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Abstract The African buffalo (Syncerus caffer) is a wild bovid with a historical distribution across much of sub-Saharan Africa. Genomic analysis can provide insights into the evolutionary history of the species, and the key selective pressures shaping populations, including assessment of population level differentiation, population fragmentation, and population genetic structure. In this study we generated the highest quality de novo genome assembly (2.65 Gb, scaffold N50 69.17 Mb) of African buffalo to date, and sequenced a further 195 genomes from across the species distribution. Principal component and admixture analyses provided little support for the currently described four subspecies. Estimating Effective Migration Surfaces analysis suggested that geographical barriers have played a significant role in shaping gene flow and the population structure. Estimated effective population sizes indicated a substantial drop occurring in all populations 5-10,000 years ago, coinciding with the increase in human populations. Finally, signatures of selection were enriched for key genes associated with the immune response, suggesting infectious disease exert a substantial selective pressure upon the African buffalo. These findings have important implications for understanding bovid evolution, buffalo conservation and population management.

Large tropical trees are rightly perceived as supporting a plethora of organisms. However, baseline data about the variety of taxa coexisting on single large tropical trees are lacking and prevent a full understanding of both the magnitude of biodiversity and the complexity of interactions among organisms in tropical rainforests. The two main aims of the research program “Life on Trees” (LOT) are (1) to establish baseline knowledge on the number of eukaryote species supported/hosted by the above-ground part of a single tropical tree and (2) to understand how these communities of organisms are assembled and distributed on or inside the tree. To achieve the first goal, we integrated a set of 36 methods for comprehensively sampling eukaryotes (plants, fungi, animals, protists) present on a tropical tree. The resulting LOT protocol was conceived and implemented during projects in the Andean Amazon region and is proposed here as a guideline for future projects of a similar nature. To address the second objective, we evaluated the microclimatic differences between tree zones and tested state-of-the-art terrestrial laser scanning (TLS) and positioning technologies incorporating satellite and fixed base station signals (dGNSS). A marked variation in temperature and relative humidity was detected along a 6-zones Johansson scheme, a tree structure subdivision system commonly used to study the stratification of epiphytic plants. Samples were collected from these six zones, including three along the trunk and three in the canopy. To better understand how different tree components (e.g., bark, leaves, fruits, flowers, dead wood) contribute to overall tree biodiversity, we categorized observations into communities based on Johansson zones and microhabitats. TLS was an essential aid in understanding the complex tree architecture. By contrast, the accuracy of positioning samples in the tree with dGNSS was low. Comprehensively sampling the biota of individual trees offers an alternative to assessing the biodiversity of fewer groups of organisms at the forest scale. Large old tropical trees provide a wealth of microhabitats that encompass a wide range of ecological conditions, thereby capturing a broad spectrum of biodiversity.

Abstract Circular RNAs (circRNAs) are covalently closed non-coding RNAs lacking the 5’ cap and the poly-A tail. Nevertheless, it has been demonstrated that certain circRNAs can undergo active translation. Therefore, aberrantly expressed circRNAs in human cancers could be an unexplored source of tumor-specific antigens, potentially mediating anti-tumor T cell responses. This study presents an immunopeptidomics workflow with a specific focus on generating a circRNA-specific protein fasta reference. The main goal of this workflow is to streamline the process of identifying and validating human leukocyte antigen (HLA) bound peptides potentially originating from circRNAs. We increase the analytical stringency of our workflow by retaining peptides identified independently by two mass spectrometry search engines and/or by applying a group-specific FDR for canonical-derived and circRNA-derived peptides. A subset of circRNA-derived peptides specifically encoded by the region spanning the back-splice junction (BSJ) are validated with targeted MS, and with direct Sanger sequencing of the respective source transcripts. Our workflow identifies 54 unique BSJ-spanning circRNA-derived peptides in the immunopeptidome of melanoma and lung cancer samples. Our approach enlarges the catalog of source proteins that can be explored for immunotherapy.

Biochars (BCs) and activated carbons (ACs) are well-known carbon-rich materials that are being increasingly studied in environmental sciences for water treatment applications to remediate pollutant sequestration in soil. This study aimed to assess the impact of Sargasso BC particle size and amendment rate on the environmental availability of DDT and DDT metabolites in two distinct Kazakh soils. These two soils were collected in the vicinity of storehouse facilities in Kyzylkairat and Beskainar that store banned pesticides. They presented very distinct concentration levels of DDT and DDT metabolites. Three different types of carbonaceous matrices were tested: Sargasso BC and two commercial ACs (ORBOTM and DARCO©). For the granulometry effect, Sargasso BC was ground, and two particle sizes were tested (150 µm) and compared to an unground material. Four distinct application rates were tested (0.25, 0.5, 1, and 2% (w/w)). After a three-month maturation period, environmental availability was assessed using an ISO/DIS 16751, part B-modified methodology. Interestingly, the best reductions in DDT environmental availability were obtained with the finest particle size (both ACs and Sargasso BC < 150 µm). More specifically, the effectiveness of the strategy seemed to depend on many factors. Firstly, a clear soil effect was demonstrated, suggesting that the more contaminated the soil, the more efficient this strategy may be. Secondly, the results showed that an increase in the amendment rate improves the immobilization of DDT and DDT metabolites. The sequestration material demonstrated different efficiency values (up to 58 ± 4% for Sargasso BC < 150 µm and 85 ± 4% for DARCO at a 2% application rate). Finally, a clear molecule effect was displayed, demonstrating the following immobilization order: p,p’-DDE > p,p’-DDD > p,p’-DDT > o,p’-DDT.

Summary: Mitochondrial function relies on the coordinated transcription of mitochondrial and nuclear genomes to assemble respiratory chain complexes. Across species, the SIN3 coregulator influences mitochondrial functions, but how its loss impacts mitochondrial homeostasis and metabolism in the context of a whole organism is unknown. Exploring this link is important because SIN3 haploinsufficiency causes intellectual disability/autism syndromes and SIN3 plays a role in tumor biology. Here we show that loss of C. elegans SIN-3 results in transcriptional deregulation of mitochondrial- and nuclear-encoded mitochondrial genes, potentially leading to mito-nuclear imbalance. Consistent with impaired mitochondrial function, sin-3 mutants show extensive mitochondrial fragmentation by transmission electron microscopy (TEM) and in vivo imaging, and altered oxygen consumption. Metabolomic analysis of sin-3 mutant animals revealed a mitochondria stress signature and deregulation of methionine flux, resulting in decreased S-adenosyl methionine (SAM) and increased polyamine levels. Our results identify SIN3 as a key regulator of mitochondrial dynamics and metabolic flux, with important implications for human pathologies.

Abstract Metabolic dysfunction‐associated steatotic liver disease (MASLD) is a major public health issue with a worldwide prevalence of 30%–32%. In animal models, voluntary exercise may be an alternative to forced physical activity, avoiding stress, potential injuries, and being logistically simpler. Here, we assessed voluntary exercise (Vex) in Sprague–Dawley rats fed a high‐fat, high‐cholesterol diet for 18 weeks to induce MASLD. We quantified workload (speed and distance) using exercise wheels and evaluated energy expenditure using calorimetric cages. MASLD progression was assessed using circulating and hepatic biochemical and gene markers of steatosis, inflammation, and fibrosis. The animals ran an average of 301 km during the study period, with the average daily distance peaking at 4937 m/day during Weeks 3–4 before decreasing to 757 m/day by the end of the study. Rats exposed to Vex showed no improvement in any of the MASLD‐associated features, such as steatosis, inflammation, or fibrosis. Rats exposed to Vex exhibited a higher total energy expenditure during the night phase (+0.35 kcal/h; p = 0.003) without resulting in any effect on body composition. We conclude that, in our experimental conditions, Vex failed to prevent MASLD progression in male Sprague–Dawley rats exposed to a high‐fat high‐cholesterol diet for 18 weeks.

Like everything for the past 2 centuries, agriculture has depended increasingly on fossil fuel energy. Pressures to shift to renewable energy and changes in the fossil fuel industry are set to massively alter the energy landscape over the next 30 years. Two near-certainties are increased overall prices and/or decreased stability of energy supplies. The impacts of these upheavals on specialty crop production and consumption are unknowable in detail but the grand lines of what will likely change can be foreseen. This foresight can guide the research, extension, and teaching needed to successfully navigate a future very unlike the recent past. Major variables that will influence outcomes include energy use in fertilizer manufacture, in farm operations, and in haulage to centers of consumption. Taking six increasingly popular fruit and vegetable crops and the top two horticultural production states as examples, here we use simple proxies for the energy requirements (in gigajoules per ton of produce) of fertilizer, farm operations, and truck transport from Florida or California to New York to compare the relative sizes of these requirements. Trucking from California is the largest energy requirement in all cases, and three times larger than from Florida. As these energy requirements themselves are all fairly fixed, but in future will likely rise in price and/or be subject to interruptions and shortages, this pilot study points to two commonsense inferences: First, that fruit and vegetable production and consumption are set to reposition to more local/regional and seasonal patterns due to increasing expenses associated with fuel, and second, that coast-to-coast produce shipment by truck will become increasingly expensive and difficult.

The host environment is of critical importance for antibiotic efficacy. By impacting bacterial machineries, stresses encountered by pathogens during infection promote the formation of phenotypic variants that are transiently insensitive to the action of antibiotics. It is assumed that these recalcitrant bacteria-termed persisters-contribute to antibiotic treatment failure and relapsing infections. Recently, we demonstrated that host reactive nitrogen species (RNS) transiently protect persisters against the action of β-lactam antibiotics by delaying their regrowth within host cells. Here, we discovered that RNS intoxication of persisters also collaterally sensitizing them to fluoroquinolones during infection, explaining the higher efficiency of fluoroquinolones against intramacrophage Salmonella. By reducing bacterial respiration and the proton-motive force, RNS inactivate the AcrAB efflux machinery of persisters, facilitating the accumulation of fluoroquinolones intracellularly. Our work shows that target inactivity is not the sole reason for Salmonella persisters to withstand antibiotics during infection, with active efflux being a major contributor to survival. Thus, understanding how the host environment impacts persister physiology is critical to optimize antibiotics efficacy during infection.

Determining the dietary spectrum of European insectivorous bats over time is the cornerstone of their conservation, as it will aid our understanding of foraging behavior plasticity in response to plummeting insect populations. Despite the global decline in insects, a restricted number of arthropod pest species thrive. Yet past research has overlooked the potential of European bats to suppress pests harmful to woodlands or livestock, in spite of their economic relevance. Here we investigated the diet composition, its breeding season variations and pest consumption of an insectivorous bat species (Myotis emarginatus), at the northern edge of its range (Wallonia, Belgium). We also explored the prey ecology to gain insight into the hunting strategies and foraging habitats of this bat species. We used DNA metabarcoding to amplify two COI markers within 195 bat droppings collected in June, July and August, thereby identifying 512 prey taxa predominated by Diptera, Araneae and Lepidoptera. Overall, in 97% of the samples we detected at least one of the 58 potential pest taxa, 41 of which targeting trees. The June samples were marked by a diet rich in orb-weaver spiders, in accordance with the archetypal diet of M. emarginatus bats. However, during the highly energy demanding July-August parturition and lactation period, roughly 55% of the dropping samples contained two cattle fly pests (Stomoxys calcitrans and Musca domestica). Moreover, among the 88 Diptera species preyed upon by M. emarginatus in July and August, these flies accounted for around 50% of the taxa occurrences. This plasticity-the switch from a spider-rich to a fly-rich diet-seems providential considering the dramatic ongoing drop in insect populations but this involves ensuring bat-friendly cattle farming. Our results revealed that bats widely consume pest entomofauna, thereby highlighting their potential role as allies of forest managers and farmers.

Grinding and flotation processes are often studied independently, despite the well-established grinding influence on flotation performance, which affects not only particle size and thus liberation but also shape and leads to complex changes in pulp chemistry affecting the particle surface properties relevant for selective bubble attachment. Yet, no study jointly investigated these possible causes and many are limited to single mineral flotation. We relate grinding conditions to changes in pulp chemistry and particle surface properties and assess their impact on upgrading. We studied three non-sulfide ores with different feed grades and valuables: scheelite, apatite, and fluorite. These were dry-, wet-, and wet conditioned-ground before flotation in a laboratory mechanical cell. Results were evaluated with bulk- and particle-specific methodologies. The selectivity of the process is higher after dry grinding for the fluorite and apatite ores and irrelevant for the scheelite ore. Variations in flotation kinetics of individual particles associated to their size and shape are not sufficient to explain these results. The higher concentration of Ca2+ and Mg2+ observed in the pulp after wet grinding, altering particle surface properties, better explains the phenomenon. Additionally, we demonstrate how particle shape impacts are system specific and related to both entrainment and true flotation.

Lung transplantation (LT) constitutes the last therapeutic option for selected patients with end-stage respiratory disease. Primary graft dysfunction (PGD) is a form of severe lung injury, occurring in the first 72 h following LT and constitutes the most common cause of early death after LT. The presence of pulmonary hypertension (PH) has been reported to favor PGD development, with a negative impact on patients’ outcomes while complicating medical management. Although several studies have suggested a potential association between pre-LT left ventricular diastolic dysfunction (LVDD) and PGD occurrence, the underlying mechanisms of such an association remain elusive. Importantly, the heterogeneity of the study protocols and the various inclusion criteria used to define the diastolic dysfunction in those patients prevents solid conclusions from being drawn. In this review, we aim at summarizing PGD mechanisms, risk factors, and diagnostic criteria, with a further focus on the interplay between LVDD and PGD development. Finally, we explore the predictive value of several diastolic dysfunction diagnostic parameters to predict PGD occurrence and severity.

This comprehensive review explores the intricate aspects of left ventricular thrombus (LVT), a potential complication in both ischemic and non-ischemic cardiomyopathies. It provides a thorough understanding of left ventricular thrombus, revealing its uncommon incidence in the general population (7 cases per 10,000 patients), predominantly linked to ischemic heart diseases (ICMs) at an 80% prevalence rate. Diagnostic tools, notably transthoracic echocardiography (TTE) and cardiac magnetic resonance imaging (CMR), demonstrate varying sensitivity but remain indispensable in specific clinical contexts related to LVT as non-invasive diagnostic modalities. A detailed comparison between ICM patients and those with non-ischemic cardiomyopathy (NICM) who have left ventricular thrombus reveals subtle distinctions with significant clinical implications. This analysis underscores the importance of these imaging techniques in distinguishing between the two conditions. Additionally, we explored the occurrence of LVT in specific non-ischemic cardiomyopathies, including Takotsubo syndrome, hypertrophic cardiomyopathy, eosinophilic myocarditis, Chagas disease, cardiac amyloidosis, and several other conditions. The article further delves into anticoagulation strategies, thoroughly examining their impact on LVT regression and patient outcomes. Pharmacological interventions, with a focus on direct oral anticoagulants, emerge as promising alternatives; however, there is insufficient information on their efficiency and safety, especially in NICM population. In conclusion, this review highlights the complex nature of LVT, incorporating a range of etiopathogenic factors, diagnostic complexities, and evolving therapeutic approaches. It emphasizes the pressing need for ongoing research in this field.