Abstract
Microbial systematics is heavily influenced by genome-based methods and challenged by an ever increasing number of taxon names and associated sequences in public data repositories. This ...poses a challenge for database systems, particularly since it is obviously advantageous if such data are based on a globally recognized approach to manage names, such as the International Code of Nomenclature of Prokaryotes. The amount of data can only be handled if accurate and reliable high-throughput platforms are available that are able to both comply with this demand and to keep track of all changes in an efficient and flexible way. The List of Prokaryotic names with Standing in Nomenclature (LPSN) is an expert-curated authoritative resource for prokaryotic nomenclature and is available at https://lpsn.dsmz.de. The Type (Strain) Genome Server (TYGS) is a high-throughput platform for accurate genome-based taxonomy and is available at https://tygs.dsmz.de. We here present important updates of these two previously introduced, heavily interconnected platforms for taxonomic nomenclature and classification, including new high-level facilities providing access to bioinformatic algorithms, a considerable expansion of the database content, and new ways to easily access the data.
Shifting the life cycle of grain crops from annual to perennial would usher in a new era of agriculture that is more environmentally friendly, resilient to climate change, and capable of soil carbon ...sequestration. Despite decades of work, transforming the annual grain crop wheat (Triticum aestivum) into a perennial has yet to be realized. Direct domestication of wild perennial grass relatives of wheat, such as Thinopyrum intermedium, is an alternative approach. Here we highlight protein coding sequences in the recently released T. intermedium genome sequence that may be orthologous to domestication genes identified in annual grain crops. Their presence suggests a roadmap for the accelerated domestication of this plant using new breeding technologies.
Current grain crops are annuals that must be sown every year, giving their root systems little time to develop during the growing season.A perennial grain crop with a long-lived extensive root system would improve soil quality, store carbon belowground, and utilize water and minerals more efficiently.Domestication genes of the annual grass wheat are highly conserved in the perennial intermediate wheatgrass (Thinopyrum intermedium), providing an opportunity for accelerated domestication of a perennial grain using a mutagenesis approach.
Irritable bowel syndrome(IBS)remains a clinical challenge in the 21st century.It’s the most commonly diagnosed gastrointestinal condition and also the most common reason for referral to ...gastroenterology clinics.Its can affect up to one in five people at some point in their lives,and has a significantly impact of life quality and health care utilization.The prevalence varies according to country and criteria used to define IBS.Various mechanisms and theories have been proposed about its etiology,but the biopsychosocial model is the most currently accepted for IBS.The complex of symptoms would be the result of the interaction between psychological,behavioral,psychosocial and environmental factors.The diagnosis of IBS is not confirmed by a specific test or structural abnormality.It is made using criteria based on clinical symptoms such as Rome criteria,unless the symptoms are thought to be atypical.Today the Rome CriteriaⅢis the current goldstandard for the diagnoses of IBS.Secure positive evidence of IBS by means of specific disease marker is currently not possible and cannot be currently recommended for routine diagnosis.There is still no clinical evidence to recommend the use of biomarkers in blood to diagnose IBS.However,a number of different changes in IBS patients were demonstrated in recent years,some of which can be used in the future as a diagnostic support.IBS has no definitive treatment but could be controlled by non-pharmacologic management eliminating of some exacerbating factors such certain drugs,stressor conditions and changes in dietary habits.The traditional pharmacologic management of IBS has been symptom based and several drugs have been used.However,the cornerstone of its therapy is a solid patient physician relationship.This review will provide a summary of pathophysiology,diagnostic criteria and current and emerging therapies for IBS.
ABSTRACT
The Magellanic Clouds (MCs) have lost most of their gas during their passage by the Milky Way, a property that has never been successfully modelled. Here, we use accurate and mesh-free ...hydrodynamic simulations to reproduce the Magellanic Stream and the MCs in the frame of a ‘ram-pressure plus collision’ model. This model reproduces many of the observed properties of the H i Stream including most of its density profile along its length and its dual filamentary structure. Besides this, ram-pressure combined with Kelvin–Helmholtz instabilities extracts amounts of ionized and H i gas consistent with those observed. The modelled scenario also reproduces the Magellanic Bridge, including the offset between young and old stars, and the collision between the Clouds, which is responsible of the very elongated morphology of the Small Magellanic Cloud along the line of sight. This model has solved most of the mysteries linked to the formation of the Magellanic Stream. The Leading Arm is not reproduced in the current model because it requires an alternative origin.
Numerous epidemiological studies have demonstrated the association between (poly)phenol-rich foods and human health. Growing consumer knowledge of the relationship between diet, good health and ...disease prevention stimulated manufacturing opportunities. Functional foods and their synergistic health benefits, beyond just being a source of individual nutrients, are highly demanded by consumers.
Therefore, the aim of this study was to review available literature focusing on the nutraceutical role of (poly)phenols, and role in functional foods production, with a specific focus on (poly)phenols derived from byproducts.
The review of the literature showed that antioxidant extracted from residual sources could prevent lipid peroxidation and protect against oxidative damage by scavenging oxygen radicals, and therefore contribute to the longer stability of foods, be used for increasing the stability of foods. These effects may also translate to humans, improving the effects on health of certain foods.
However, careful monitoring of production is needed in order to maximize the (poly)phenol content of plant foods.
Abstract
The thermally pulsing asymptotic giant branch (TP-AGB) experienced by low- and intermediate-mass stars is one of the most uncertain phases of stellar evolution and the models need to be ...calibrated with the aid of observations. To this purpose, we couple high-quality observations of resolved stars in the Small Magellanic Cloud (SMC) with detailed stellar population synthesis simulations computed with the trilegal
code. The strength of our approach relies on the detailed spatially resolved star formation history of the SMC, derived from the deep near-infrared photometry of the VISTA survey of the Magellanic Clouds, as well as on the capability to quickly and accurately explore a wide variety of parameters and effects with the colibri
code for the TP-AGB evolution. Adopting a well-characterized set of observations – star counts and luminosity functions – we set up a calibration cycle along which we iteratively change a few key parameters of the TP-AGB models until we eventually reach a good fit to the observations. Our work leads to identify two best-fitting models that mainly differ in the efficiencies of the third dredge-up and mass-loss in TP-AGB stars with initial masses larger than about 3 M⊙. On the basis of these calibrated models, we provide a full characterization of the TP-AGB stellar population in the SMC in terms of stellar parameters (initial masses, C/O ratios, carbon excess, mass-loss rates). Extensive tables of isochrones including these improved models are publicly available.
Neoantigens, which are derived from tumour-specific protein-coding mutations, are exempt from central tolerance, can generate robust immune responses
and can function as bona fide antigens that ...facilitate tumour rejection
. Here we demonstrate that a strategy that uses multi-epitope, personalized neoantigen vaccination, which has previously been tested in patients with high-risk melanoma
, is feasible for tumours such as glioblastoma, which typically have a relatively low mutation load
and an immunologically 'cold' tumour microenvironment
. We used personalized neoantigen-targeting vaccines to immunize patients newly diagnosed with glioblastoma following surgical resection and conventional radiotherapy in a phase I/Ib study. Patients who did not receive dexamethasone-a highly potent corticosteroid that is frequently prescribed to treat cerebral oedema in patients with glioblastoma-generated circulating polyfunctional neoantigen-specific CD4
and CD8
T cell responses that were enriched in a memory phenotype and showed an increase in the number of tumour-infiltrating T cells. Using single-cell T cell receptor analysis, we provide evidence that neoantigen-specific T cells from the peripheral blood can migrate into an intracranial glioblastoma tumour. Neoantigen-targeting vaccines thus have the potential to favourably alter the immune milieu of glioblastoma.
The discovery that dentine is a reservoir of bioactive molecules that can be recruited on demand has attracted efforts to develop new protocols and materials for vital pulp therapy (VPT). The ...noncollagenous proteins (NCPs) present in the dentine extracellular matrix (ECM) include growth factors (TGF‐β1, BMP‐7, FGF‐2, IGF‐1 and IGF‐2, NGF and GDNF), extracellular matrix molecules (DSP, DPP, BSP, DMP‐1 and DSPP) and both anti‐inflammatory and pro‐inflammatory chemokines and cytokines (TNF‐α, IL‐1, IL‐6 and IL‐10). Molecules such as DSP and DPP are mainly expressed by odontoblasts, and they are cleaved products from dentine sialophosphoprotein (DSPP). Some molecules, such as TGF‐β1, specifically interact with decorin/biglycan in dentine. Although TGF‐β1 increases the expression and secretion of NGF in human pulp cells, NGF induces mineralization and increases the expression of DSPP and DMP‐1. Furthermore, GDNF may act as a cell survival factor and mitogen during tooth injury and repair. Pulp capping materials, such as MTA and calcium hydroxide, can solubilize bioactive dentine molecules (TGF‐β1, NGF and GDNF) that stimulate tertiary dentinogenesis. The binding of these signalling molecules leads to activation of several signalling transduction pathways involved in dentinogenesis, odontoblast differentiation and inflammatory responses, such as the p38 MAPK, NF‐kβ and Wnt/β‐catenin signalling pathways. Understanding the cascade of cellular and molecular events underlying the repair and regeneration processes provides a reasonable new approach to VPT through a targeted interaction between tooth tissue and bioactive molecules.
Personal neoantigen vaccines have been envisioned as an effective approach to induce, amplify and diversify antitumor T cell responses. To define the long-term effects of such a vaccine, we evaluated ...the clinical outcome and circulating immune responses of eight patients with surgically resected stage IIIB/C or IVM1a/b melanoma, at a median of almost 4 years after treatment with NeoVax, a long-peptide vaccine targeting up to 20 personal neoantigens per patient ( NCT01970358 ). All patients were alive and six were without evidence of active disease. We observed long-term persistence of neoantigen-specific T cell responses following vaccination, with ex vivo detection of neoantigen-specific T cells exhibiting a memory phenotype. We also found diversification of neoantigen-specific T cell clones over time, with emergence of multiple T cell receptor clonotypes exhibiting distinct functional avidities. Furthermore, we detected evidence of tumor infiltration by neoantigen-specific T cell clones after vaccination and epitope spreading, suggesting on-target vaccine-induced tumor cell killing. Personal neoantigen peptide vaccines thus induce T cell responses that persist over years and broaden the spectrum of tumor-specific cytotoxicity in patients with melanoma.
P4 ATPases (i.e., lipid flippases) are eukaryotic enzymes that transport lipids across membrane bilayers. In plants, P4 ATPases are named Aminophospholipid ATPases (ALAs) and are organized into five ...phylogenetic clusters. Here we generated an Arabidopsis mutant lacking all five cluster‐2 ALAs (ala8/9/10/11/12), which is the most highly expressed ALA subgroup in vegetative tissues. Plants harboring the quintuple knockout (KO) show rosettes that are 2.2‐fold smaller and display chlorotic lesions. A similar but less severe phenotype was observed in an ala10/11 double KO. The growth and lesion phenotypes of ala8/9/10/11/12 mutants were reversed by expressing a NahG transgene, which encodes an enzyme that degrades salicylic acid (SA). A role for SA in promoting the lesion phenotype was further supported by quantitative PCR assays showing increased mRNA abundance for an SA‐biosynthesis gene ISOCHORISMATE SYNTHASE 1 (ICS1) and two SA‐responsive genes PATHOGENESIS‐RELATED GENE 1 (PR1) and PR2. Lesion phenotypes were also reversed by growing plants in liquid media containing either low calcium (~0.1 mM) or high nitrogen concentrations (~24 mM), which are conditions known to suppress SA‐dependent autoimmunity. Yeast‐based fluorescent lipid uptake assays revealed that ALA10 and ALA11 display overlapping substrate specificities, including the transport of LysoPC signaling lipids. Together, these results establish that the biochemical functions of ALA8–12 are at least partially overlapping, and that deficiencies in cluster‐2 ALAs result in an SA‐dependent autoimmunity phenotype that has not been observed for flippase mutants with deficiencies in other ALA clusters.
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