Miracle-dz/UniFAR-FTUs huggingface dataset:
A mitochondrial electron transport chain with atypical subunit composition confers oxygen sensitivity to a mammalian chemoreceptor

The carotid body (CB) is the major chemoreceptor for blood oxygen in the control of ventilation in mammals, contributing to physiological adaptation to high altitude, pregnancy, and exercise, and its hyperactivity is linked to chronic conditions such as sleep-disorder breathing, hypertension, chronic heart failure, airway constriction, and metabolic syndrome (1–3). Upon acute hypoxia (PO2=100 mmHg to <80 mmHg), K+ channels on CB glomus cells are inhibited, causing membrane depolarization to trigger Ca+2 influx and neurotransmitter release that stimulates afferent nerves (1–3). A longstanding model proposes that the CB senses hypoxia through atypical mitochondrial electron transport chain (ETC) metabolism that is more sensitive to decreases in oxygen than other tissues. This model is supported by observations that ETC inhibition by pharmacology and gene knockout activates CB sensory activity and that smaller decreases in oxygen concentration inhibit ETC activity in CB cells compared to other cells (1–5). Determining the composition of atypical ETC subunits in the CB and their specific activities is essential to delineate molecular mechanisms underlying the mitochondrial hypothesis of oxygen sensing. Here, we identify HIGD1C, a novel hypoxia inducible gene domain factor isoform, as an ETC Complex IV (CIV) protein highly and selectively expressed in glomus cells that mediates acute oxygen sensing by the CB. We demonstrate that HIGD1C negatively regulates oxygen consumption by CIV and acts with the hypoxia-induced CIV subunit COX4I2 to enhance the sensitivity of CIV to hypoxia, constituting an important component of mitochondrial oxygen sensing in the CB. Determining how HIGD1C and other atypical CIV proteins expressed in the CB work together to confer exquisite oxygen sensing to the ETC will help us better understand how tissue- and condition-specific CIV subunits contribute to physiological function and disease (6) and allow us to potentially target these proteins to treat chronic diseases characterized by CB dysfunction (7).
T cell stimulation remodels the latently HIV-1 infected cell population by differential activation of proviral chromatin

The reservoir of latently HIV-1 infected cells is heterogeneous. To achieve an HIV-1 cure, the reservoir of activatable proviruses should be eliminated while permanently silenced proviruses may be tolerated. We have developed a method to assess the proviral nuclear microenvironment in single cells. In latently HIV-1 infected cells, a zinc finger protein tethered to the HIV-1 promoter produced a fluorescent signal as a protein of interest came in its proximity, such as the viral transactivator Tat when recruited to the nascent RNA. Tat is essential for viral replication. In these cells we assessed the proviral activation and chromatin composition. By linking Tat recruitment to proviral activity, we dissected the mechanisms of HIV-1 latency reversal and the consequences of HIV-1 production. A pulse of promoter-associated Tat was identified that contrasted to the continuous production of viral proteins. As expected, promoter H3K4me3 led to substantial expression of the provirus following T cell stimulation. However, the activation-induced cell cycle arrest and death led to a surviving cell fraction with proviruses encapsulated in repressive chromatin. Further, this cellular model was used to reveal mechanisms of action of small molecules. In a proof-of-concept study we determined the effect of an enhancer specific CBP/P300-inhibitor on HIV-1 latency reversal. Only proviruses resembling active enhancers, associated with H3K4me1 and H3K27ac, efficiently recruited Tat. Tat-independent HIV-1 latency reversal of unknown significance still occurred. We present a method for single cell assessment of the microenvironment of the latent HIV-1 proviruses, used here to reveal how T cell stimulation modulates the proviral activity and how the subsequent fate of the infected cell depends on the chromatin context.
Sex Differences in Behavioral Responding and Dopamine Release during Pavlovian Learning

Visual Abstract Learning associations between cues and rewards require the mesolimbic dopamine system. The dopamine response to cues signals differences in reward value in well trained animals. However, these value-related dopamine responses are absent during early training sessions when cues signal differences in the reward rate. These findings suggest cue-evoked dopamine release conveys differences between outcomes only after extensive training, though it is unclear whether this is unique to when cues signal differences in reward rate, or whether this is also evident when cues signal differences in other value-related parameters such as reward size. To address this, we used a Pavlovian conditioning task in which one audio cue was associated with a small reward (one pellet) and another audio cue was associated with a large reward (three pellets). We performed fast-scan cyclic voltammetry to record changes in dopamine release in the nucleus accumbens of male and female rats throughout learning. While female rats exhibited higher levels of conditioned responding, a faster latency to respond, and elevated post-reward head entries relative to male rats, there were no sex differences in the dopamine response to cues. Multiple training sessions were required before cue-evoked dopamine release signaled differences in reward size. Reward-evoked dopamine release scaled with reward size, though females displayed lower reward-evoked dopamine responses relative to males. Conditioned responding related to the decrease in the peak reward-evoked dopamine response and not to cue-evoked dopamine release. Collectively, these data illustrate sex differences in behavioral responding as well as in reward-evoked dopamine release during Pavlovian learning.
Applications of the indole-alkaloid gramine modulate the assembly of individual members of the barley rhizosphere microbiota

Microbial communities proliferating at the root-soil interface, collectively referred to as the rhizosphere microbiota, represent an untapped beneficial resource for plant growth, development and health. Integral to a rational manipulation of the microbiota for sustainable agriculture is the identification of the molecular determinants of these communities. In plants, biosynthesis of allelochemicals is centre stage in defining inter-organismal relationships in the environment. Intriguingly, this process has been moulded by domestication and breeding selection. The indole-alkaloid gramine, whose occurrence in barley (Hordeum vulgare L.) is widespread among wild genotypes but has been counter selected in several modern varieties, is a paradigmatic example of this phenomenon. This prompted us to investigate how exogenous applications of gramine impacted on the rhizosphere microbiota of two, gramine-free, elite barley varieties grown in a reference agricultural soil. High throughput 16S rRNA gene amplicon sequencing revealed that applications of gramine interfere with the proliferation of a subset of soil microbes with a relatively broad phylogenetic assignment. Strikingly, growth of these bacteria appeared to be rescued by barley plants in a genotype- and dosage-independent manner. In parallel, we discovered that host recruitment cues can interfere with the impact of gramine application in a host genotype-dependent manner. Interestingly, this latter effect displayed a bias for members of the phyla Proteobacteria. These initial observations indicate that gramine can act as a determinant of the prokaryotic communities inhabiting the root-soil interface.
Editorial: Managing for the Future: Challenges and Approaches for Disentangling the Relative Roles of Environmental Change and Fishing in Marine Ecosystems

Citation: Bundy A, Renaud PE, Coll M, Koenigstein S, Niiranen S, Pennino MG, Tam JC and Travers-Trolet M (2021) Editorial: Managing for the Future: Challenges and Approaches for Disentangling the Relative Roles of Environmental Change and Fishing in Marine Ecosystems. Front. Mar. Sci. 8:753459. doi: 10.3389/fmars.2021. 753459 Editorial: Managing for the Future: Challenges and Approaches for Disentangling the Relative Roles of Environmental Change and Fishing in Marine Ecosystems
Pandemic Preparedness Against Influenza: DNA Vaccine for Rapid Relief

The 2009 “swine flu” pandemic outbreak demonstrated the limiting capacity for egg-based vaccines with respect to global vaccine supply within a timely fashion. New vaccine platforms that efficiently can quench pandemic influenza emergences are urgently needed. Since 2009, there has been a profound development of new vaccine platform technologies with respect to prophylactic use in the population, including DNA vaccines. These vaccines are particularly well suited for global pandemic responses as the DNA format is temperature stable and the production process is cheap and rapid. Here, we show that by targeting influenza antigens directly to antigen presenting cells (APC), DNA vaccine efficacy equals that of conventional technologies. A single dose of naked DNA encoding hemagglutinin (HA) from influenza/A/California/2009 (H1N1), linked to a targeting moiety directing the vaccine to major histocompatibility complex class II (MHCII) molecules, raised similar humoral immune responses as the adjuvanted split virion vaccine Pandemrix, widely administered in the 2009 pandemic. Both vaccine formats rapidly induced serum antibodies that could protect mice already 8 days after a single immunization, in contrast to the slower kinetics of a seasonal trivalent inactivated influenza vaccine (TIV). Importantly, the DNA vaccine also elicited cytotoxic T-cell responses that reduced morbidity after vaccination, in contrast to very limited T-cell responses seen after immunization with Pandemrix and TIV. These data demonstrate that DNA vaccines has the potential as a single dose platform vaccine, with rapid protective effects without the need for adjuvant, and confirms the relevance of naked DNA vaccines as candidates for pandemic preparedness.
Climate Change and Coffee Quality: Systematic Review on the Effects of Environmental and Management Variation on Secondary Metabolites and Sensory Attributes of Coffea arabica and Coffea canephora

Climate change is impacting crop performance and agricultural systems around the world with implications for farmers and consumers. We carried out a systematic review to synthesize evidence regarding the effects of environmental factors associated with climate change and management conditions associated with climate adaptation on the crop quality of a culturally-relevant perennial crop, coffee (Coffea arabica and Coffea canephora). Seventy-three articles were identified that addressed the study's research question including 42 articles on environmental factors, 20 articles on management conditions, and 11 articles on both. While variation was found between studies, findings highlight that coffee quality is vulnerable to changes in light exposure, altitude, water stress, temperature, carbon dioxide, and nutrient management. Both increases as well as decreases were found in secondary metabolites and sensory attributes that determine coffee quality in response to shifts in environmental and management conditions. The most consistent evidence identified through this systematic review includes the following two trends: (1) increased altitude is associated with improved sensory attributes of coffee and; (2) increased light exposure is associated with decreased sensory attributes of coffee. Research gaps were found regarding the effects of shifts in carbon dioxide, water stress, and temperature on the directionality (increase, decrease, or non-linear) of coffee quality and how this varies with location, elevation, and management conditions. This systematic review further identified the following research needs: (1) long-term studies that examine the interactive effects of multiple environmental factors and management conditions on coffee quality; (2) studies that examine the interaction between sensory attributes and secondary metabolites that determine coffee quality and; (3) studies on the feasibility of various climate-adaptation strategies for mitigating the effects of climate change on coffee quality. Evidence-based innovations are needed to mitigate climate impacts on coffee quality toward enhanced sustainability and resilience of the coffee sector from farm to cup.
Crustal Structure of the Seismogenic Volume of the 2010–2014 Pollino (Italy) Seismic Sequence From 3D P- and S-Wave Tomographic Images

A tomographic analysis of Mt. Pollino area (Italy) has been performed using earthquakes recorded in the area during an intense seismic sequence that occurred between 2010 and 2014. 870 local earthquakes with magnitude ranging from 1.8 to 5.0 were selected considering the number of recording stations, the signal quality, and the hypocenter distribution. P- and S-wave arrival times were manually picked and used to compute 3D velocity models through tomographic seismic inversion. The resulting 3D distributions of VP and VS are characterized by high resolution in the central part of the investigated area and from surface to about 10 km below sea level. The aim of the work is to obtain high-quality tomographic images to correlate with the main lithological units that characterize the study area. The results will be important to enhance the seismic hazard assessment of this complex tectonic region. These images show the ductile Apennine platform (VP = 5.3 km/s) overlaying the brittle Apulian platform (VP = 6.0 km/s) at depth of around 5 km. The central sector of the area shows a clear fold and thrust interface. Along this structure, most of the seismicity occurred, including the strongest event of the sequence (MW 5.0). High VP (>6.8 km/s) and high VP/VS (>1.9) patterns, intersecting the southern edge of this western seismogenic volume, have been interpreted as water saturated rocks, in agreement with similar geological context in the Apennines. These fluids could have played a role in nucleation and development of the seismic sequence. A recent study revealed the occurrence of clusters of earthquakes with similar waveforms along the same seismogenic volume. The hypocenters of these cluster events have been compared with the events re-located in this work. Jointly, they depict a 10 km × 4 km fault plane, NW-SE oriented, deepening towards SW with a dip angle of 40–45°. Instead, the volume of seismicity responsible for the ML 4.3 earthquake developed as a mainshock-aftershock sequence, occurring entirely within the average-to-low VP/VS Apennine platform. Our results agree with other independent geophysical analyses carried out in this area, and they could significantly improve the actual knowledge of the main lithologic units of this complex tectonic area.
Increased Predictive Accuracy of Multi-Environment Genomic Prediction Model for Yield and Related Traits in Spring Wheat (Triticum aestivum L.)

Genomic selection (GS) has the potential to improve the selection gain for complex traits in crop breeding programs from resource-poor countries. The GS model performance in multi-environment (ME) trials was assessed for 141 advanced breeding lines under four field environments via cross-predictions. We compared prediction accuracy (PA) of two GS models with or without accounting for the environmental variation on four quantitative traits of significant importance, i.e., grain yield (GRYLD), thousand-grain weight, days to heading, and days to maturity, under North and Central Indian conditions. For each trait, we generated PA using the following two different ME cross-validation (CV) schemes representing actual breeding scenarios: (1) predicting untested lines in tested environments through the ME model (ME_CV1) and (2) predicting tested lines in untested environments through the ME model (ME_CV2). The ME predictions were compared with the baseline single-environment (SE) GS model (SE_CV1) representing a breeding scenario, where relationships and interactions are not leveraged across environments. Our results suggested that the ME models provide a clear advantage over SE models in terms of robust trait predictions. Both ME models provided 2–3 times higher prediction accuracies for all four traits across the four tested environments, highlighting the importance of accounting environmental variance in GS models. While the improvement in PA from SE to ME models was significant, the CV1 and CV2 schemes did not show any clear differences within ME, indicating the ME model was able to predict the untested environments and lines equally well. Overall, our results provide an important insight into the impact of environmental variation on GS in smaller breeding programs where these programs can potentially increase the rate of genetic gain by leveraging the ME wheat breeding trials.
Bycatch Estimates From a Pacific Tuna Longline Fishery Provide a Baseline for Understanding the Long-Term Benefits of a Large, Blue Water Marine Sanctuary

Bycatch on pelagic tuna longlines has contributed to population declines in several far-ranging, oceanic species and presents a conservation challenge that area-based management tools are increasingly promoted to address. In January 2020 the Republic of Palau, concerned about the impacts of longline fishing in its waters, closed 80% of its exclusive economic zone to all extractive activities, reserving the remaining 20% for a domestic fishing zone (DFZ). One of a growing number of very large marine protected areas, the Palau National Marine Sanctuary (PNMS) spans ∼500,000 km2 and was established inter alia to allow for the recovery of fish stocks adversely impacted by tuna longline fleets. Given that the main tuna stocks targeted in the western Pacific are not overexploited, the benefits of protection potentially afforded by the sanctuary are likely greater for vulnerable bycatch species. Evaluations of the sanctuary’s performance require, in part, a baseline of historical catch rates and effort distribution in the distant-water fleet (DWF) and locally based fleet (LBF) operating in Palau prior to sanctuary implementation. We describe the fishing effort, catch rates, catch estimates and fishing mortality in Palau’s longline fishery based on logbook, observer and electronic monitoring data. We defined bycatch as any species, retained or discarded, other than targeted tunas. Between 2010 and 2020, 104.8 million hooks were deployed, catching over 2 million individuals from 117 taxa at an overall target:bycatch ratio of 1:1, with a retention rate of ∼62%. Pronounced differences in fishing strategies and spatial distribution of effort between fleets were associated with large variations in catch rates and composition. The LBF had a larger effect on populations of at-risk species relative to the DWF, with higher catch rates and magnitudes for several vulnerable species and higher observable fishing mortality rates (64% vs 50% in the DWF). The sanctuary reshaped Palau’s longline fishery, contracting the fishery’s area and capacity. The relocation of the DFZ eliminated the LBF and constrained the DWF to an area where the fleet’s total catch rates and those of a number of vulnerable species were historically lower relative to former fishing grounds now closed by the sanctuary. Our results highlight the importance of consistent bycatch monitoring and emphasize the need for regional area-based approaches for managing longline fisheries.
Nursing Students' Perceptions on Healthcare-Associated Infection Control and Prevention Teaching and Learning Experience: Development and Validation of a Scale in Four European Countries

Healthcare-associated infections are one of the major concerns worldwide. This study presents the development and the validation process of the InovSafeCare scale and aimed at identifying and measuring the ecosystem variables related to healthcare-associated infection (HCAI) prevention and control practices in European nurse students. Qualitative and quantitative approaches were used to (1) elaborate an item pool related to the educational environment, the healthcare setting environment, and the attitudes, beliefs, and performance of the nursing students regarding HCAI prevention and control and (2) analyze psychometric properties of the scale using factor analysis. The validated InovSafeCare scale was applied to undergraduate nursing students of five European Higher Education Institutions. The partial least square structural equation modeling (PLS-SEM) method with SMART-PLS3 software was used. The study sample consists of 657 nursing students, who responded a self-report inventory. From the analyzed data were identified 14 factors. The InovSafeCare scale reveals good validity and reliability of the dimensions in different European countries.
Integrative Systems Biology Analysis Elucidates Mastitis Disease Underlying Functional Modules in Dairy Cattle

Background: Mastitis is the most prevalent disease in dairy cattle and one of the most significant bovine pathologies affecting milk production, animal health, and reproduction. In addition, mastitis is the most common, expensive, and contagious infection in the dairy industry. Methods: A meta-analysis of microarray and RNA-seq data was conducted to identify candidate genes and functional modules associated with mastitis disease. The results were then applied to systems biology analysis via weighted gene coexpression network analysis (WGCNA), Gene Ontology, enrichment analysis for the Kyoto Encyclopedia of Genes and Genomes (KEGG), and modeling using machine-learning algorithms. Results: Microarray and RNA-seq datasets were generated for 2,089 and 2,794 meta-genes, respectively. Between microarray and RNA-seq datasets, a total of 360 meta-genes were found that were significantly enriched as “peroxisome,” “NOD-like receptor signaling pathway,” “IL-17 signaling pathway,” and “TNF signaling pathway” KEGG pathways. The turquoise module (n = 214 genes) and the brown module (n = 57 genes) were identified as critical functional modules associated with mastitis through WGCNA. PRDX5, RAB5C, ACTN4, SLC25A16, MAPK6, CD53, NCKAP1L, ARHGEF2, COL9A1, and PTPRC genes were detected as hub genes in identified functional modules. Finally, using attribute weighting and machine-learning methods, hub genes that are sufficiently informative in Escherichia coli mastitis were used to optimize predictive models. The constructed model proposed the optimal approach for the meta-genes and validated several high-ranked genes as biomarkers for E. coli mastitis using the decision tree (DT) method. Conclusion: The candidate genes and pathways proposed in this study may shed new light on the underlying molecular mechanisms of mastitis disease and suggest new approaches for diagnosing and treating E. coli mastitis in dairy cattle.