ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization

Microbiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences of changes in the intestinal microbiome may provide more power for studying their impact on inflammation and immune responses. Although 16S rRNA analysis is one of the most popular and a cost-effective method to profile the microbial compositions, marker-gene sequencing cannot provide direct information about the functional genes that are present in the genomes of community members. Bioinformatic tools have been developed to predict microbiome function with 16S rRNA gene data. Among them, PICRUSt2 has become one of the most popular functional profile prediction tools, which generates community-wide pathway abundances. However, no state-of-art inference tools are available to test the differences in pathway abundances between comparison groups. We have developed ggpicrust2, an R package, to do extensive differential abundance(DA) analyses and provide publishable visualization to highlight the signals.Comment: 4 pages, 1 figur

DOF-binding sites additively contribute to guard cell-specificity of AtMYB60 promoter

<p>Abstract</p> <p>Background</p> <p>We previously demonstrated that the <it>Arabidopsis thaliana </it>AtMYB60 protein is an R2R3MYB transcription factor required for stomatal opening. <it>AtMYB60 </it>is specifically expressed in guard cells and down-regulated at the transcriptional levels by the phytohormone ABA.</p> <p>Results</p> <p>To investigate the molecular mechanisms governing <it>AtMYB60 </it>expression, its promoter was dissected through deletion and mutagenesis analyses. By studying different versions of <it>AtMYB60 </it>promoter::GUS reporter fusions in transgenic plants we were able to demonstrate a modular organization for the <it>AtMYB60 </it>promoter. Particularly we defined: a minimal promoter sufficient to confer guard cell-specific activity to the reporter gene; the distinct roles of different DOF-binding sites organised in a cluster in the minimal promoter in determining guard cell-specific expression; the promoter regions responsible for the enhancement of activity in guard cells; a promoter region responsible for the negative transcriptional regulation by ABA. Moreover from the analysis of single and multiple mutants we could rule out the involvement of a group of DOF proteins, known as CDFs, already characterised for their involvement in flowering time, in the regulation of <it>AtMYB60 </it>expression.</p> <p>Conclusions</p> <p>These findings shed light on the regulation of gene expression in guard cells and provide new promoter modules as useful tools for manipulating gene expression in guard cells, both for physiological studies and future biotechnological applications.</p

The Attrition of Young Physician-Scientists: Problems and Potential Solutions

Physician-scientists have played a prominent role as thought leaders in American medicine over the past century. This group has produced many basic scientific advances and pioneered the translation of these advances into clinical practice. Now that we are in the post-genomic era, there is a greater need than ever for the continued participation of this group because of their unique ability to bridge the "bench to bedside." However, the number of physicians pursuing this career is static and their average age is rising. Recent data indicate that the many benefits of this career path are seen as being outweighed by so many negative factors, as to prompt the question, "Is this a career that a reasonable person should undertake in 2007 and beyond?" The following analysis suggests that the current answer is "no." We have identified the lack of professional security as a major factor that prompts young physicians to abandon the physician-scientist track. Because this problem has not been sufficiently emphasized, we believe current efforts are unlikely to reverse this disturbing trend. We propose strategies that seek to address this problem and help sustain young physician-scientists at career transition points at which they are most vulnerable to give up

Critical role of endothelial P-selectin glycoprotein ligand 1 in chronic murine ileitis

L-selectin ligands might be relevant for inflammatory cell trafficking into the small intestine in a spontaneous model of chronic ileitis (i.e., SAMP1/YitFc mice). Immunoblockade of peripheral node addressin or mucosal addressin cell adhesion molecule 1 failed to ameliorate ileitis, whereas P-selectin glycoprotein ligand 1 (PSGL-1) neutralization attenuated both the adoptively transferred and spontaneous disease. PSGL-1 was detected in venules of mesenteric lymph node and small intestine by immunohistochemistry and confirmed by real-time reverse transcription polymerase chain reaction and flow cytometry. In addition, reconstitution of wild-type mice with PSGL-1−/− bone marrow demonstrated that PSGL-1 messenger RNA and PSGL-1 protein expression remained on endothelium, localized within mesenteric lymph node and small intestine. Endothelial PSGL-1 bound P-selectin–IgG and its blockade or genetic deletion altered the recruitment of lymphocytes to the small intestine, as revealed by intravital microscopy and homing studies. Endothelial expression of PSGL-1 adds a new dimension to the various cellular interactions involved in small intestinal recruitment. Thus, the multiple roles of PSGL-1 may explain why targeting this single adhesion molecule results in attenuation of chronic murine ileitis, a disease previously resistant to antiadhesion molecule strategies

The grapevine guard cell-related VvMYB60 transcription factor is involved in the regulation of stomatal activity and is differentially expressed in response to ABA and osmotic stress

- Background: Under drought, plants accumulate the signaling hormone abscisic acid (ABA), which induces the rapid closure of stomatal pores to prevent water loss. This event is trigged by a series of signals produced inside guard cells which finally reduce their turgor. Many of these events are tightly regulated at the transcriptional level, including the control exerted by MYB proteins. In a previous study, while identifying the grapevine R2R3 MYB family, two closely related genes, VvMYB30 and VvMYB60 were found with high similarity to AtMYB60, an Arabidopsis guard cell-related drought responsive gene. - Results: Promoter-GUS transcriptional fusion assays showed that expression of VvMYB60 was restricted to stomatal guard cells and was attenuated in response to ABA. Unlike VvMYB30, VvMYB60 was able to complement the loss-of-function atmyb60-1 mutant, indicating that VvMYB60 is the only true ortholog of AtMYB60 in the grape genome. In addition, VvMYB60 was differentially regulated during development of grape organs and in response to ABA and drought-related stress conditions. - Conclusions: These results show that VvMYB60 modulates physiological responses in guard cells, leading to the possibility of engineering stomatal conductance in grapevine, reducing water loss and helping this species to tolerate drought under extreme climatic conditions

Clinical Effects of Gamma-Radiation-Resistant Aspergillus sydowii on Germ-Free Mice Immunologically Prone to Inflammatory Bowel Disease

We report and investigated a case of inadvertent contamination of 125 mice (housed in two germ-free positive-pressurized isolators) with emerging human and coral pathogen Aspergillus sydowii. The infected mice correspond to genetic line SAMP1/YitFc, which have 100% immune predisposition to develop Crohn&apos;s disease-like spontaneous pathologies, namely, inflammatory bowel disease (IBD). Pathogen update based on a scoping review of the literature and our clinical observations and experimentation are discussed. The unwanted infection of germ-free mice (immunologically prone to suffer chronic inflammation) with human pathogen A. sydowii resulted in no overt signs of clinical disease over 3-week exposure period, or during DSS-induced colitis experiments. Results and observations suggest that A. sydowii alone has limited clinical effect in immunocompromised germ-free mice or that other commensal microbial flora is required for Aspergillus-associated disease to occur

Interleukin-1β blockade reduces intestinal inflammation in a murine model of Tumor Necrosis Factor-independent ulcerative colitis

Background &amp; aimsInflammatory bowel diseases (IBDs) are multifactorial diseases commonly treated with either immunomodulatory drugs or anti-tumor necrosis factor (TNF). Currently, failure to respond to anti-TNF therapy (assessed not prior to 8-12 weeks after starting treatment) occurs in 20-40% of patients enrolled in clinical trials and 10-20% in clinical practice. Murine models of IBD provide important tools to better understand disease mechanism(s). In this context and among the numerous models available, Winnie-TNF-KO mice were recently reported to display characteristics of ulcerative colitis (UC) that are independent of TNF, and with increased IL-1β production.MethodsHerein, the efficacy of recombinant (r) IL-1 receptor antagonist (IL-1Ra, Anakinra) administration was evaluated in Winnie-TNF-KO mice, utilized as an UC model of primary anti-TNF non-responders.ResultsWe analyzed gut mucosal biopsies and circulating cytokine profiles of a cohort of 30 UC patients; approximately 75% of primary non-responders were characterized by abundant IL-1β in both the serum and local intestinal tissues. In Winnie-TNF-KO mice, administration of Anakinra efficiently reduced the histological score of the distal colon, which represents the most common site of inflammation in Winnie mice. Furthermore, among lamina propria and mesenteric lymph node-derived T cells, IFNγ-expressing CD8+ T cells were significantly reduced following Anakinra administration.ConclusionsOur study provides new insight and alternative approaches to treat UC patients, and point to anti-IL-1 strategies (i.e., Anakinra) that may be a more effective therapeutic option for primary non-responders to anti-TNF therapy

Genetic Dissection of the Cellular Pathways and Signaling Mechanisms in Modeled Tumor Necrosis Factor–induced Crohn's-like Inflammatory Bowel Disease

Recent clinical evidence demonstrated the importance of tumor necrosis factor (TNF) in the development of Crohn's disease. A mouse model for this pathology has previously been established by engineering defects in the translational control of TNF mRNA (TnfΔAREmouse). Here, we show that development of intestinal pathology in this model depends on Th1-like cytokines such as interleukin 12 and interferon γ and requires the function of CD8+ T lymphocytes. Tissue-specific activation of the mutant TNF allele by Cre/loxP-mediated recombination indicated that either myeloid- or T cell–derived TNF can exhibit full pathogenic capacity. Moreover, reciprocal bone marrow transplantation experiments using TNF receptor–deficient mice revealed that TNF signals are equally pathogenic when directed independently to either bone marrow–derived or tissue stroma cell targets. Interestingly, TNF-mediated intestinal pathology was exacerbated in the absence of MAPKAP kinase 2, yet strongly attenuated in a Cot/Tpl2 or JNK2 kinase–deficient genetic background. Our data establish the existence of redundant cellular pathways operating downstream of TNF in inflammatory bowel disease, and demonstrate the therapeutic potential of selective kinase blockade in TNF-mediated intestinal pathology

Phosphocaveolin-1 enforces tumor growth and chemoresistance in rhabdomyosarcoma

Caveolin-1 (Cav-1) can ambiguously behave as either tumor suppressor or oncogene depending on its phosphorylation state and the type of cancer. In this study we show that Cav-1 was phosphorylated on tyrosine 14 (pCav-1) by Src-kinase family members in various human cell lines and primary mouse cultures of rhabdomyosarcoma (RMS), the most frequent soft-tissue sarcoma affecting childhood. Cav-1 overexpression in the human embryonal RD or alveolar RH30 cells yielded increased pCav-1 levels and reinforced the phosphorylation state of either ERK or AKT kinase, respectively, in turn enhancing in vitro cell proliferation, migration, invasiveness and chemoresistance. In contrast, reducing the pCav-1 levels by administration of a Src-kinase inhibitor or through targeted Cav-1 silencing counteracted the malignant in vitro phenotype of RMS cells. Consistent with these results, xenotransplantation of Cav-1 overexpressing RD cells into nude mice resulted in substantial tumor growth in comparison to control cells. Taken together, these data point to pCav-1 as an important and therapeutically valuable target for overcoming the progression and multidrug resistance of RMS

The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn’s Disease–Like Ileitis

We thank John D. Ward and Lindsey N. Kaydo for their technical support and Dr. Wei Xin for the histological scoring of ileitis severity. ARP is an Assistant Professor of Medicine at CWRU School of Medicine. Metagenomic sequencing was conducted in the laboratory of Dr. Skip Virgin at Washington University, School of Medicine, St. Louis, MO. Raw sequencing data files will be available upon request.Peer reviewedPostprin