Miracle-dz/UniFAR-FTUs huggingface dataset:
A predictive model of gene expression reveals the role of network motifs in the mating response of yeast

Signaling network motifs ensure appropriate transcriptional responses to distinct pheromone dynamics in yeast. Motifs in mating responses In the mating response in yeast, pheromone stimulation initiates a MAPK signaling cascade that alleviates the repression of the transcription factor Ste12 by Dig1 and Dig2, resulting in transcriptional changes, and that activates a factor called Far1, which promotes Ste12 degradation. Pomeroy et al. found that pheromone-induced transcriptional regulation showed persistence after pheromone removal and long-term adaptation upon prolonged pheromone exposure. They generated a model trained on transcriptional data generated in response to different temporal patterns of pheromone stimulation. The model predicted that persistence and long-term adaptation required four network motifs: feedforward, positive feedback, and negative feedback loops between MAPKs, Ste12, and Far1; and the rebinding of Dig1 and Dig2 to Ste12. These predictions were experimentally validated with mutant yeast strains. Thus, multiple network motifs ensure that gene expression is appropriately regulated in response to different patterns of pheromone exposure. Cells use signaling pathways to receive and process information about their environment. These nonlinear systems rely on feedback and feedforward regulation to respond appropriately to changing environmental conditions. Mathematical models describing signaling pathways often lack predictive power because they are not trained on data that encompass the diverse time scales on which these regulatory mechanisms operate. We addressed this limitation by measuring transcriptional changes induced by the mating response in Saccharomyces cerevisiae exposed to different dynamic patterns of pheromone. We found that pheromone-induced transcription persisted after pheromone removal and showed long-term adaptation upon sustained pheromone exposure. We developed a model of the regulatory network that captured both characteristics of the mating response. We fit this model to experimental data with an evolutionary algorithm and used the parameterized model to predict scenarios for which it was not trained, including different temporal stimulus profiles and genetic perturbations to pathway components. Our model allowed us to establish the role of four architectural elements of the network in regulating gene expression. These network motifs are incoherent feedforward, positive feedback, negative feedback, and repressor binding. Experimental and computational perturbations to these network motifs established a specific role for each in coordinating the mating response to persistent and dynamic stimulation.
Understanding multiethnic and multiracial experiences globally: towards a conceptual framework of mixedness

ABSTRACT This special issue brings together nine articles on the experiences of multiracial and multiethnic individuals from nine different countries across the globe – the United Kingdom, Sweden, Ireland, Spain, Canada, the United States, Japan, Singapore and Israel. The articles in this volume address the diverse experiences of the identification, socialising and mainstreaming of multiethnic and multiracial individuals in different national contexts. The collection consists of both qualitative and quantitative research from various disciplines in the social sciences and thus contributes to an interdisciplinary understanding and a multi-method approach to this reality. Through a cross-country analysis of the results provided by each paper, this Introduction proposes a conceptual framework for better understanding the realities of mixedness globally.
Influence of geogenic CO2 on mineral and organic soil constituents on a mofette site in the NW Czech Republic

Geogenic CO2 emission on mofette sites may be a factor in soil formation. To demonstrate a CO2 effect, we studied soils (0–60 cm depth) along a transect across a mofette in the NW Czech Republic. We determined CO2 partial pressures (p(CO2)), and the contents in the soil of carbon (C), nitrogen (N), sulphur and dithionite‐ and oxalate‐extractable iron and manganese. X‐ray diffractometry (XRD) and Fourier‐transform infrared (FTIR) spectroscopy methods were applied to the soils' particle‐size fractions. The CO2 partial pressures varied considerably (0.001–1) along the transect and were positively correlated with both the Corg contents (5.5–432.9 g kg−1) and the C:N ratio (9.3–32.2), indicating a decreased turnover of organic parent material with increasing CO2. When the soil atmosphere was entirely composed of CO2, pedogenic Fe oxide contents were small (minimum 0.5 g dithionite‐extractable Fe kg−1) and poorly crystalline. XRD and FTIR spectroscopy revealed primary and secondary minerals such as quartz, feldspars, mica, illite, kaolinite and halloysite irrespective of CO2 contents. A pronounced effect of CO2 was found for soil organic matter (SOM), because the FTIR spectra did not reveal a normal accumulation of alkyl C and lipids of microbial origin in the clay fraction. This indicates that microbial synthesis and/or degradation of plant‐derived aliphatic species were reduced. We did not detect more organo–mineral associations, microbially formed polypeptides or pectin in clay fractions in comparison with the clay‐plus‐silt fractions at large p(CO2). This indicates relatively unaltered particulate OM in the clay fraction. At large p(CO2) values, the IR bands indicative of lignin became detectable and that of aryl ketones in lignin was positively correlated with p(CO2). Thus, we suggest that microbial formation of SOM and degradation of lignin is restricted under an increased CO2 atmosphere. We attribute less humification at increased CO2 in the soil atmosphere to a decrease in oxidative transformations and decreased microbial activity.
Does Filial Piety Still Matter? A Filiality-based Perspective on Intergenerational Solidarity and Cooperation

ABSTRACT The Republic of Korea has its own tradition of intergenerational solidarity based on long-lasting social norms and values. This paper explores the issues associated with filial piety for elderly parents and older relatives, and its impact on intergenerational relationships in Korean culture. An exploratory study was conducted as data were collected from 17 individual interviews between 2018 and 2019 across the nation. Thematic analysis was used to develop themes through interaction with the data. The findings show that the core principle of filial piety continues to constitute a major component of intergenerational relationships and practices in contemporary Korean society.
Community-Based Resistance Strategies among a Group of Trans Women in Lima, Peru during the COVID-19 Pandemic

ABSTRACT This study explores the community-based strategies that a group of trans women living in Lima, Peru, employed to resist the negative impact of the COVID-19 pandemic on their wellbeing. Data was collected through participant observation and focus group discussions during the implementation of a social aid campaign targeted to this population and analyzed through reflexive theoretical thematic analysis. Resistance strategies were understood as forms of social capital grounded in relations of support and connectedness. Results underscored the importance of social cohesion to ameliorate increasing levels of precarity, community leaders as key for linking trans women across different networks, and unified efforts of social groups who share values to influence institutional power. The analysis also captured barriers and challenges that could hinder the development and articulation of social capital. Fostering trust relations and community-organization should be fundamental components for advocacy programs that seek to support the trans women community.
Interrelated Factors for Return to Work of Sick-Listed Employees in Sweden

Abstract Purpose: Long-term sickness absence is a significant human and economic cost in many countries, including Sweden making research on factors which impact on return to work (RTW) relevant. This study has two aims: (1) provide an overview of factors that impact RTW expectations in a national sample of Swedish workers on long-term sickness absence; and (2) gain an understanding of the interrelationships among these factors using a socioecological framework and decision tree analysis. Method: A survey, designed to capture information about demographic variables, health and work ability, workplace contact, supervisor support and expectations of return to work, was mailed to 1,112 randomly selected sick-listed people in Sweden and completed by 534, representing a response rate of 48%. Results: The most important factors affecting RTW expectations were work ability and burnout. Employees reporting high levels of work ability were more likely to expect to RTW compared to those reporting low levels, and this was dependent on their relative burnout score. Those with a high burnout score were less likely to expect to RTW, while for those with a low burnout score RTW expectations were dependent on age, country of birth, and supervisor support. For young employees reporting low work ability and low burnout score, RTW expectations were lower. Conclusions: Our results suggest a more nuanced approach to delivery of RTW services is required, whereby practitioners need to understand the socioecology of the range of factors that impact RTW expectations. The use of decision tree analysis facilitates this understanding by describing the interrelationships between these factors.
α α-tocopherol and amygdalin contents of selected almond (Prunus amygdalus Batsch.) genotypes

Phenolic compounds may be regarded as one factor contributing to quality of fruits and juice because of high antioxidative effects. Limited information is available concerning the qualitative and quantitative composition of polyphenolic compounds in almonds. The phenolic acids, αtocopherol and amygdalin contents of the 14 selected almond genotypes were investigated in the study. Catechin was the major phenolic acid ranging from 11.1 to 227.2 µg/g, followed by caffeic acid (2.9-32.1 µg/g), epicatechin (2.0-23.5 µg/g) and gallic acid (2.4-16.1 µg/g). α-Tocopherol contents of genotypes were between 143.97 and 462.78 µg/g, and significant differences were observed amongst genotypes. The highest amygdalin content was detected in slightly bitter almond genotype Isp-9 (22.53 mg/g). Amygdalin contents of sweet almond genotypes ranged from 1.53 to 11.56 mg/g. The results showed large variability amongst genotypes in phenolic acids, α-tocopherol and amygdalin contents.
Mitochondrial Fission Regulates Transcription of Ribosomal Protein Genes in Embryonic Hearts

Mitochondrial dysfunction causes severe congenital heart diseases and prenatal/neonatal lethality. The lack of sufficient knowledge regarding how mitochondrial abnormalities affect cardiogenesis poses a major barrier for the development of clinical applications that target inborn heart defects due to mitochondrial deficiency. Mitochondrial morphology, which is regulated by fission and fusion, plays key roles in determining mitochondrial activity. Drp1 encodes a dynamin-related GTPase required for mitochondrial fission. To investigate the role of mitochondrial fission on cardiogenesis during the embryonic metabolic shift period, we specifically inactivated Drp1 in second heart field derived structures. Deletion of Drp1 in embryonic cardiomyocytes led to severe defects in mitochondrial morphology, ultrastructure, and activity. These defects caused increased cell death, decreased cell survival, disorganized cardiomyocytes, and embryonic lethality. Through characterizing this model, we reveal a novel AMPK-SIRT7-GABPB axis that relays the mitochondrial fission anomaly to reduced transcription of ribosomal protein genes in mutant cardiomyocytes. We therefore provide the first mouse genetic evidence to show that mitochondrial fission is essential for embryonic heart development. Furthermore, we uncovered a novel signaling cascade that mediates the crosstalk between mitochondrial dysfunction and protein synthesis. Our research provides further mechanistic insight regarding how mitochondrial dysfunction causes pathological molecular and cellular alterations during cardiogenesis.
Upregulation of bundle sheath electron transport capacity under limiting light in C4 Setaria viridis

C4 photosynthesis is a biochemical pathway that operates across mesophyll and bundle sheath (BS) cells to increase CO2 concentration at the site of CO2 fixation. C4 plants benefit from high irradiance but their efficiency decreases under shade causing a loss of productivity in crop canopies. We investigated shade acclimation responses of a model NADP-ME monocot Setaria viridis focussing on cell-specific electron transport capacity. Plants grown under low light (LL) maintained CO2 assimilation rates similar to high light plants but had an increased chlorophyll and light-harvesting-protein content, predominantly in BS cells. Photosystem II (PSII) protein abundance, oxygen-evolving activity and the PSII/PSI ratio all increased in LL BS cells indicating a higher capacity for linear electron flow. PSI, ATP synthase, Cytochrome b6f and the chloroplastic NAD(P) dehydrogenase complex, which constitute the BS cyclic electron flow machinery, were all upregulated in LL plants. A decline in PEP carboxylase activity in mesophyll cells and a consequent shortage of reducing power in BS chloroplasts was associated with the more oxidised redox state of the plastoquinone pool in LL plants and the formation of PSII - light-harvesting complex II supercomplexes with an increased oxygen evolution rate. Our results provide evidence of a redox regulation of the supramolecular composition of Photosystem II in BS cells in response to shading. This newly identified link contributes to understanding the regulation of PSII activity in C4 plants and will support strategies for crop improvement including the engineering of C4 photosynthesis into C3 plants. Significance statement The efficiency of C4 photosynthesis decreases under low irradiance causing a loss of productivity in crop canopies. We investigate shade acclimation of a model NADP-ME monocot, analysing cell-specific protein expression and electron transport capacity. We propose a regulatory pathway controlling abundance and activity of Photosystem II in bundle sheath cells in response to irradiance.
Retrospective Study on the Health Problems of Falcons in Al Ain, United Arab Emirates

Background Falcons are important animals in sociocultural events of the society of the United Arab Emirates (UAE). Like any other birds, falcons can be affected by different health problems. This study was conducted to investigate the major health problems of falcons presented to the City Vet Clinic in Al Ain during 2019. Methods Data were extracted from the records of 906 falcons presented to City Vet Clinic in 2019. Data extraction was made on the diagnostic methods used, diagnosed health problems and the type of treatment/veterinary services given to falcons. Analysis was done using descriptive statistics. Results The overall incidence rate of health problems detected in falcons presented to City Vet Clinic in 2019 was 26.5% (95% confidence interval, CI, 23.6-29.5%). The most incident health problems were ingluvitis (inflammation of crop), aspergillosis and bacterial enteritis with incidence rates of 8.1% (95%CI: 6.4–10.0%), 5.8% (95%CI: 4.4-7.6%) and 2.4% (95%CI: 1.5-3.7%), respectively. The relationship between the number of cases of falcon and months was polynomial with a regression (R2) of 42% indicating that only 42% of the variation in the number cases could be explained by monthly variation. The three main medical treatments given for the diagnosed health problems included antibiotics, anti-fungal and anti-parasitic with frequencies of 46.3% (95%CI: 39.8-52.8%), 21.7% (95%CI: 16.6-27.4%) and 12.0% (95%CI: 8.2-16.9%), respectively. Conclusion The major health problems of falcons were ingluvitis, aspergillosis and bacterial enteritis. Infections that occur in falcons can also be transmitted to owners. Therefore, regular check-up and control of diseases of falcons is recommended.
Profiling of histone H 1 variants and changes on genome architecture and gene expression upon histone H 1 depletion in breast cancer cells

1 Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, 08028, Spain 2 CNAG-CRG, Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona, 08028, Spain 3 Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Carrer del Doctor Aiguader 88, Barcelona, 08003, Spain 4 Pompeu Fabra University, Doctor Aiguader 88, Barcelona, 08003, Spain 5 ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
Mutation bias implicates RNA editing in a wide range of mammalian RNA viruses

The rapid evolution of RNA viruses has been long considered to result from a combination of high copying error frequencies during RNA replication, short generation times and the consequent extensive fixation of neutral or adaptive changes over short periods. While both the identities and sites of mutations are typically modelled as being random, recent investigations of sequence diversity of SARS coronavirus 2 (SARS-CoV-2) have identified a preponderance of C->U transitions, potentially driven by an APOBEC-like RNA editing process. The current study investigated whether this phenomenon could be observed in the more genetically diverse datasets of other RNA viruses. Using a 5% divergence filter to infer directionality, 18 from 32 datasets of aligned coding region sequences from a diverse range of mammalian RNA viruses (including Picornaviridae, Flaviviridae, Matonaviridae, Caliciviridae and Coronaviridae) showed a >2-fold base composition normalised excess of C->U transitions compared to U->C (range 2.1x–7.5x). C->U transitions showed a favoured 5’ U upstream context consistent with previous analyses of APOBEC-mediated RNA targeting. Amongst several genomic compositional and structural parameters, the presence of genome scale RNA secondary structure (GORS) was associated with C->U/U->C transition asymmetries (p < 0.001), potentially reflecting the documented structure dependence of APOBEC-mediated RNA editing. Using the association index metric, C->U changes were specifically over-represented at phylogenetically uninformative sites, consistent with extensive homoplasy documented in SARS-CoV-2. Excess C->U substitutions accounted for 15-20% of standing sequence variability of HCV and other RNA viruses; RNA editing may therefore represent a potent driver of RNA virus sequence diversification and longer term evolution. Author Summary The rapid evolution of RNA viruses is thought to arise from high mutation frequencies during replication and the rapid accumulation of genetic changes over time in response to its changing environments. This study describes an additional potent factor that contributes to the evolution of RNA infecting mammals, the deliberate mutation of the viral genome by host antiviral pathways active within the cell when it becomes infected. This so called “genome editing” by one or more APOBEC enzymes leads to characteristic C->U mutations that damage the virus’s ability to replicate. While this pathway is well characterised as an antiviral defence against HIV and other retroviruses, this study provides evidence for its activity against a wide range of human and veterinary viruses, including HCV and foot and mouth disease virus. APOBEC-driven mutations accounted for 15-20% of standing sequence variability of RNA virus groups, representing a potent driver of RNA virus sequence diversification.
gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae

Members of the bacterial genus Vibrio utilise chitin both as a metabolic substrate and a signal to activate natural competence. Vibrio cholerae is a bacterial enteric pathogen, sub-lineages of which can cause pandemic cholera. However, the chitin metabolic pathway in V. cholerae has been dissected using only a limited number of laboratory strains of this species. Here, we survey the complement of key chitin metabolism genes amongst 195 diverse V. cholerae. We show that the gene encoding GbpA, known to be an important colonisation and virulence factor in pandemic isolates, is not ubiquitous amongst V. cholerae. We also identify a putatively novel chitinase, and present experimental evidence in support of its functionality. Our data indicate that the chitin metabolic pathway within the V. cholerae species is more complex than previously thought, and emphasise the importance of considering genes and functions in the context of a species in its entirety, rather than simply relying on traditional reference strains. Impact statement It is thought that the ability to metabolise chitin is ubiquitous amongst Vibrio spp. , and that this enables these species to survive in aqueous and estuarine environmental contexts. Although chitin metabolism pathways have been detailed in several members of this genus, little is known about how these processes vary within a single Vibrio species. Here, we present the distribution of genes encoding key chitinase and chitin-binding proteins across diverse Vibrio cholerae, and show that our canonical understanding of this pathway in this species is challenged when isolates from non-pandemic V. cholerae lineages are considered alongside those linked to pandemics. Furthermore, we show that genes previously thought to be species core genes are not in fact ubiquitous, and we identify novel components of the chitin metabolic cascade in this species, and present functional validation for these observations. Data summary The authors confirm that all supporting data, code, and protocols have been provided within the article or through supplementary data files. No whole-genome sequencing data were generated in this study. Accession numbers for the publicly-available sequences used for these analyses are listed in Supplementary Table 1, Table 2, and the Methods. All other data which underpin the figures in this manuscript, including pangenome data matrices, modified and unmodified sequence alignments and phylogenetic trees, original images of gels and immunoblots, raw fluorescence data, amplicon sequencing reads, and the R code used to generate Figure 7, are available in Figshare: https://dx.doi. org/10.6084/m9.figshare. 13169189 (Note for peer-review: Figshare DOI is inactive but will be activated upon publication, please use temporary URL https://figshare.com/s/7795a2d80c13f694f8fa for review).