Biodepot Launcher: an app to install, manage and launch bioinformatics workflows.

We present the Biodepot Launcher, a desktop application that facilitates installation, management and deployment of bioinformatics workflows using the Biodepot-workflow-builder (Bwb). With the new app, Bwb can be started by double-clicking on an icon, eliminating the need for typing cryptic start up commands into the terminal. This creates an end-to-end graphical and easy-to-use interface to manage and launch containerized workflows on the local computer or cloud instances.

T-follicular helper cells are epigenetically poised to transdifferentiate into T-regulatory type 1 cells.

Chronic antigenic stimulation can trigger the formation of interleukin 10 (IL-10)-producing T-regulatory type 1 (TR1) cells in vivo. We have recently shown that murine T-follicular helper (TFH) cells are precursors of TR1 cells and that the TFH-to-TR1 cell transdifferentiation process is characterized by the progressive loss and acquisition of opposing transcription factor gene expression programs that evolve through at least one transitional cell stage. Here, we use a broad range of bulk and single-cell transcriptional and epigenetic tools to investigate the epigenetic underpinnings of this process.

Transcriptional re-programming of liver-resident iNKT cells into T-regulatory type-1-like liver iNKT cells involves extensive gene de-methylation.

Unlike conventional CD4+ T cells, which are phenotypically and functionally plastic, invariant NKT (iNKT) cells generally exist in a terminally differentiated state. Naïve CD4+ T cells can acquire alternative epigenetic states in response to different cues, but it remains unclear whether peripheral iNKT cells are epigenetically stable or malleable. Repetitive encounters of liver-resident iNKT cells (LiNKTs) with alpha-galactosylceramide (αGalCer)/CD1d-coated nanoparticles (NPs) can trigger their differentiation into a LiNKT cell subset expressing a T regulatory type 1 (TR1)-like (LiNKTR1) transcriptional signature.

Transcriptional re-programming of insulin B-chain epitope-specific T-follicular helper cells into anti-diabetogenic T-regulatory type-1 cells.

Systemic delivery of nanoparticles (NPs) coated with mono-specific autoimmune disease-relevant peptide-major histocompatibility complex class II (pMHCII) molecules can resolve organ inflammation in various disease models in a disease-specific manner without impairing normal immunity. These compounds invariably trigger the formation and systemic expansion of cognate pMHCII-specific T-regulatory type 1 (TR1) cells. By focusing on type 1 diabetes (T1D)-relevant pMHCII-NP types that display an epitope from the insulin B-chain bound to the same MHCII molecule (IA) on three different registers, we show that pMHCII-NP-induced TR1 cells invariably co-exist with cognate T-Follicular Helper (TFH)-like cells of quasi-identical clonotypic composition and are oligoclonal, yet transcriptionally homogeneous.

A T follicular helper cell origin for T regulatory type 1 cells.

Chronic antigenic stimulation can trigger the differentiation of antigen-experienced CD4 T cells into T regulatory type 1 (TR1) cells, a subset of interleukin-10-producing Treg cells that do not express FOXP3. The identities of the progenitor(s) and transcriptional regulators of this T-cell subset remain unclear. Here, we show that the peptide-major histocompatibility complex class II (pMHCII) monospecific immunoregulatory T-cell pools that arise in vivo in different genetic backgrounds in response to pMHCII-coated nanoparticles (pMHCII-NPs) are invariably comprised of oligoclonal subpools of T follicular helper (TFH) and TR1 cells with a nearly identical clonotypic composition but different functional properties and transcription factor expression profiles.

Re-programming mouse liver-resident invariant natural killer T cells for suppressing hepatic and diabetogenic autoimmunity.

Invariant NKT (iNKT) cells comprise a heterogeneous group of non-circulating, tissue-resident T lymphocytes that recognize glycolipids, including alpha-galactosylceramide (αGalCer), in the context of CD1d, but whether peripheral iNKT cell subsets are terminally differentiated remains unclear. Here we show that mouse and human liver-resident αGalCer/CD1d-binding iNKTs largely correspond to a novel Zbtb16Tbx21Gata3MafRorc subset that exhibits profound transcriptional, phenotypic and functional plasticity. Repetitive in vivo encounters of these liver iNKT (LiNKT) cells with intravenously delivered αGalCer/CD1d-coated nanoparticles (NP) trigger their differentiation into immunoregulatory, IL-10+IL-21-producing Zbtb16MafTbx21Gata3Rorc cells, termed LiNKTR1, expressing a T regulatory type 1 (TR1)-like transcriptional signature.

Immunomodulatory and immunoregulatory nanomedicines for autoimmunity.

Autoimmune diseases, caused by cellularly and molecularly complex immune responses against self-antigens, are largely treated with broad-acting, non-disease-specific anti-inflammatory drugs. These compounds can attenuate autoimmune inflammation, but tend to impair normal immunity against infection and cancer, cannot restore normal immune homeostasis and are not curative. Nanoparticle (NP)- and microparticle (MP)-based delivery of immunotherapeutic agents affords a unique opportunity to not only increase the specificity and potency of broad-acting immunomodulators, but also to elicit the formation of organ-specific immunoregulatory cell networks capable of inducing bystander immunoregulation.

Danger-associated molecular pattern molecules and the receptor for advanced glycation end products enhance ANCA-induced responses.

Objectives: The pro-inflammatory activities of the calgranulins and HMGB1 can be counteracted by sRAGE, the soluble form of their shared receptor. To understand the role of these molecules in AAV and their potential as therapeutic targets we have studied (i) the relationship between these DAMPS and disease activity; (ii) the expression of RAGE and sRAGE in biopsy tissue and peripheral blood; and (iii) the effect of these molecules on ANCA-mediated cytokine production.

Methods: We examined circulating levels of calgranulins (S100A8/A9 and S100A12), HMGB1 and sRAGE by ELISA.

Increased yields and biological potency of knob-into-hole-based soluble MHC class II molecules.

Assembly of soluble peptide-major histocompatibility complex class II (pMHCII) monomers into multimeric structures enables the detection of antigen-specific CD4 T cells in biological samples and, in some configurations, their reprogramming in vivo. Unfortunately, current MHCII-αβ chain heterodimerization strategies are typically associated with low production yields and require the use of foreign affinity tags for purification, precluding therapeutic applications in humans. Here, we show that fusion of peptide-tethered or empty MHCII-αβ chains to the IgG1-Fc mutated to form knob-into-hole structures results in the assembly of highly stable pMHCII monomers.

Ibero⁻American Consensus on Low- and No-Calorie Sweeteners: Safety, Nutritional Aspects and Benefits in Food and Beverages.

International scientific experts in food, nutrition, dietetics, endocrinology, physical activity, paediatrics, nursing, toxicology and public health met in Lisbon on 2⁻4 July 2017 to develop a Consensus on the use of low- and no-calorie sweeteners (LNCS) as substitutes for sugars and other caloric sweeteners. LNCS are food additives that are broadly used as sugar substitutes to sweeten foods and beverages with the addition of fewer or no calories. They are also used in medicines, health-care products, such as toothpaste, and food supplements.

Use of experimental design to investigate biodiesel production by multiple-stage Ultra-Shear reactor.

This work presents biodiesel production from soybean oil and bioethanol by multiple-stage Ultra-Shear reactor (USR). The experiments were carried out in the following conditions: reaction time from 6 to 12 min; catalyst concentration from 0.5% to 1.

Double-scale roughness and superhydrophobicity on metalized Toray carbon fiber paper.

A simple, inexpensive route for the fabrication of a superhydrophobic metal surface is described. Carbon-carbon composite paper (Toray TGP-H) is electroplated with copper. The copper layer is made hydrophobic by self-assembling a monolayer of dodecanethiol.

Cria alpaca body weight and perinatal survival in relation to age of the dam.

The present study with alpacas determined effect of dam's age on body weight and survival of cria during the first week of life. Pregnant dams (n=424) and their crias were used in the study. Cria body weight (kg) was determined at time of placenta expulsion.

Cortisol concentrations in the perinatal and weaning periods of alpacas.

Cortisol concentrations were determined during the perinatal and weaning periods in alpacas. Fifty males and 50 females were chosen at random (25 at each period) for blood collection on day of parturition, 3 and 5 days after birth. For the weaning period, blood samples were collected 2 days before, on the day of weaning (0), and at days 3 and 5 after weaning.

The effect of enzymes on semen viscosity in Llamas and Alpacas.

The effect of four enzymes: collagenase, fibrinolysin, hyalurodinase, and trypsin were recorded on the viscosity, motility, percent live spermatozoa and acrosome integrity of Llama and Alpaca semen. Semen samples were collected using a modified artificial vagina for each of the five llamas and five alpacas. A 25% solution of the of enzyme at a concentration of 1mg/ml was added to the ejaculate.

Acetylation of the HIV-1 Tat protein by p300 is important for its transcriptional activity.

The human immunodeficiency virus 1 (HIV-1) Tat protein activates transcriptional elongation by recruiting the positive transcription elongation factor (pTEFb) complex to the TAR RNA element, which is located at the 5' extremity of all viral transcripts [1-3]. Tat also associates in vitro and in vivo with the transcriptional coactivator p300/CBP [4-6]. This association has been proposed to recruit the histone acetyltransferase (HAT) activity of p300 to the integrated HIV-1 promoter.

Collection of semen and artificial insemination of alpacas.

Semen collection and artificial insemination have not yet been fully developed in the alpaca. Thus, we collected semen from 7 males using a modified artificial vagina placed inside a dummy. Forty adult female alpacas, previously induced to ovulate with hCG, were artificially inseminated with fresh undiluted semen by laparoscopy or by cervix.

Induction of parturition in alpacas and subsequent survival of neonates.

Objective: To evaluate use of fluprostenol, dexamethasone, and oxytocin for induction of parturition in alpacas, and to determine viability of the newborn crias.

Design: Prospective, randomized, controlled trial.

Animals: 36 pregnant alpacas within 10 days of parturition.