Miracle-dz/UniFAR-FTUs huggingface dataset:
Pseudomonas aeruginosa kills Staphylococcus aureus in a polyphosphate-dependent manner

Due to their frequent coexistence in many polymicrobial infections, including in patients with burn or chronic wounds or cystic fibrosis, recent studies have started to investigate the mechanistic details of the interaction between the opportunistic pathogens Pseudomonas aeruginosa and Staphylococcus aureus. P. aeruginosa rapidly outcompetes S. aureus under in vitro co-cultivation conditions, which is mediated by several of P. aeruginosa’s virulence factors. Here, we report that polyphosphate (polyP), an efficient stress defense system and virulence factor in P. aeruginosa, plays a role for the pathogen’s ability to inhibit and kill S. aureus in a contact-independent manner. We show that P. aeruginosa cells characterized by low polyP level are less detrimental to S. aureus growth and survival while the gram-positive pathogen is significantly more compromised by the presence of P. aeruginosa cells that produce high level of polyP. We show that the polyP-dependent phenotype could be a direct effect by the biopolymer, as polyP is present in the spent media and causes significant damage to the S. aureus cell envelope. However, more likely is that polyP’s effects are indirect through the regulation of one of P. aeruginosa’s virulence factors, pyocyanin. We show that pyocyanin production in P. aeruginosa occurs polyP-dependent and harms S. aureus through membrane damage and the generation of reactive oxygen species, resulting in increased expression of antioxidant enzymes. In summary, our study adds a new component to the list of biomolecules that the gram-negative pathogen P. aeruginosa generates to compete with S. aureus for resources. IMPORTANCE How do interactions between microorganisms shape the course of polymicrobial infections? Previous studies have provided evidence that the two opportunistic pathogens P. aeruginosa and S. aureus generate molecules that modulate their interaction with potentially significant impact on disease outcomes. Our study identified the biopolymer polyP as a new effector molecule that impacts P. aeruginosa’s interaction with S. aureus. We show that P. aeruginosa kills S. aureus in a polyP-dependent manner, which occurs primarily through the polyP-dependent production of the P. aeruginosa virulence factor pyocyanin. Our findings add a new role for polyP to an already extensive list of functions. A more in-depth understanding of how polyP influences interspecies interactions is critical, as targeting polyP synthesis in bacteria such as P. aeruginosa may have a significant impact on other microorganisms and potentially result in dynamic changes in the microbial composition.
Absence, multiplicity and the boundaries of research? Reflections on online asynchronous focus groups

During the COVID 19 pandemic, Online Asynchronous Focus Groups (OAFG) through WhatsApp were conducted to explore women’s experiences in the context of Congenital Syphilis prevention in Colombia. This paper discusses issues raised by the OAFGs (not least in relation to face-to-face focus groups). After a review of the literature on online and offline focus groups, there is a consideration of some key features of our OAFGs. In particular, we note how silence, presence, attention, continuity and multiplicity manifested in our OAFGs. We suggest that rather than regarding OAFGs as inferior to the ‘gold standard’ of face-to-face focus groups, our OAFGs raise important questions about our assumptions about focus group methodology. For instance, what counts as participant engagement, what comprises ‘useful’ social data, and what constitute the boundaries of a focus group all emerge as critical issues. We go on to reflect on some of the implications of these issues for the fruitfulness of OAFG methods.
Can antimicrobial blue light contribute to resistance development? Genome-wide analysis revealed aBL-protective genes in Escherichia coli

ABSTRACT Antimicrobial blue light (aBL) is a promising non-antibiotic approach to fighting multidrug-resistant bacteria. However, the complete mechanism of aBL action is not fully understood yet. This study contributes to a better understanding that the response to aBL depends on many factors and that it is hardly possible to identify a predominant mechanism underlying microbial sensitivity to photoinactivation. The results of this study provide insights into genetic changes that may lead to bacterial survival at higher aBL doses, giving rise to aBL-resistant strains. To our best knowledge, this is the first study concerning genome-wide mutant testing of aBL. We managed to identify 64 single-gene mutants that lacked certain protective genes expressing aBL-increased sensitivity. IMPORTANCE Increasing antibiotic resistance and the lack of new antibiotic-like compounds to combat bacterial resistance are significant problems of modern medicine. The development of new alternative therapeutic strategies is extremely important. Antimicrobial blue light (aBL) is an innovative approach to combat multidrug-resistant microorganisms. aBL has a multitarget mode of action; however, the full mechanism of aBL antibacterial action requires further investigation. In addition, the potential risk of resistance development to this treatment should be considered. Increasing antibiotic resistance and the lack of new antibiotic-like compounds to combat bacterial resistance are significant problems of modern medicine. The development of new alternative therapeutic strategies is extremely important. Antimicrobial blue light (aBL) is an innovative approach to combat multidrug-resistant microorganisms. aBL has a multitarget mode of action; however, the full mechanism of aBL antibacterial action requires further investigation. In addition, the potential risk of resistance development to this treatment should be considered.
Conserved autism-associated genes tune social feeding behavior in C. elegans

Animal foraging is an essential and evolutionarily conserved behavior that occurs in social and solitary contexts, but the underlying molecular pathways are not well defined. We discover that conserved autism-associated genes (NRXN1(nrx-1), NLGN3(nlg-1), GRIA1,2,3(glr-1), GRIA2(glr-2), and GLRA2,GABRA3(avr-15)) regulate aggregate feeding in C. elegans, a simple social behavior. NRX-1 functions in chemosensory neurons (ADL and ASH) independently of its postsynaptic partner NLG-1 to regulate social feeding. Glutamate from these neurons is also crucial for aggregate feeding, acting independently of NRX-1 and NLG-1. Compared to solitary counterparts, social animals show faster presynaptic release and more presynaptic release sites in ASH neurons, with only the latter requiring nrx-1. Disruption of these distinct signaling components additively converts behavior from social to solitary. Aggregation induced by circuit activation is also dependent on nrx-1. Collectively, we find that aggregate feeding is tuned by conserved autism-associated genes through complementary synaptic mechanisms, revealing molecular principles driving social feeding. TEASER Conserved autism-associated genes mediate distinct molecular and circuit signaling components that cooperate to tune C. elegans social feeding behavior.
Three-dimensional histology reveals dissociable human hippocampal long axis gradients of Alzheimer’s pathology

INTRODUCTION Three-dimensional (3D) histology analyses are essential to overcome sampling variability and understand pathological differences beyond the dissection axis. We present Path2MR, the first pipeline allowing 3D reconstruction of sparse human histology without an MRI reference. We implemented Path2MR with post-mortem hippocampal sections to explore pathology gradients in Alzheimer’s Disease. METHODS Blockface photographs of brain hemisphere slices are used for 3D reconstruction, from which an MRI-like image is generated using machine learning. Histology sections are aligned to the reconstructed hemisphere and subsequently to an atlas in standard space. RESULTS Path2MR successfully registered histological sections to their anatomical position along the hippocampal longitudinal axis. Combined with histopathology quantification, we found an expected peak of tau pathology at the anterior end of the hippocampus, while amyloid-β displayed a quadratic anterior-posterior distribution. CONCLUSION Path2MR, which enables 3D histology using any brain bank dataset, revealed significant differences along the hippocampus between tau and amyloid-β.
The facial microbiome and metabolome across different geographic regions

ABSTRACT Facial skin is more exposed to the outside environment, and it is usually affected by environmental factors. Characterization of the skin microbiome and metabolome of individuals from different geographic regions will help to understand the factors behind the prevalence of skin disorders and support skincare product development. In the current study, volunteers from northern, southern, and northwestern China were recruited. Facial skin samples were collected for amplicon sequencing and metabolomic liquid chromatography‒mass spectrometry (LC–MS/MS) analyses. We demonstrated significant alterations in the abundances of multiple microorganisms and skin lipid compositions between individuals. People living in the northwest, which has a dry climate and high altitude, showed lower level of total lipids, and lower abundance of Malassezia, but higher levels of ceramides and fatty acids. Malassezia had a positive correlation with eicosanoids and a negative correlation with ceramides. This work highlights the effects of geographic factors on the skin microbial structures and skin lipids. IMPORTANCE Characterization of the skin microbiome and metabolome across geography will help uncover the climate factors behind the prevalence of skin disorders and provide suggestions for skincare products for people living in different geographic regions. Characterization of the skin microbiome and metabolome across geography will help uncover the climate factors behind the prevalence of skin disorders and provide suggestions for skincare products for people living in different geographic regions.
The Effects of African Easterly Wave Suppression by Wave Track on Atlantic Tropical Cyclones

It is well established that African easterly waves (AEWs) can serve as seedling disturbances for Atlantic tropical cyclones (TCs). However, research has shown that AEWs are not necessary to maintain specifically basin‐wide TC frequency. Here, we for the first time investigate the effects of AEW suppression by wave track on Atlantic TC activity. Regional model simulations were performed, where AEWs were either prescribed or suppressed from the eastern lateral boundary condition. We found that without AEWs, there was an increase in TC frequency and strength, with the most pronounced increases occurring when the waves were suppressed in the south track. These changes coincided with more favorable environmental conditions and disturbances associated with increased convective activity over the Atlantic. Our results indicate that AEWs are not a limiting factor for TCs, and that AEW suppression, specifically in the south track, can affect the large‐scale environment to enhance favorability for TC genesis.
Mapping surface water-groundwater interactions and associated geological faults using temperature profiling

ABSTRACT In this study temperature profiling was used as a mapping tool to investigate surface water-groundwater interactions associated with low-permeability faults in the south-eastern part ofthe Netherlands. Data obtained from temperature profiling were simulated using a simple waterand energy balance model. The model was used to quantify groundwater seepage rates nearthe faults. The model simulated the surface water temperature transects very well, but themodel-based seepage rates are much higher than those reported in the literature for comparablehydrological settings. Of all the assumptions made in the model, the adopted values for theparameters that control the heat exchange between the water and the atmosphere are believedto be the most uncertain. Despite these uncertainties, temperature profiling proved to be avery useful tool to investigate surface water-groundwater interactions and to map groundwaterseepage zones. The strength of using temperature as a tracer is that it is measured directly in thefield with relative ease and using low cost equipment.
Molybdenite Re/Os isochron age of the Wunugetu Shan porphyry Cu/Mo deposit, Inner Mongolia and its implication for metallogenic geodynamics.

The Wunugetu Shan porphyry Cu/Mo deposit,Inner Mongolia,is one of the largest Cu/Mo deposits in Northeast China. The Re/Os isotopic model ages of five molybdenite samples range from 166.1±2.0 to 176.4±2.8Ma,and yield an isochron age of 178±10Ma(1σ,MSWD=3.3),which is interpreted to be the hydrothermal metallogenic age of the deposit.The metallogenic porphyry-fluid system developed around 183±6Ma.In the regional tectonic evolution,the Wunugetu Shan porphyry Cu/Mo deposit was formed under a decompression-geothermal increasing regime during continental collision,instead of a magmatic arc related to B-type subduction.
Control of asparagine homeostasis in Bacillus subtilis: identification of promiscuous amino acid importers and exporters

ABSTRACT The Gram-positive model bacterium B. subtilis is able to import all proteinogenic amino acids from the environment as well as to synthesize them. However, the players involved in the acquisition of asparagine have not yet been identified for this bacterium. In this work, we used d-asparagine as a toxic analog of l-asparagine to identify asparagine transporters. This revealed that d- but not l-asparagine is taken up by the malate/lactate antiporter MleN. Specific strains that are sensitive to the presence of l-asparagine due to the lack of the second messenger cyclic di-AMP or due to the intracellular accumulation of this amino acid were used to isolate and characterize suppressor mutants that were resistant to the presence of otherwise growth-inhibiting concentrations of l-asparagine. These screens identified the broad-spectrum amino acid importers AimA and BcaP as responsible for the acquisition of l-asparagine. The amino acid exporter AzlCD allows detoxification of l-asparagine in addition to 4-azaleucine and histidine. This work supports the idea that amino acids are often transported by promiscuous importers and exporters. However, our work also shows that even stereo-enantiomeric amino acids do not necessarily use the same transport systems. IMPORTANCE Transport of amino acid is a poorly studied function in many bacteria, including the model organism Bacillus subtilis. The identification of transporters is hampered by the redundancy of transport systems for most amino acids as well as by the poor specificity of the transporters. Here, we apply several strategies to use the growth-inhibitive effect of many amino acids under defined conditions to isolate suppressor mutants that exhibit either reduced uptake or enhanced export of asparagine, resulting in the identification of uptake and export systems for l-asparagine. The approaches used here may be useful for the identification of transporters for other amino acids both in B. subtilis and in other bacteria. Transport of amino acid is a poorly studied function in many bacteria, including the model organism Bacillus subtilis. The identification of transporters is hampered by the redundancy of transport systems for most amino acids as well as by the poor specificity of the transporters. Here, we apply several strategies to use the growth-inhibitive effect of many amino acids under defined conditions to isolate suppressor mutants that exhibit either reduced uptake or enhanced export of asparagine, resulting in the identification of uptake and export systems for l-asparagine. The approaches used here may be useful for the identification of transporters for other amino acids both in B. subtilis and in other bacteria.
AQUATIC INVERTEBRATE COMMUNITY STRUCTUREIN THE NIOBRARA RIVER, AGATE FOSSIL BEDSNATIONAL MONUMENT, NEBRASKA, 1996-2009

Aquatic invertebrates were sampled annually in the Niobrara River, Nebraska, during the period 1996-2009 using Hester-Dendy multiplate samplers. Collections indicated the invertebrate community in the river has shifted from one dominated by Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa to one dominated by Chironomidae and Amphipoda. Generally, EPT richness and percentage abundance ofEPT of the total community, as well as percentage abundance ofHeptageniidae and Leptophlebiidae, has declined across the years. During that same period, percentage abundance of Amphipoda and Chironomidae, taxa evenness, Shannon's Index, and the HilsenhoffBiotic Index have increased. Stream discharge decreased significantly during the IS-year period when invertebrates were collected (Mann-Kendall trend test, P = 0.04). Water-surface elevation of the river measured with staff gages also gradually increased over time, although the trends were not significant (P ;::: 0.15). Although not analyzed statistically, water temperature eG), conductivity (IlS/cm), and pH gradually increased over time while dissolved oxygen concentration (mg/liter) decreased over time. Although other factors cannot be ruled out, a proposed reason for the observed changes in invertebrate community structure may be related to changes in the physical habitat condition in the Niobrara River associated with encroachment of the nonnative and invasive emergent aquatic plant, yellow flag (Iris pseudacorus L.). This weed has expanded into the stream channel, where it blocks streamflow.
Dynamics of brainstem arousal systems and pupil size predict cortical interactions for flexible decision-making

Most perceptual decisions entail a flexible mapping from sensory input to motor output. Flexible input-output mapping is reflected in correlated variability within the cortical network involved in perceptual decisions. Here, we tested the idea that brainstem arousal systems are involved in flexible input-output mapping and changes in cortical correlated variability. We combined brainstem fMRI, pupillometry, and time-resolved assessment of the intrinsic correlations between cortical population codes for stimulus and action. Human participants reported the orientation of visual stimuli by button presses, while the required stimulus-response mapping rule could undergo hidden and unpredictable changes. Rule switches evoked brainstem and pupil responses as well as changes in computational model-inferred, latent variables. These variables governed participants’ rule-switching behavior and pupil responses. Brainstem activity and pupil dilation preceded increases in the strength of correlations between cortical stimulus and action codes. Brainstem arousal systems may promote the reorganization of sensorimotor cortical pathways for flexible decisions.
Effects of atmospheric CO2 concentration on transpiration and leaf elongation responses to drought in wheat, perennial ryegrass and tall fescue

We studied the effects of atmospheric CO2 concentration ([CO2]) on the leaf growth response to drought in perennial ryegrass, tall fescue and wheat. Plants were grown in growth chambers at either 200 or 800 ppm of CO2. At leaf 6-7 unfolding, half of the plants were subjected to severe drought. Leaf elongation rate (LER) was measured daily, while plant transpiration was continuously recorded gravimetrically. Water-soluble carbohydrate concentration, water and osmotic potentials in the leaf growing zone were measured at drought onset, at mid-drought and at the time of leaf growth cessation. [CO2] caused stomata closure and therefore reduction of instantaneous transpiration rate and water loss. As a result, CO2 mitigated the impacts of drought on LER and delayed growth cessation for all three species. For ryegrass, LER and soil relative water content (SRWC) relation was improved with CO2, presumably due to a better stomatal regulation. CO2 did not affect nighttime water potential nor osmotic potential of the growing zone. Related to leaf growth, we observed the main effect of CO2 on tillering but no effect on the plant development. In total, water consumption was similar (wheat, tall fescue) or greater (ryegrass) with CO2.
Beaming of intense AKR seen from the Interball‐2 spacecraft

We present results of intense auroral kilometric radiation (AKR) sources direction finding based on single‐spacecraft k→ vector source location performed in the frame of Interball‐2 mission (POLRAD experiment on board Auroral Probe). With our swept frequency analyzer we are not able to work with single AKR bursts generated in small, elementary sources, but we improve our signal‐to‐noise (s/n) ratio and determine direction to the AKR source region averaging data over 10 consecutive 4 kHz frequency steps. Measurements of directions to the AKR sources confirm recent Mutel et al. ( ) findings based on Cluster Very Long Baseline Interferometry (VLBI) data—AKR rays are mostly confined to the direction tangent to the auroral oval as measured in Mutel's tangent plane (TP) coordinates. In this paper we use additional coordinate system rotated with respect to TP coordinates in order to determine azimuths of AKR rays with respect to the auroral oval. We see cases of AKR propagation significantly deflected from the tangent plane. Additional information concerning geometry of auroral arc at the AKR source can help to distinguish between propagation along and propagation across the auroral cavity. Examples of instantaneous AKR visibility maps defined in this paper for both coordinate systems are shown and discussed. Using such map (valid for our spacecraft for relatively short observational periods of the order of 10 min), it is possible for known positions of the AKR sources in invariant latitude‐magnetic local time coordinates to visualize direction angles of AKR beams reaching the observer.
Tardigrade secretory proteins protect biological structures from desiccation

Tardigrades, microscopic animals that survive a broad range of environmental stresses, express a unique set of proteins termed tardigrade-specific intrinsically disordered proteins (TDPs). TDPs are often expressed at high levels in tardigrades upon desiccation, and appear to mediate stress adaptation. Here, we focused on the proteins belonging to the secretory family of tardigrade proteins termed secreted-abundant heat soluble (“SAHS”) proteins, and investigated their ability to protect diverse biological structures. Recombinantly expressed SAHS proteins prevented desiccated liposomes from fusion, and enhanced desiccation tolerance of E. coli and Rhizobium tropici upon extracellular application. Molecular dynamics simulation and comparative structural analysis suggest a model by which SAHS proteins may undergo a structural transition upon desiccation, in which removal of water and solutes from a large internal cavity in SAHS proteins destabilizes the beta-sheet structure. These results highlight the potential application of SAHS proteins as stabilizing molecules for preservation of cells.