Miracle-dz/UniFAR-FTUs huggingface dataset:
Standard and Non-Standard Measurements of Acidity and the Bacterial Ecology of Northern Temperate Mineral Soils

Databases of soil pH values today guide the decisions of land managers and the experimental designs of microbiologists and biogeochemists. Soil acidity underpins fundamental properties and functions in the soil, such as the solubilities of exchangeable ions and nutrients, or bacterial use of gradients of internal and external acidity to generate ATP and turn flagellar motors. Therefore, it is perhaps unsurprising that soil pH has emerged as the strongest predictor of soil bacterial community composition. However, the measurement of these particular values today does not address whether soil pH accurately represents the in situ acidity of soil microhabitats where microorganisms survive and reproduce. This study analyzes and compares soils of a large-scale natural soil pH gradient and a long-term experimental soil pH gradient for the purposes of testing new methods of measuring and interpreting soil acidity when applied to soil ecology. We extracted and prepared soil solutions using laboratory simulation of levels of carbon dioxide and soil moisture more typical of soil conditions while also miniaturizing extraction methods using a centrifuge for extractions. The simulation of in situ soil conditions resulted in significantly different estimates of soil pH. Furthermore, for soils from the long-term experimental soil pH gradient trial, the simulated soil pH values substantially improved predictions of bacterial community composition (from R2 = 0.09 to R2 = 0.16). We offer suggestions and cautions for researchers considering how to better represent soil pH as it exists in situ.
New kindergarten teachers’ career development trajectories in China: A problem-solving perspective

Since the 1960s, concerns for beginning teachers have attracted extensive attention. High attrition rates among beginning teachers have been an international challenge, which is costly for a nation’s budget. To improve the retention of new teachers, it is imperative to understand what beginning teachers have experienced in their professional practice. This qualitative research examined the career development trajectories of beginning kindergarten teachers in China. The experiences of 23 kindergarten teachers from Nanjing were investigated through semi-structured interviews. Using grounded theory, this research identified four main themes and four career development trajectories. Themes include orientation, mastery, re-examination and self-validation, while career development trajectories reveal that teacher career development is not unilinear, but diverse. These findings are crucial in raising the awareness of researchers and practitioners about the diversities and possibilities of teacher career development trajectories. Further implications for researchers, teacher educators and kindergarten teachers are discussed.
Physiological response of cauliflower in relation to manganese-boron interaction

SummaryCauliflower (Brassica oleracea L. var. botrytis) was grown in refined sand at low (0.0011 mg l−1), normal (0.55 mg l−1) and excess (5.5 mg l−1) Mn, each at three levels of B, deficient (0.0033 mg l−1), normal (0.33 mg H) and excess (3.3 mg l−1). In Mn deficient cauliflowers a deficiency of B accentuated visible symptoms of Mn deficiency and aggravated the Mn deficiency effects i.e. a decrease in dry matter, leaf Mn, sugars, starch, chlorophyll, Hill reaction and specific activity of aldolase and an increase in the concentrations of proline and inorganic phosphorus. In cauliflowers exhibiting B toxicity symptoms under conditions of excess B, excess Mn increased leaf Mn, sugars, nucleic acids, protein P, nucleic acid P, acid-labile P and leaf B. Excess Mn decreased the concentrations of DNA, protein nitrogen, chlorophyll and activities of peroxidase, aldolase and leaf B, leaf Mn in boron deficient cauliflowers.
Adhesion to type I collagen fibrous gels induces E- to N-cadherin switching without other EMT-related phenotypes in lung carcinoma cell A549

In culture system, environmental factors, such as increasing exogenous growth factors and adhesion to type I collagen (Col-I) induce epithelial-to-mesenchymal transition (EMT) in cells. Col-I molecules maintain a non-fibril form under acidic conditions, and they reassemble into fibrils under physiological conditions. Col-I fibrils often assemble to form three-dimensional gels. The gels and non-gel-form of Col-I can be utilized as culture substrates and different gel-forming state often elicit different cell behaviors. However, gel-form dependent effects on cell behaviors, including EMT induction, remain unclear. EMT induction in lung cancer cell line A549 has been reported via adhesion to Col-I but the effects of gel form dependency are unelucidated. This study investigated the changes in EMT-related behaviors in A549 cells cultured on Col-I gels. We examined cell morphology, proliferation, single-cell migration and expression of EMT-related features in A549 cells cultured on gels or non-gel form of Col-I and non-treated dish with or without transforming growth factor (TGF)-β1. On Col-I gels, some cells kept cell–cell contacts and formed clusters, others maintained single-cell form. In cell–cell contact regions, E-cadherin expression was downregulated, whereas that of N-cadherin was upregulated. Vimentin and integrins α2 and β1 expression were not increased. In TGF-β1-treated A549 cells, cadherin switched from E- to N-cadherin. Their morphology changed to a mesenchymal form and cells scattered with no cluster formation. Vimentin, integrins α2 and β1 expression were upregulated. Thus, we concluded that culture on Col-I fibrous gels induced E- to N-cadherin switching without other EMT-related phenotypes in A549 cells.
Development and pilot screen of novel high content assay for down regulators of expression of heterogenous nuclear ribonuclear protein H2

Despite recent advances in melanoma drug discovery, the average overall survival of patients with late stage metastatic melanoma is approximately 3 years, suggesting a need for new approaches and melanoma therapeutic targets. Previously we identified heterogeneous nuclear ribonucleoprotein H2 as a potential target of anti-melanoma compound 2155-14 (Palrasu et al, Cell Physiol Biochem 2019;53:656-86). In the present study, we endeavored to develop an assay to enable a high throughput screening campaign to identify drug-like molecules acting via down regulation of heterogeneous nuclear ribonucleoprotein H that can be used for melanoma therapy and research. Results We established a cell-based platform using metastatic melanoma cell line WM266-4 expressing hnRNPH2 conjugated with green fluorescent protein to enable assay development and screening. High Content Screening assay was developed and validated in 384 well plate format, followed by miniaturization to 1,536 well plate format. All plate-based QC parameters were acceptable: %CV = 6.7±0.3, S/B = 21±2.1, Z’ = 0.75±0.04. Pilot screen of FDA-approved drug library (n=1,400 compounds) demonstrated hit rate of 0.5%. Two compounds demonstrated pharmacological response and were authenticated by western blot analysis. Conclusions We developed a highly robust HTS-amenable high content screening assay capable of monitoring down regulation of hnRNPH2. This assay is thus capable of identifying authentic down regulators of hnRNPH1 and 2 in a large compound collection and, therefore, is amenable to a large-scale screening effort.
VARIOUS METHODS OF CHILLING AND HIGH-VOLTAGE ELECTRICAL STIMULATION APPLIED IN SUSTAINABLE BEEF PRODUCTION SYSTEMS

Entrepreneurs implementing the concept of sustainable development of meat production are highly interested in combining various red meat chilling systems with quality-improving techniques. Therefore, we analyzed the impact of high-voltage electrical stimulation (HVES) and selected chilling methods on changes in quality characteristics and weight loss of beef. We also studied energy consumption based on the heat balance of chilling chambers during the fast chilling of varying amounts of raw material. The HVES and the fast chilling method yielded positive economic (meat weight loss), technological (high quality, hot-boning), energetic (lower electricity consumption), and organizational effects (increased chilling speed, reducing of storage surfaces and expenditures for staff wages) compared to the slow and accelerated methods. Reaching the desired final temperature with an increased amount of chilled meat enabled a few-fold reduction in the total heat collected from the chambers and in meat weight loss. This allows recommending the above actions to be undertaken by entrepreneurs in the pursuit of sustainable meat production.
Late cortical potentials are not a reliable marker of somatosensory awareness

Two types of scalp-recorded event-related potentials have been proposed as neural correlates of perceptual awareness in humans: an early, modality-specific negativity and a late, modality-independent positivity. However, whether these potentials genuinely reflect perception or result from task demands remains controversial. To address this question, we compared results from a classical somatosensory detection task (direct report task) to a somatosensory-visual matching task, in which overt reports were decorrelated from target detection, equated the behavioural relevance of detected and undetected stimuli, and mitigated the influence of attentional processes. By means of Bayesian model selection, we show that the early N140 component was the first to reflect target detection in both tasks, whereas the late P300 component was task dependent, with strong detection effects in the direct report task that were absent in the matching task. We conclude that the P300 is not a genuine correlate of somatosensory awareness but reflects postperceptual processing.
LC-MS/MS analysis of lesional and normally looking psoriatic skin reveals significant changes in protein metabolism and RNA processing

Background Plaque psoriasis is a chronic autoimmune disorder characterized by the development of red scaly plaques. To date psoriasis lesional skin transcriptome has been extensively studied, whereas only few proteomic studies of psoriatic skin are available. Aim The aim of this study was to compare protein expression patterns of lesional and normally looking skin of psoriasis patients with skin of the healthy volunteers, reveal differentially expressed proteins and identify changes in cell metabolism caused by the disease. Methods Skin samples of normally looking and lesional skin donated by psoriasis patients (n = 5) and samples of healthy skin donated by volunteers (n = 5) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). After protein identification and data processing, the set of differentially expressed proteins was subjected to protein ontology analysis to characterize changes in biological processes, cell components and molecular functions in the patients’ skin compared to skin of the healthy volunteers. Results The performed analysis identified 405 and 59 differentially expressed proteins in lesional and normally looking psoriatic skin compared to healthy control. We discovered decreased expression of KNG1, APOE, HRG, THBS1 and PLG in normally looking skin of the patients. Presumably, these changes were needed to protect the epidermis from spontaneous activation of kallikrein-kinin system and delay the following development of inflammatory response. In lesional skin, we identified several large groups of proteins with coordinated expression. Mainly, these proteins were involved in different aspects of protein and RNA metabolism, namely ATP synthesis and consumption; intracellular trafficking of membrane-bound vesicles, pre-RNA processing, translation, chaperoning and degradation in proteasomes/immunoproteasomes. Conclusion Our findings explain the molecular basis of metabolic changes caused by disease in skin lesions, such as faster cell turnover and higher metabolic rate. They also indicate on downregulation of kallikrein-kinin system in normally looking skin of the patients that would be needed to delay exacerbation of the disease. Data are available via ProteomeXchange with identifier PXD021673.
An Etiological Study on Mass Mortality of Cultured Colorcarp Juveniles Showing Edema

An etiological study was conducted to identify the causative agent of contagious edema of cultured juvenile colorcarp, Cyprinus carpio, in Japan. The disease outbreaks were often observed during the rainy season, extending from late June to late July, and the mortality frequently reached 80-100%. High mortality with edema was demonstrated among carp fry (0.10-0.26g) exposed to the filtered homogenates of diseased fish. Repeated infection trials demonstrated that the disease was transmissible by using filtered homogenates even after 12 times passage.Pox-like virus particles, 335 (300-400) nm in length and 265 (245-290) nm in width, were detected in the gilllamellar epithelial cells from both spontaneously affected and experimentally infected fish. Pancreas, kidney, spleen, and intestine of experimentally infected fish showed histopathological changes, but pox-like virus or other pathogenic organisms were not found in these organs. In the case of experimentally infected fish, more than 80%of infectivity was found in gills when the titers were compared by quantitative infection trials. Although the virus has not been successfully isolated, the facts mentioned above indicate that the pox-like virus observed in gill epithelial cells is the pathogen of this disease. We suggest that this infectious disease be termed “viral edema of carp”.
Intrusive Experiences In Post-Traumatic Stress Disorder: Treatment Response Induces Changes In The Effective Connectivity of The Anterior Insula

Background One of the core features of posttraumatic stress disorder (PTSD) is reexperiencing the trauma. The anterior insula (AI) was proposed to play a crucial role in these intrusive experiences. However, the dynamic function of the AI in reexperiencing trauma, as well as its putative modulation by effective therapy, still need to be specified. Methods Thirty PTSD patients were enrolled and exposed to traumatic memory reactivation therapy. Resting-state fMRI scans were acquired before and after treatment. To explore AI directed influences over the rest of the brain, we referred to a mixed-model using pre/post Granger causality analysis seeded on the AI as a within-subject factor and treatment response as a between-subject factor. To further identify correlates of reexperiencing trauma, we investigated how intrusive severity affected: (i) causality maps and (ii) the spatial stability of other intrinsic brain networks. Results We observed dynamic changes in AI effective connectivity in PTSD patients. Many within- and between-network causal paths were found to be less influenced by the AI after effective therapy. Insular influences were found positively correlated with flashback severity, while reexperiencing was linked with a stronger default mode network (DMN) and more unstable central executive network (CEN) connectivity. Conclusion We showed that directed changes in AI signaling to the DMN and CEN at rest may underlie the degree of intrusive symptoms in PTSD. A positive response to treatment further induced changes in network-to-network anticorrelated patterns. Such findings may guide targeted neuromodulation strategies in PTSD patients not suitably improved by conventional treatment.
Abscission Checkpoint Bodies Reveal a New Facet of Abscission Checkpoint Control

The abscission checkpoint regulates the ESCRT membrane fission machinery and thereby delays cytokinetic abscission to protect genomic integrity in response to residual mitotic errors. The checkpoint is maintained by Aurora B kinase, which phosphorylates multiple targets, including CHMP4C, a regulatory ESCRT-III subunit necessary for this checkpoint. We now report the discovery that cytoplasmic abscission checkpoint bodies (ACBs) containing phospho-Aurora B and tri-phospho-CHMP4C develop in telophase under an active checkpoint. ACBs are derived from Mitotic Interchromatin Granules (MIGs), transient mitotic structures whose components are housed in splicing-related nuclear speckles during interphase. ACB formation requires CHMP4C, and the ESCRT factor ALIX also contributes. ACB formation is conserved across cell types and under multiple circumstances that activate the checkpoint. Finally, ACBs retain a population of ALIX, and their presence correlates with delayed recruitment of ALIX to the midbody where it would normally promote abscission. Thus, a cytoplasmic mechanism helps regulate midbody machinery to delay abscission.
The Species-specific Acquisition and Diversification of a Novel Family of Killer Toxins in Budding Yeasts of the Saccharomycotina

Killer toxins are extracellular antifungal proteins that are produced by a wide variety of fungi, including Saccharomyces yeasts. Although many Saccharomyces killer toxins have been previously identified, their evolutionary origins remain uncertain given that many of the se genes have been mobilized by double-stranded RNA (dsRNA) viruses. A survey of yeasts from the Saccharomyces genus has identified a novel killer toxin with a unique spectrum of activity produced by Saccharomyces paradoxus. The expression of this novel killer toxin is associated with the presence of a dsRNA totivirus and a satellite dsRNA. Genetic sequencing of the satellite dsRNA confirmed that it encodes a killer toxin with homology to the canonical ionophoric K1 toxin from Saccharomyces cerevisiae and has been named K1-like (K1L). Genomic homologs of K1L were identified in six non-Saccharomyces yeast species of the Saccharomycotina subphylum, predominantly in subtelomeric regions of the yeast genome. The sporadic distribution of these genes supports their acquisition by horizontal gene transfer followed by diversification, with evidence of gene amplification and positive natural selection. When ectopically expressed in S. cerevisiae from cloned cDNAs, both K1L and its homologs can inhibit the growth of competing yeast species, confirming the discovery of a new family of biologically active killer toxins. The phylogenetic relationship between K1L and its homologs suggests gene flow via dsRNAs and DNAs across taxonomic divisions to enable the acquisition of a diverse arsenal of killer toxins for use in niche competition.
H-tSNE: Hierarchical Nonlinear Dimensionality Reduction

Dimensionality reduction (DR) is often integral when analyzing high-dimensional data across scientific, economic, and social networking applications. For data with a high order of complexity, nonlinear approaches are often needed to identify and represent the most important components. We propose a novel DR approach that can incorporate a known underlying hierarchy. Specifically, we extend the widely used t-Distributed Stochastic Neighbor Embedding technique (t-SNE) to include hierarchical information and demonstrate its use with known or unknown class labels. We term this approach “H-tSNE. ” Such a strategy can aid in discovering and understanding underlying patterns of a dataset that is heavily influenced by parent-child relationships. Without integrating information that is known a priori, we suggest that DR cannot function as effectively. In this regard, we argue for a DR approach that enables the user to incorporate known, relevant relationships even if their representation is weakly expressed in the dataset. Availability github.com/Cobanoglu-Lab/h-tSNE
Genetic requirements for cell division in a genomically minimal cell

Genomically minimal cells, such as JCVI-syn3.0, offer a platform to clarify genes underlying core physiological processes. While this minimal cell includes genes essential for population growth, the physiology of its single cells remained uncharacterized. To investigate striking morphological variation in JCVI-syn3.0 cells, we present an approach to characterize cell propagation and determine genes affecting cell morphology. Microfluidic chemostats allowed observation of intrinsic cell dynamics resulting in irregular morphologies. The addition of 19 genes not retained in JCVI-syn3.0 generated JCVI-syn3A, which presents significantly less morphological variation than JCVI-syn3.0. We further identified seven of these 19 genes, including two known cell division genes ftsZ and sepF and five genes of unknown function, required together to restore cell morphology and division similar to JCVI-syn1.0. This surprising result emphasizes the polygenic nature of cell morphology, as well as the importance of a Z-ring and membrane properties in the physiology of genomically minimal cells.
Simulating digital micromirror devices for patterning coherent excitation light in structured illumination microscopy

Digital micromirror devices (DMDs) are spatial light modulators that employ the electro-mechanical movement of miniaturized mirrors to steer and thus modulate the light reflected of a mirror array. Their wide availability, low cost and high speed make them a popular choice both in consumer electronics such as video projectors, and scientific applications such as microscopy. High-end fluorescence microscopy systems typically employ laser light sources, which by their nature provide coherent excitation light. In super-resolution microscopy applications that use light modulation, most notably structured illumination microscopy (SIM), the coherent nature of the excitation light becomes a requirement to achieve optimal interference pattern contrast. The universal combination of DMDs and coherent light sources, especially when working with multiple different wavelengths, is unfortunately not straight forward. The substructure of the tilted micromirror array gives rise to a blazed grating, which has to be understood and which must be taken into account when designing a DMD-based illumination system. Here, we present a set of simulation frameworks that explore the use of DMDs in conjunction with coherent light sources, motivated by their application in SIM, but which are generalizable to other light patterning applications. This framework provides all the tools to explore and compute DMD-based diffraction effects and to simulate possible system alignment configurations computationally, which simplifies the system design process and provides guidance for setting up DMD-based microscopes.
Edition of complex gene families in tobacco with GoldenBraid 4.0, a multipurpose web-based platform for plant genome engineering

CRISPR/Cas ability to target several loci simultaneously (multiplexing) is a game-changer in plant breeding. Multiplexing not only accelerates trait pyramiding but also can unveil traits hidden by functional redundancy in polyploid crops. Furthermore, multiplexing enhances dCas-based programmable gene expression and enables cascade-like gene regulation. However, multiplex constructs comprising tandemly arrayed gRNAs are difficult to assemble, this hampering more widespread use. Here we present a comprehensive upgrade of the popular cloning platform GoldenBraid (GB), in which, on top of its classical multigene cloning software, we integrate new assembly tools for two-dimensions gRNA multiplexing with both Cas9 and Cas12a, using the gRNA-tRNA-spaced and the gRNA unspaced approaches, respectively. As functional validation, we show, among others, the assembly of up to 17 tandemly-arrayed gRNAs constructs against a subset of the Squamosa-Promoter Binding Protein-Like (SPL) gene family in tobacco. With these constructs we generated a collection of Cas9-free SPL mutants harboring up to 9 biallelic mutations in a single generation. The functionality of GB-assembled dCas9 and dCas12a-based CRISPR activators and repressors using single and multiplexing gRNAs is also validated. With the incorporation of the new CRISPR tools and part’s collection, GB4.0 turns an unprecedentedly comprehensive open platform for plant genetic engineering.