We hypothesized that due to the absence of specialist herbivores in introduced ranges, invasive plants have evolved decreased allocation to carbohydrate storage for regrowth ability and as a consequence allocate more to growth. In this study, we compared plant growth, carbohydrate storage and regrowth ability of invasive and native Jacobaea vulgaris in response to complete shoot defoliation. We used invasive J. vulgaris genotypes from three geographically and climactically distinct regions and compared these with native genotypes from Europe. We found that invasive genotypes initially grew larger while native genotypes regrew larger after defoliation. Before defoliation, the carbohydrate storage in roots of invasive genotypes was 38% lower than native genotypes. Biomass after regrowth increased with root carbohydrate storage while it decreased with structural root mass, showing that it is crucial to study root storage and structural components separately in order to investigate plant regrowth. All studied traits of invasive populations from the three geographically and climatologically distinct regions changed in the same expected direction suggesting that the shifts in herbivore guild were causal to the observed change in growth and regrowth ability rather than environmental factors.

Medulloblastoma is the most common malignant brain tumor of childhood. Group 3 medulloblastoma, the most aggressive molecular subtype, frequently disseminates through the leptomeningeal cerebral spinal fluid (CSF) spaces in the brain and spinal cord. The mechanism of dissemination through the CSF remains poorly understood, and the molecular pathways involved in medulloblastoma metastasis and self-renewal are largely unknown. Here we show that NOTCH1 signaling pathway regulates both the initiation of metastasis and the self-renewal of medulloblastoma. We identify a mechanism in which NOTCH1 activates BMI1 through the activation of TWIST1. NOTCH1 expression and activity are directly related to medulloblastoma metastasis and decreased survival rate of tumor-bearing mice. Finally, medulloblastoma-bearing mice intrathecally treated with anti-NRR1, a NOTCH1 blocking antibody, present lower frequency of spinal metastasis and higher survival rate. These findings identify NOTCH1 as a pivotal driver of Group 3 medulloblastoma metastasis and self-renewal, supporting the development of therapies targeting this pathway.

Enrichment of calf diets with exogenous butyrate has shown promise as a promotor of calf growth and intestinal development. However, the impact of dietary derived butyrate on the gut microbiota and their potential role, in turn, as mediators of its effect on calf growth and development is not known. Here, the effects of butyrate supplementation on rumen and hindgut microbiota and fermentation profiles were assessed in 16 Holstein-Friesian bull calves randomly assigned to one of two groups: Control (CON) fed conventional milk replacer or Sodium-Butyrate (SB - added to milk replacer) from days 7 to 56 of life. In the colon, total short chain fatty acid (SCFA), propionate and acetate concentrations were increased by SB (P < 0.05). 16S rRNA gene amplicon sequencing showed cecal abundance of butyrate producers Butyrivibrio and Shuttleworthia were decreased by SB (P < 0.05), while that of the propionate producer Phascolarctobacterium was higher (P < 0.05). Mogibacterium is associated with impaired gut health and was reduced in the cecum of SB calves (P < 0.05). These data show that the beneficial effects of SB on growth and performance occur in tandem with changes in the abundance of important SCFA producing and health-associated bacteria in the hindgut in milk-fed calves.

Selecting the most appropriate protein sequences is critical for precision drug design. Here we describe Haplosaurus, a bioinformatic tool for computation of protein haplotypes. Haplosaurus computes protein haplotypes from pre-existing chromosomally-phased genomic variation data. Integration into the Ensembl resource provides rapid and detailed protein haplotypes retrieval. Using Haplosaurus, we build a database of unique protein haplotypes from the 1000 Genomes dataset reflecting real-world protein sequence variability and their prevalence. For one in seven genes, their most common protein haplotype differs from the reference sequence and a similar number differs on their most common haplotype between human populations. Three case studies show how knowledge of the range of commonly encountered protein forms predicted in populations leads to insights into therapeutic efficacy. Haplosaurus and its associated database is expected to find broad applications in many disciplines using protein sequences and particularly impactful for therapeutics design.

Topoisomerases II (Top2s) are a group of essential enzymes involved in replication, transcription, chromosome condensation, and segregation via altering DNA topology. The mechanism of the Top2s poisons such as etoposide (VP-16) was reported as stabilizing the Top2-DNA complex and engendering permanent DNA breakage. As the structurally similar compound of VP-16, a novel 4β-sulfur-substituted 4'-demethylepipodophyllotoxin (DMEP) derivative (compound C-Bi) with superior antitumor activity was developed in our previous study. To understand the structural basis of the compound action, the crystal structure (2.54 Å) of human Top2 β-isoform (hTop2β) cleavage complexes stabilized by compound C-Bi was determined. However, compound C-Bi was not visible in the crystal structure. Through the comparison of the structures of hTop2β-DNA-etoposide ternary complex and hTop2β-DNA binary complex, it could be observed that the distance between drug-binding sites Arg503 of the two monomers was 26.62 Å in hTop2β-DNA-etoposide ternary complex and 34.54 Å in hTop2β-DNA binary complex, respectively. Significant twist were observed in the DNA chains of binary complex. It suggested that compound C-Bi played antitumor roles through increasing spacing of hTop2β monomers. The changes in hTop2β structure further caused double changes in the torsional direction and migration distance of the DNA chains, resulting in impeding religation of DNA.

Human APOBEC3H (A3H) is a single-stranded DNA cytosine deaminase that inhibits HIV-1. Seven haplotypes (I-VII) and four splice variants (SV154/182/183/200) with differing antiviral activities and geographic distributions have been described, but the genetic and mechanistic basis for variant expression and function remains unclear. Using a combined bioinformatic/experimental analysis, we find that SV200 expression is specific to haplotype II, which is primarily found in sub-Saharan Africa. The underlying genetic mechanism for differential mRNA splicing is an ancient intronic deletion [del(ctc)] within A3H haplotype II sequence. We show that SV200 is at least fourfold more HIV-1 restrictive than other A3H splice variants. To counteract this elevated antiviral activity, HIV-1 protease cleaves SV200 into a shorter, less restrictive isoform. Our analyses indicate that, in addition to Vif-mediated degradation, HIV-1 may use protease as a  counter-defense mechanism against A3H in >80% of sub-Saharan African populations.

Impaired immunity in patients with late-stage cancer is not limited to antitumor responses, as demonstrated by poor vaccination protection and high susceptibility to infection1-3. This has been largely attributed to chemotherapy-induced impairment of innate immunity, such as neutropenia2, whereas systemic effects of tumors on hematopoiesis and adoptive immunity remain incompletely understood. Here we observed anemia associated with severe deficiency of CD8+ T cell responses against pathogens in treatment-naive mice bearing large tumors. Specifically, we identify CD45+ erythroid progenitor cells (CD71+TER119+; EPCs) as robust immunosuppressors. CD45+ EPCs, induced by tumor growth-associated extramedullary hematopoiesis, accumulate in the spleen to become a major population, outnumbering regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs). The CD45+ EPC transcriptome closely resembles that of MDSCs, and, like MDSCs, reactive oxygen species production is a major mechanism underlying CD45+ EPC-mediated immunosuppression. Similarly, an immunosuppressive CD45+ EPC population was detected in patients with cancer who have anemia. These findings identify a major population of immunosuppressive cells that likely contributes to the impaired T cell responses commonly observed in patients with advanced cancer.

Available corrector drugs are unable to effectively rescue the folding defects of CFTR-ΔF508 (or CFTR-F508del), the most common disease-causing mutation of the cystic fibrosis transmembrane conductance regulator, a plasma membrane (PM) anion channel, and thus to substantially ameliorate clinical phenotypes of cystic fibrosis (CF). To overcome the corrector efficacy ceiling, here we show that compounds targeting distinct structural defects of CFTR can synergistically rescue mutant expression and function at the PM. High-throughput cell-based screens and mechanistic analysis identified three small-molecule series that target defects at nucleotide-binding domain (NBD1), NBD2 and their membrane-spanning domain (MSD) interfaces. Although individually these compounds marginally improve ΔF508-CFTR folding efficiency, function and stability, their combinations lead to ~50-100% of wild-type-level correction in immortalized and primary human airway epithelia and in mouse nasal epithelia. Likewise, corrector combinations were effective against rare missense mutations in various CFTR domains, probably acting via structural allostery, suggesting a mechanistic framework for their broad application.

Some of the most unique and compelling survival strategies in the natural world are fixed in isolated species1. To date, molecular insight into these ancient adaptations has been limited, as classic experimental genetics has focused on interfertile individuals in populations2. Here we use a new mapping approach, which screens mutants in a sterile interspecific hybrid, to identify eight housekeeping genes that underlie the growth advantage of Saccharomyces cerevisiae over its distant relative Saccharomyces paradoxus at high temperature. Pro-thermotolerance alleles at these mapped loci were required for the adaptive trait in S. cerevisiae and sufficient for its partial reconstruction in S. paradoxus. The emerging picture is one in which S. cerevisiae improved the heat resistance of multiple components of the fundamental growth machinery in response to selective pressure. Our study lays the groundwork for the mapping of genotype to phenotype in clades of sister species across Eukarya.

Microglia, the resident immune cells of the brain, have multiple functions in physiological and pathological conditions, including Alzheimer's disease (AD). The use of primary microglial cell cultures has proved to be a valuable tool to study microglial biology under various conditions. However, more advanced transfection methodologies for primary cultured microglia are still needed, as current methodologies provide low transfection efficiency and induce cell death and/or inflammatory activation of the microglia. Here, we describe an easy, and effective method based on the Glial-Mag method (OZ Biosciences) using magnetic nanoparticles and a magnet to successfully transfect primary microglia cells with different small interfering RNAs (siRNAs). This method does not require specialist facilities or specific training and does not induce cell toxicity or inflammatory activation. We demonstrate that this protocol successfully decreases the expression of two key genes associated with AD, the triggering receptor expressed in myeloid cells 2 (TREM2) and CD33, in primary microglia cell cultures.

Background: There is paucity in the literature regarding the role of the interoceptive pathway through the insular cortex (IC), as well as heart rate variability (HRV) in relation to Osteopathic Manipulative Therapy (OMT) and deep-touch. Aims: The present study investigated whether both OMT treatment and deep-touch (a newly hypothesized treatment option) was effective at altering the interoceptive pathway and HRV, whilst OMT was only expected to be effective for increasing Range of Motion (ROM). Methods: Thirty-five healthy volunteers were randomly allocated into three conditions in a repeated measures crossover design; a control (laying supine on a plinth); deep-touch (head cradling); and an osteopathic mobilization therapeutic technique on the temporomandibular joint (TMJ). Interoceptive accuracy (IAc), HRV, as well as range of motion (ROM) for the TMJ area as well as the cervical spine (Csp) right and left measures were taken pre and post each condition setting. Results: Significant condition effects emerged from the deep-touch and mobilization interventions for IAc where increases were identified through planned comparisons. For the HRV measure (RMSSD), a significant effect emerged in the deep-touch condition (increase) but not in the mobilization or control conditions. ROM did not increase for any condition. IAc correlated with post-ROM outcomes in many cases and HRV moderated some of these relations. Conclusion: These results are discussed in the context of clinical practice, where cranial deep-touch maybe an effective treatment and modulator of the parasympathetic nervous systems, as well as the interoceptive system.

One of the most influential synaptic learning rules explored in the past decades is activity dependent spike-timing-dependent plasticity (STDP). In STDP, synapses are either potentiated or depressed based on the order of pre- and postsynaptic neuronal activation within narrow, milliseconds-long, time intervals. STDP is subject to neuromodulation by dopamine (DA), a potent neurotransmitter that significantly impacts synaptic plasticity and reward-related behavioral learning. Previously, we demonstrated that GABAergic synapses onto ventral tegmental area (VTA) DA neurons are able to express STDP (Kodangattil et al., 2013), however it is still unclear whether DA modulates inhibitory STDP in the VTA. Here, we used whole-cell recordings in rat midbrain slices to investigate whether DA D1-like and/or D2-like receptor (D1R/D2R) activation is required for induction of STDP in response to a complex pattern of spiking. We found that VTA but not Substantia nigra pars compact (SNc) DA neurons exhibit long-term depression (LTDGABA) in response to a combination of positive (pre-post) and negative (post-pre) timing of spiking (a complex STDP protocol). Blockade of either D1Rs or D2Rs prevented the induction of LTDGABA while activation of D1Rs did not affect the plasticity in response to this complex STDP protocol in VTA DA neurons.Our data suggest that this DA-dependent GABAergic STDP is selectively expressed at GABAergic synapses onto VTA DA neurons which could be targeted by drugs of abuse to mediate drug-induced modulation of DA signaling within the VTA, as well as in VTA-projection areas, thereby affecting reward-related learning and drug-associated memories.

We developed a novel, pH-sensitive drug delivery microparticle based on N-palmitoyl chitosan (NPCS) to transport the superparamagnetic iron oxide (SPIO) and anticancer drug doxorubicin (DOX). The characteristics of NPCS were characterized through nuclear magnetic resonance. Our results based on testing of volume swelling in multiple pH aqueous solutions revealed that the modified chitosan had a pH-sensitive property. The morphology and size of the DOX-SPIO/NPCS microparticles were investigated using transmission electron microscopy and scanning electron microscopy. The statistical result of microparticles had diameter of 185 ± 87 nm. Surface chemical moieties of DOX-SPIO/NPCS microparticles were confirmed using attenuated total reflection Fourier transform infrared spectroscopy and indicated the existence of mostly hydrophilic groups such as -OH, -C=O, and -C-O-C-. Transmission electron microscopy revealed the dark contrast of SPIO dots encapsulated in the NPCS matrix. Nuclear magnetic resonance T2-weighted magnetic resonance imaging confirmed that the produced DOX-SPIO/NPCS microparticles still exhibited T2 relaxation durations as short as 37.68 ± 8.69 ms (under administration of 2.5 μg/mL), which is comparable to the clinically required dosage. In the drug release profile, the DOX-SPIO/NPCS drug delivery microparticle was accelerated in an acidic environment (pH 6.5) compared with that in a basic environment. Microparticles in a cytotoxicity assay (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide assay) revealed that DOX-SPIO/NPCS microparticles had better antitumor ability than did free-form of DOX. Additionally, microparticles loaded with 0.5-5 μg/mL DOX in an acidic environment (pH 6.5) demonstrated higher efficacy against Hep G2 cell growth, possibly because of the swelling effect of NPCS, resulting in volume expansion and easy drug release. Accordingly, these large DOX-SPIO/NPCS microparticles showed potential for application as a pH-sensitive drug delivery system and as chemoembolization particles for hepatic carcinoma therapy.

Introduction: Borderline Personality Disorder (BPD) is a prevalent condition that is often under-treated. This is partly because very few psychotherapists offer treatment for this disabling disorder. Internet-based self-management interventions could contribute to reducing the treatment gap but-mainly due to safety concerns-these have never been tested for BPD in controlled trials. Methods: Patients with BPD will be recruited primarily via the internet and randomized to two groups: care as usual (CAU) alone) or the self-management intervention priovi® in addition to CAU. At the end of the diagnostic interview, all participants will discuss an emergency plan. The main outcome measure is the clinician-rated symptom severity using the BPD Severity Index (BPDSI). Secondary outcome measures include a range of self-reported scales, an SCID-diagnosis of BPD and several safety parameters including serious adverse events (e.g., a life-threatening event, hospitalization or suicide attempt). Discussion: This trial will evaluate the effectiveness of the self-management intervention, priovi, in reducing symptoms of BPD. It will also assess the safety of its use in this target population. If successful, this intervention would be the first comprehensive internet intervention for the treatment of BPD and complement the wide range of internet interventions effective in treating other mental disorders, particularly depression and anxiety disorders. Trial Registration: NCT03418142 (clinicaltrials.gov) on January 23rd 2018. Trial status: recruiting, currently N = 108 (July 2018).

Background and objective: Phase difference enhanced imaging (PADRE), a new phase-related MRI technique, can enhance both paramagnetic and diamagnetic substances, and select which phases to be enhanced. Utilizing these characteristics, we developed color map of PADRE (Color PADRE), which enables simultaneous visualization of myelin-rich structures and veins. Our aim was to determine whether Color PADRE is sufficient to delineate the characteristics of non-gadolinium-enhancing T2-hyperintense regions related with metastatic tumors (MTs), diffuse astrocytomas (DAs) and glioblastomas (GBs), and whether it can contribute to the differentiation of MTs from GBs. Methods: Color PADRE images of 11 patients with MTs, nine with DAs and 17 with GBs were created by combining tissue-enhanced, vessel-enhanced and magnitude images of PADRE, and then retrospectively reviewed. First, predominant visibility of superficial white matter and deep medullary veins within non-gadolinium-enhancing T2-hyperintense regions were compared among the three groups. Then, the discriminatory power to differentiate MTs from GBs was assessed using receiver operating characteristic analysis. Results: The degree of visibility of superficial white matter was significantly better in MTs than in GBs (p = 0.017), better in GBs than in DAs (p = 0.014), and better in MTs than in DAs (p = 0.0021). On the contrary, the difference in the visibility of deep medullary veins was not significant (p = 0.065). The area under the receiver operating characteristic curve to discriminate MTs from GBs was 0.76 with a sensitivity of 80% and specificity of 64%. Conclusion: Visibility of superficial white matter on Color PADRE reflects inferred differences in the proportion of vasogenic edema and tumoral infiltration within non-gadolinium-enhancing T2-hyperintense regions of MTs, DAs and GBs. Evaluation of peritumoral areas on Color PADRE can help to distinguish MTs from GBs.

Background: The osteogenic differentiation of vascular smooth muscle cell (VSMCs) is important for the development of vascular calcification (VC), particularly in diabetes. Exosomes derived from Mesenchymal Stromal Cells (MSCs) are effective against cardiovascular diseases, yet their role in VC remains unclear. Advanced glycation end products (AGEs) inhibit bone marrow stromal cell osteogenesis by targeting osteogenesis-associated genes. Thus, we investigated the role of exosomes derived from MSCs pretreated with AGEs-BSA in VC and its potential mechanisms. Methods: Primary VSMCs and MSCs were isolated from the aorta and bone marrow of Sprague-Dawley rats, respectively. VSMCs were cultured with AGEs-BSA to induce osteogenic differentiation. Exosomes were harvested from MSCs by ultracentrifugation. MSCs and VSMCs were cocultured in Transwells, and exosomes were added to VSMC culture medium to assess their effects on osteogenic differentiation. Double luciferase reporter assay was applied to confirm that miR-146a directly targets the 3' UTR of the thioredoxin-interacting protein (TXNIP) gene. Results: Pretreatment of VSMCs with AGEs-BSA increased the expression of thioredoxin-interacting protein (TXNIP) by inhibiting that of miR-146a, resulting in enhanced ROS production and VSMC calcification. By contrast, the expression of miR-146a in MSCs was increased by AGEs-BSA treatment. Thus, miR-146a was transferred from AGEs-BSA-pretreated or miR-146a-transfected MSCs to VSMCs via exosomes. After coculture with miR-146a-containing exosomes, the AGEs-BSA-mediated increase in VSMC calcification was diminished, accompanied by decreased TXNIP expression and ROS production. Furthermore, TXNIP overexpression counteracted the anti-calcification effects of MSC-derived miR-146a-containing exosomes. In addition, TXNIP was identified as a target gene of miR-146a, and the results of double luciferase reporter assay confirmed that TXNIP was the direct target gene of miR-146a. Conclusions: Exosomes secreted by MSCs pretreated with AGEs-BSA contained a high level of miR-146a, which was transferred to VSMCs and inhibited AGEs-BSA-induced calcification in a TXNIP-dependent manner. Thus, miR-146a-containing exosomes may be a potential therapeutic target for VC.

The last years have witnessed a breakthrough in the development of cell-based tolerance-inducing cell therapies for the treatment of autoimmune diseases and solid-organ transplantation. Indeed, the use of tolerogenic dendritic cells (tolDC) and regulatory macrophages (Mreg) is currently being tested in Phase I and Phase II clinical trials worldwide, with the aim of finding an effective therapy able to abrogate the inflammatory processes causing these pathologies without compromising the protective immunity of the patients. However, there exists a wide variety of different protocols to generate human tolDC and Mreg and, consequently, the characteristics of each product are heterogeneous. For this reason, the identification of biomarkers able to define their functionality (tolerogenicity) is of great relevance, on the one hand, to guarantee the safety of tolDC and Mreg before administration and, on the other hand, to compare the results between different cell products and laboratories. In this article, we perform an exhaustive review of protocols generating human tolDC and Mreg in the literature, aiming to elucidate if there are any common transcriptomic signature or potential biomarkers of tolerogenicity among the different approaches. However, and although several effectors seem to be induced in common in some of the most reported protocols to generate both tolDC or Mreg, the transcriptomic profile of these cellular products strongly varies depending on the approach used to generate them.

ImmuneDB is a system for storing and analyzing high-throughput immune receptor sequencing data. Unlike most existing tools, which utilize flat-files, ImmuneDB stores data in a well-structured MySQL database, enabling efficient data queries. It can take raw sequencing data as input and annotate receptor gene usage, infer clonotypes, aggregate results, and run common downstream analyses such as calculating selection pressure and constructing clonal lineages. Alternatively, pre-annotated data can be imported and analyzed data can be exported in a variety of common Adaptive Immune Receptor Repertoire (AIRR) file formats. To validate ImmuneDB, we compare its results to those of another pipeline, MiXCR. We show that the biological conclusions drawn would be similar with either tool, while ImmuneDB provides the additional benefits of integrating other common tools and storing data in a database. ImmuneDB is freely available on GitHub at https://github.com/arosenfeld/immunedb, on PyPi at https://pypi.org/project/ImmuneDB, and a Docker container is provided at https://hub.docker.com/r/arosenfeld/immunedb. Full documentation is available at http://immunedb.com.

The experiment was conducted during two consecutive seasons (years 2016 and 2017) in an organic apple orchard of the cultivar Jonathan. Several biostimulants were tested (10 in total), including humic acids, macro and micro seaweed extracts, alfalfa protein hydrolysate, amino acids alone or in combination with zinc, B-group vitamins, chitosan and a commercial product containing silicon. Treatments were performed at weekly intervals, starting from the end of May until mid-August. The macroseaweed extract was effective in stimulate tree growth potential in both years, as shown by a significantly larger leaf area (+20% as compared to control) and by an higher chlorophyll content and leaf photosynthetic rate in year 2016. As for the yield performances and apples quality traits at harvest (average fruit weight, soluble solids content, titratable acidity, and flesh firmness), they were generally affected by the different climatic conditions that characterized the two growing seasons (year 2017 being characterized by higher maximal and average temperatures and by limited rainfalls at the beginning of the season). Treatments with macroseaweed extract, B-group vitamins and alfalfa protein hydrolysate were able to significantly improve the intensity and extension of the red coloration of apples at harvest. Correspondingly, the anthocyanin content in the skin of apples treated with the same biostimulants resulted significantly higher than control, highlighting the potential influence of these substances on the synthesis of secondary metabolites in apple. The incidence of physiological disorders was also monitored during apple storage period. Amino acids plus zinc application was effective in reducing (more than 50%) the incidence of the "Jonathan spot," the main post-harvest disorder for this cultivar.

Common walnut (Juglans regia L.) is an economically important hardwood tree species cultivated worldwide for its high quality wood and edible nuts. It is generally accepted that after the last glaciation J. regia survived and grew in almost completely isolated stands in Asia, and that ancient humans dispersed walnuts across Asia and into new habitats via trade and cultural expansion. The history of common walnut in China is a matter of debate, however. We estimated the genetic diversity and spatial genetic structure of 31 walnut populations sampled across its Chinese range using 22 microsatellite markers (13 neutral and 9 non-neutral). Using historical data and population genetic analysis, including approximate Bayesian analysis (ABC), we reconstructed the demographic history of J. regia in China. The genetic data indicated the likely presence of J. regia in glacial refugia in the Xinjiang province (Northwest China), Northeastern China (Beijing, Shandong, and Changbai Mountains), Central China (Qinling and Baishan Mountains and Xi'an), and Southwestern China (Tibet, Yunnan, Guizhou, and Sichuan provinces). Based on DIY-ABC analysis, we identified three ancient lineages of J. regia in China. Two lineages (subpopulation A and subpopulation B+C) diverged about 2.79 Mya, while Southwestern China, and Qinling and Baishan Mountains lineages diverged during the Quaternary glaciations (about 1.13 Mya). Remnants of these once-distinct genetic clusters of J. regia may warrant ecological management if they are to be retained as in situ resources. A population size expansion in Northeastern China was detected in the last five centuries. The present distribution of walnut in China resulted from the combined effects of expansion/contraction from multiple refugia after the Last Glacial Maximum and later human exploitation.