Vaccines against classical swine fever have proven very effective in protecting pigs from this deadly disease. However, little is known about how vaccination impacts the selective pressures acting on the classical swine fever virus (CSFV). Here we use high-throughput sequencing of viral genomes to investigate evolutionary changes in virus populations following the challenge of naïve and vaccinated pigs with the highly virulent CSFV strain "Koslov". The challenge inoculum contained an ensemble of closely related viral sequences, with three major haplotypes being present, termed A, B, and C. After the challenge, the viral haplotype A was preferentially located within the tonsils of naïve animals but was highly prevalent in the sera of all vaccinated animals. We find that the viral population structure in naïve pigs after infection is very similar to that in the original inoculum. In contrast, the viral population in vaccinated pigs, which only underwent transient low-level viremia, displayed several distinct changes including the emergence of 16 unique non-synonymous single nucleotide polymorphisms (SNPs) that were not detectable in the challenge inoculum. Further analysis showed a significant loss of heterogeneity and an increasing positive selection acting on the virus populations in the vaccinated pigs. We conclude that vaccination imposes a strong selective pressure on viruses that subsequently replicate within the vaccinated animal.

The effects of high-pressure homogenization (HPH) on the structural, physical, and rheological properties of lily pulp (15%, w/w) were investigated. Different pressures ranging from 0 MPa to 100 MPa were used. The focus was on evaluating the changes in the particle size distribution (PSD), structure, pulp sedimentation behavior, serum cloudiness (SC), total soluble solids (TSS), color, and rheological behavior of the pulps. PSD analysis showed that the diameter of suspended lily particles significantly decreased with an increasing homogenization pressure. The suspended particles observed through optical microscopy became small after homogenization, highlighting the effect of HPH on disrupting the suspended particles. Compared with the untreated pulp, the SC and sedimentation velocity of the homogenized pulps decreased due to the disruption of the suspended particles. The effects of HPH on the sedimentation index and SC exhibited an asymptotic behavior similar to that of the changes in the particle size of lily pulp. Moreover, HPH processing reduced the viscosity of lily pulp and increased the TSS and lightness of the homogenized pulps. HPH significantly modified the structural, physical, and rheological properties of lily pulp. The pulp homogenized above 60 MPa had good suspension stability. This finding indicates that HPH technology can be used to improve the stability of lily pulp.

Mycophenolic acid (MPA) is the active metabolite of mycophenolate mofetil, a drug that is widely used for immunosuppression in organ transplantation and autoimmune diseases, as well as anticancer chemotherapy. It inhibits IMP dehydrogenase, a rate-limiting enzyme in de novo synthesis of guanidine nucleotides. MPA treatment interferes with transcription elongation, resulting in a drastic reduction of pre-rRNA and pre-tRNA synthesis, the disruption of the nucleolus, and consequently cell cycle arrest. Here, we investigated the mechanism whereby MPA inhibits RNA polymerase III (Pol III) activity, in both yeast and mammalian cells. We show that MPA rapidly inhibits Pol III by depleting GTP. Although MPA treatment can activate p53, this is not required for Pol III transcriptional inhibition. The Pol III repressor MAF1 is also not responsible for inhibiting Pol III in response to MPA treatment. We show that upon MPA treatment, the levels of selected Pol III subunits decrease, but this is secondary to transcriptional inhibition. Chromatin immunoprecipitation (ChIP) experiments show that Pol III does not fully dissociate from tRNA genes in yeast treated with MPA, even though there is a sharp decrease in the levels of newly transcribed tRNAs. We propose that in yeast, GTP depletion may lead to Pol III stalling.

In response to stress conditions, autophagy activity in multicellular organisms is systemically modulated to ensure maintenance of cellular homeostasis at an organismal level. Very little is known about the intercellular signals that elicit the long-range organism-wide autophagy response. Here we showed that during Caenorhabditis elegans development, loss of cuticle annular furrow collagens elicits autophagy in the hypodermis, intestine, and muscle. The cilia of sensory neurons with cuticle-localized endings are essential for triggering this systemic response. The TGFβ-like molecule DAF-7, which is secreted in part from a specific pair of ciliated neurons, acts as a systemic factor that activates a canonical TGFβ signaling pathway in distant tissues to induce autophagy. We also showed that AAK-2/AMPK and the STAT-like protein STA-2 act differentially in different tissues for autophagy activation. Our study reveals a circuit that senses and transduces the signal from the damaged cuticle to activate systemic autophagy during animal development.

Ferroptosis is a novel form of programmed cell death in which the accumulation of intracellular iron promotes lipid peroxidation, leading to cell death. Recently, the induction of autophagy has been suggested during ferroptosis. However, this relationship between autophagy and ferroptosis is still controversial and the autophagy-inducing mediator remains unknown. In this study, we confirmed that autophagy is indeed induced by the ferroptosis inducer erastin. Furthermore, we show that autophagy leads to iron-dependent ferroptosis by degradation of ferritin and induction of transferrin receptor 1 (TfR1) expression, using wild-type and autophagy-deficient cells, BECN1+/- and LC3B-/-. Consistently, autophagy deficiency caused depletion of intracellular iron and reduced lipid peroxidation, resulting in cell survival during erastin-induced ferroptosis. We further identified that autophagy was triggered by erastin-induced reactive oxygen species (ROS) in ferroptosis. These data provide evidence that ROS-induced autophagy is a key regulator of ferritin degradation and TfR1 expression during ferroptosis. Our study thus contributes toward our understanding of the ferroptotic processes and also helps resolve some of the controversies associated with this phenomenon.

Knowledge about the past, current and future distribution of the human population is fundamental for tackling many global challenges. Censuses are used to collect information about population within a specified spatial unit. The spatial units are usually arbitrarily defined and their numbers, size and shape tend to change over time. These issues make comparisons between areas and countries difficult. We have in related work proposed that the shape of the lit area derived from nighttime lights, weighted by its intensity can be used to analyse characteristics of the population distribution, such as the mean centre of population. We have processed global nighttime lights data for the period 1992-2013 and derived centroids for administrative levels 0-2 of the Database of Global Administrative Areas, corresponding to nations and two levels of sub-divisions, that can be used to analyse patterns of global or local population changes. The consistency of the produced dataset was investigated and distance between true population centres and derived centres are compared using Swedish census data as a benchmark.

Despite their early experimental production and observation, the unambiguous molecular structures of metal-containing boron nitride (BN) nanocages still remain mysterious. It has been commonly assumed that this family of compounds has the metal atom confined inside the cage, just like their isoelectronic cousins, carbon metallofullerenes do. Here, we demonstrate that Ti(BN)[Formula: see text] ([Formula: see text] = 12-24) complexes have, unexpectedly, an exohedral structure instead of an endohedral one, which could be verified by collision-induced dissociation experiments. The predicted global minimum structures exhibit some common bonding features accounting for their high stability, and could be readily synthesized under typical conditions for generating BN nanoclusters. The Ti doping dramatically changes not only the cage topology, but the arrangement of B and N atoms, endowing the resultant compounds with potential for CO[Formula: see text] capture and nitrogen fixation. These findings may expand or alter the understanding of BN nanostructures functionalized with other transition metals.

Malaria caused by Plasmodium affects millions people worldwide. Plasmodium consumes hemoglobin during its intraerythrocytic stage leaving toxic heme. Parasite detoxifies free heme through formation of hemozoin (β-hematin) pigment. Proteolysis of hemoglobin and formation of hemozoin are two main targets for antimalarial drugs. Quinoline antimarial drugs and analogs (β-carbolines or nitroindazoles) were studied as inhibitors of β-hematin formation. The most potent inhibitors were quinacrine, chloroquine, and amodiaquine followed by quinidine, mefloquine and quinine whereas 8-hydroxyquinoline and β-carbolines had no effect. Compounds that inhibited β-hematin increased free hemin that promoted peroxidative reactions as determined with TMB and ABTS substrates. Hemin-catalyzed peroxidative reactions were potentiated in presence of proteins (i.e. globin or BSA) while antioxidants and peroxidase inhibitors decreased peroxidation. Free hemin increased by chloroquine action promoted oxidative reactions resulting in inhibition of proteolysis by three cysteine proteases: papain, ficin and cathepsin B. Glutathione reversed inhibition of proteolysis. These results show that active quinolines inhibit hemozoin and increase free hemin which in presence of H2O2 that abounds in parasite digestive vacuole catalyzes peroxidative reactions and inhibition of cysteine proteases. This work suggests a link between the action of quinoline drugs with biochemical processes of peroxidation and inhibition of proteolysis.

The search for biomarkers associated with obesity-related diseases is ongoing, but it is not clear whether plasma and serum can be used interchangeably in this process. Here we used high-throughput screening to analyze 358 proteins and 76 lipids, selected because of their relevance to obesity-associated diseases, in plasma and serum from age- and sex-matched lean and obese humans. Most of the proteins/lipids had similar concentrations in plasma and serum, but a subset showed significant differences. Notably, a key marker of cardiovascular disease PAI-1 showed a difference in concentration between the obese and lean groups only in plasma. Furthermore, some biomarkers showed poor correlations between plasma and serum, including PCSK9, an important regulator of cholesterol homeostasis. Collectively, our results show that the choice of biofluid may impact study outcome when screening for obesity-related biomarkers and we identify several markers where this will be the case.

Alzheimer's disease (AD) is characterized by a progressive loss of neurons and cognitive functions. Therefore, early diagnosis of AD is critical. The development of practical and non-invasive diagnostic tests for AD remains, however, an unmet need. In the present proof-of-concept study we investigated tear fluid as a novel source of disease-specific protein and microRNA-based biomarkers for AD development using samples from patients with mild cognitive impairment (MCI) and AD. Tear protein content was evaluated via liquid chromatography-mass spectrometry and microRNA content was profiled using a genome-wide high-throughput PCR-based platform. These complementary approaches identified enrichment of specific proteins and microRNAs in tear fluid of AD patients. In particular, we identified elongation initiation factor 4E (eIF4E) as a unique protein present only in AD samples. Total microRNA abundance was found to be higher in tears from AD patients. Among individual microRNAs, microRNA-200b-5p was identified as a potential biomarker for AD with elevated levels present in AD tear fluid samples compared to controls. Our study suggests that tears may be a useful novel source of biomarkers for AD and that the identification and verification of biomarkers within tears may allow for the development of a non-invasive and cost-effective diagnostic test for AD.

In the Arctic, sea-ice plays a central role in the functioning of marine food webs and its rapid shrinking has large effects on the biota. It is thus crucial to assess the importance of sea-ice and ice-derived resources to Arctic marine species. Here, we used a multi-biomarker approach combining Highly Branched Isoprenoids (HBIs) with δ13C and δ15N to evaluate how much Arctic seabirds rely on sea-ice derived resources during the pre-laying period, and if changes in sea-ice extent and duration affect their investment in reproduction. Eggs of thick-billed murres (Uria lomvia) and northern fulmars (Fulmarus glacialis) were collected in the Canadian Arctic during four years of highly contrasting ice conditions, and analysed for HBIs, isotopic (carbon and nitrogen) and energetic composition. Murres heavily relied on ice-associated prey, and sea-ice was beneficial for this species which produced larger and more energy-dense eggs during icier years. In contrast, fulmars did not exhibit any clear association with sympagic communities and were not impacted by changes in sea ice. Murres, like other species more constrained in their response to sea-ice variations, therefore appear more sensitive to changes and may become the losers of future climate shifts in the Arctic, unlike more resilient species such as fulmars.

Metabolism and mitochondrial biology have gained a prominent role as determinants of stem cell fate and function. In the context of regenerative medicine, innovative parameters predictive of therapeutic efficacy could be drawn from the association of metabolic or mitochondrial parameters to different degrees of stemness and differentiation potentials. Herein, this possibility was addressed in human mesenchymal stromal/stem cells (hMSC) previously shown to differ in lifespan and telomere length. First, these hMSC were shown to possess significantly distinct proliferation rate, senescence status and differentiation capacity. More potential hMSC were associated to higher mitochondrial (mt) DNA copy number and lower mtDNA methylation. In addition, they showed higher expression levels of oxidative phosphorylation subunits. Consistently, they exhibited higher coupled oxygen consumption rate and lower transcription of glycolysis-related genes, glucose consumption and lactate production. All these data pointed at oxidative phosphorylation-based central metabolism as a feature of higher stemness-associated hMSC phenotypes. Consistently, reduction of mitochondrial activity by complex I and III inhibitors in higher stemness-associated hMSC triggered senescence. Finally, functionally higher stemness-associated hMSC showed metabolic plasticity when challenged by glucose or glutamine shortage, which mimic bioenergetics switches that hMSC must undergo after transplantation or during self-renewal and differentiation. Altogether, these results hint at metabolic and mitochondrial parameters that could be implemented to identify stem cells endowed with superior growth and differentiation potential.

A number of bifidobacterial species are found at a particularly high prevalence and abundance in faecal samples of healthy breastfed infants, a phenomenon that is believed to be, at least partially, due to the ability of bifidobacteria to metabolize Human Milk Oligosaccharides (HMOs). In the current study, we isolated a novel strain of Bifidobacterium kashiwanohense, named APCKJ1, from the faeces of a four-week old breastfed infant, based on the ability of the strain to utilise the HMO component fucosyllactose. We then determined the full genome sequence of this strain, and employed the generated data to analyze fucosyllactose metabolism in B. kashiwanohense APCKJ1. Transcriptomic and growth analyses, combined with metabolite analysis, in vitro hydrolysis assays and heterologous expression, allowed us to elucidate the pathway for fucosyllactose metabolism in B. kashiwanohense APCKJ1. Homologs of the key genes for this metabolic pathway were identified in particular in infant-derived members of the Bifdobacterium genus, revealing the apparent niche-specific nature of this pathway, and allowing a broad perspective on bifidobacterial fucosyllactose and L-fucose metabolism.

The bacterial ribosome is an important drug target for antibiotics that can inhibit different stages of protein synthesis. Among the various classes of compounds that impair translation there are, however, no known small-molecule inhibitors that specifically target ribosomal release factors (RFs). The class I RFs are essential for correct termination of translation and they differ considerably between bacteria and eukaryotes, making them potential targets for inhibiting bacterial protein synthesis. We carried out virtual screening of a large compound library against 3D structures of free and ribosome-bound RFs in order to search for small molecules that could potentially inhibit termination by binding to the RFs. Here, we report identification of two such compounds which are found both to bind free RFs in solution and to inhibit peptide release on the ribosome, without affecting peptide bond formation.

Joint actions often require agents to track others' actions while planning and executing physically incongruent actions of their own. Previous research has indicated that this can lead to visuomotor interference effects when it occurs outside of joint action. How is this avoided or overcome in joint actions? We hypothesized that when joint action partners represent their actions as interrelated components of a plan to bring about a joint action goal, each partner's movements need not be represented in relation to distinct, incongruent proximal goals. Instead they can be represented in relation to a single proximal goal - especially if the movements are, or appear to be, mechanically linked to a more distal joint action goal. To test this, we implemented a paradigm in which participants produced finger movements that were either congruent or incongruent with those of a virtual partner, and either with or without a joint action goal (the joint flipping of a switch, which turned on two light bulbs). Our findings provide partial support for the hypothesis that visuomotor interference effects can be reduced when two physically incongruent actions are represented as mechanically interdependent contributions to a joint action goal.

Ancient evidence of human presence in Europe is recorded in several Early Pleistocene archaeopalaeontological sites from Spain, France and Italy. This is the case of Barranco León (BL) and Fuente Nueva-3 (FN-3), two localities placed near the town of Orce (depression of Baza and Guadix, SE Spain) and dated to ~1.4 Ma. At these sites, huge assemblages of Oldowan tools and evidence of defleshing, butchering and marrow processing of large mammal bones have been recovered together with a deciduous tooth of Homo sp. in the case of level BL-D. In this study, we: (i) describe in detail the anthropic marks found in the bone assemblages from these sites; (ii) analyse patterns of defleshment, butchery and marrow processing, based on the modifications identified in the cortical surface of the fossils; and (iii) discuss on the subsistence strategies of the first hominins that inhabited the European subcontinent during Early Pleistocene times.

Autistic individuals experience significantly elevated rates of childhood trauma, self-harm and suicidal behaviour and ideation (SSBI). Is this purely the result of negative environmental experiences, or does this interact with genetic predisposition? In this study we investigated if a genetic predisposition for autism is associated with childhood trauma using polygenic scores (PGS) and genetic correlations in the UK Biobank (105,222 < N < 105,638), and tested potential mediators and moderators of the association between autism, childhood trauma and SSBI. Autism PGS were significantly associated with childhood trauma (max R2 = 0.096%, P < 2 × 10-16), self-harm ideation (max R2 = 0.108%, P < 2 × 10-16), and self-harm (max R2 = 0.13%, P < 2 × 10-16). Supporting this, we identified significant genetic correlations between autism and childhood trauma (rg = 0.36 ± 0.05, P = 8.13 × 10-11), self-harm ideation (rg = 0.49 ± 0.05, P = 4.17 × 10-21) and self-harm (rg = 0.48 ± 0.05, P = 4.58 × 10-21), and an over-transmission of PGS for the two SSBI phenotypes from parents to autistic probands. Male sex negatively moderated the effect of autism PGS on childhood trauma (β = -0.023 ± 0.005, P = 6.74 × 10-5). Further, childhood trauma positively moderated the effect of autism PGS on self-harm score (β = 8.37 × 10-3 ± 2.76 × 10-3, P = 2.42 × 10-3) and self-harm ideation (β = 7.47 × 10-3 ± 2.76 × 10-3, P = 6.71 × 10-3). Finally, depressive symptoms, quality and frequency of social interactions, and educational attainment were significant mediators of the effect of autism PGS on SSBI, with the proportion of effect mediated ranging from 0.23 (95% CI: 0.09-0.32) for depression to 0.008 (95% CI: 0.004-0.01) for educational attainment. Our findings identify that a genetic predisposition for autism is associated with adverse life-time outcomes, which represent complex gene-environment interactions, and prioritizes potential mediators and moderators of this shared biology. It is important to identify sources of trauma for autistic individuals in order to reduce their occurrence and impact.

Apart from its well-known prodeath activity, p53 is also implicated in promoting cell survival. How p53 can mediate such seemingly opposing effects is largely unclear. We report here a novel mechanism in which p53-mediated proapoptosis is switched to antiapoptosis via its interaction with a p53 isoform, Δ133p53. We show that the expression of Δ133p53 is induced by mild or a moderate level of stress via an HIF1-dependent mechanism. Increased Δ133p53 levels contribute to the adaptive response by shifting the p53 binding at the Bcl2 promoter from suppressive responsive elements (RE) to activating REs, resulting in induction of Bcl2. In accordance with this mode of action, pretreatment of mice with mild stress induces Δ133p53 and Bcl2, which is associated with protection of animals from toxicity caused by high doses of DNA damage agents. Collectively, our work uncovers a novel functional interplay between p53 and Δ133p53 determining cell fate; survival or death in response to stress.

The isotropic or anisotropic organization of biological extracellular matrices has important consequences for tissue function. We study emergent anisotropy using fibroblasts that generate varying degrees of matrix alignment from uniform starting conditions. This reveals that the early migratory paths of fibroblasts are correlated with subsequent matrix organization. Combined experimentation and adaptation of Vicsek modelling demonstrates that the reorientation of cells relative to each other following collision plays a role in generating matrix anisotropy. We term this behaviour 'cell collision guidance'. The transcription factor TFAP2C regulates cell collision guidance in part by controlling the expression of RND3. RND3 localizes to cell-cell collision zones where it downregulates actomyosin activity. Cell collision guidance fails without this mechanism in place, leading to isotropic matrix generation. The cross-referencing of alignment and TFAP2C gene expression signatures against existing datasets enables the identification and validation of several classes of pharmacological agents that disrupt matrix anisotropy.

The generation of tissue-resident memory T cells (TRM) is an essential aspect of immunity at mucosal surfaces, and it has been suggested that preferential generation of TRM is one of the principal advantages of mucosally administered vaccines. We have previously shown that antigen-specific, IL-17-producing CD4+ T cells can provide capsular antibody-independent protection against nasal carriage of Streptococcus pneumoniae; but whether pneumococcus-responsive TRM are localized within the nasal mucosa and are sufficient for protection from carriage has not been determined. Here, we show that intranasal administration of live or killed pneumococci to mice generates pneumococcus-responsive IL-17A-producing CD4+ mucosal TRM. Furthermore, we show that these cells are sufficient to mediate long-lived, neutrophil-dependent protection against subsequent pneumococcal nasal challenge. Unexpectedly, and in contrast with the prevailing paradigm, we found that parenteral administration of killed pneumococci also generates protective IL-17A+CD4+ TRM in the nasal mucosa. These results demonstrate a critical and sufficient role of TRM in prevention of pneumococcal colonization, and further that these cells can be generated by parenteral immunization. Our findings therefore have important implications regarding the generation of immune protection at mucosal surfaces by vaccination.