We find that B. anthracis RsiP is not degraded in the presence of β-lactams. Altering the B. anthracis RsiP site 1 cleavage site by a single residue to resemble B. thuringiensis RsiP results in β-lactam-dependent degradation of RsiP. We show that mutation of the B. thuringiensis RsiP cleavage site to resemble the sequence of B. anthracis RsiP blocks degradation by SipP. The change in the cleavage site likely explains many reasons why B. anthracis strains are sensitive to β-lactams. IMPORTANCE β-Lactam antibiotics are important for the treatment of many bacterial infections. However, resistance mechanisms have become increasingly more prevalent. Understanding how β-lactam resistance is conferred and how bacteria control expression of β-lactam resistance is important for informing the future treatment of bacterial infections. σP is an alternative σ factor that controls the transcription of genes that confer β-lactam resistance in Bacillus thuringiensis, Bacillus cereus, and Bacillus anthracis. Here, we identify a signal peptidase as the protease required for initiating activation of σP by the degradation of the anti-σ factor RsiP. The discovery that the signal peptidase SipP is required for σP activation highlights an increasing role for signal peptidases in signal transduction, as well as in antibiotic resistance.