Alex Palacios - Academia.edu (original) (raw)

Papers by Alex Palacios

The Journal of Immunology

Intestinal CD4+ T helper (TH) cells are subject to extensive regulation by microbiota. By contras... more Intestinal CD4+ T helper (TH) cells are subject to extensive regulation by microbiota. By contrast, it is not known whether or how TH cells interface with other, host-derived intestinal metabolites. Here we show that bile acids directly regulate mucosal TH cell function in the distal small intestine (i.e., ileum) via the xenobiotic transporter, Mdr1. Using both Mdr1-dependent dye efflux and a novel CRISPR-generated Mdr1 reporter mouse, we show that wild type RORγt+IL-17A+ (Th17) and RORγt-IFNγ+ (Th1) cells upregulate Mdr1 expression upon migration into the ileum. By contrast, germline ablation or shRNAmir-mediated knockdown of Mdr1 in Th17 and Th1 cells results in local dysfunction in the ileum, and these cells transfer Crohn’s disease-like ileitis in Rag1−/− hosts. Mdr1 enforces Th17 and Th1 cell survival and limits pro-inflammatory cytokine (TNFα, IFNγ) expression in the presence of conjugated bile acids (CBAs), which are actively reabsorbed through the ileal mucosa as a function ...

Gut Microbes, 2022

ABSTRACT Parabacteroides distasonis (Pdis) is the type species for the new Parabacteroides genus,... more ABSTRACT Parabacteroides distasonis (Pdis) is the type species for the new Parabacteroides genus, and a gut commensal of the Bacteroidetes phylum. Emerging reports (primarily based on reference strain/ATCC-8503) concerningly propose that long-known opportunistic pathogen Pdis is a probiotic. We posit there is an urgent need to characterize the pathogenicity of Pdis strain-strain variability. Unfortunately, no methods/insights exist to classify Bacteroidetes for this purpose. Herein, we developed a virulence gene-based classification system for Pdis and Bacteroidetes to facilitate pathogenic-vs-probiotic characterization. We used DNA in silico methods to develop a system based on the virulence (lipopolysaccharide/bacterial wall) ‘rfbA O-antigen-synthesis gene’. We then performed phylogenetic analysis of rfbA from fourteen Pdis complete genomes (21 genes), other Parabacteroides, Bacteroidetes, and Enterobacteriaceae; and proposed a PCR-based Restriction-Fragment Length Polymorphism method. Cluster analysis revealed that Pdis can be classified into four lineages (based on gene gaps/insertions) which we designated rfbA-Types I, II, III, and IV. In context, we found 14 additional rfbA-types (I–XVIII) interspersed with numerous Bacteroidetes and pathogenic Enterobacteriaceae forming three major “rfbA-superclusters.” For laboratory rfbA-Typing implementation, we developed a PCR-primer strategy to amplify Pdis rfbA genes (100%-specificity) to conduct MboII-RFLP and sub-classify Pdis. In-silico primers for other Bacteroidetes are proposed/discussed. Comparative analysis of lipopolysaccharide/lipid-A gene lpxK confirmed rfbA as highly discriminant. In conclusion, rfbA-Typing classifies Bacteroidetes/Pdis into unique clusters/superclusters given rfbA copy/sequence variability. Analysis revealed that most pathogenic Pdis strains are single-copy rfbA-Type I . The relevance of the rfbA strain variability in disease might depend on their hypothetical modulatory interactions with other O-antigens/lipopolysaccharides and TLR4 lipopolysaccharide-receptors in human/animal cells.

Door Signs ready for printing to motivate the wearing of face covers / cloth facemasks in public ... more Door Signs ready for printing to motivate the wearing of face covers / cloth facemasks in public to help control of dissemination of respiratory droplets and environmental contamination.<br>Oral and respiratory droplets, which may carry respiratory pathogens, including COVID-19, are always produced as we talk, cough, or sneeze.________________________________Current health guidelines suggest the use of cloth masks. Unfortunately, their use in public is not widely adopted.A great choice to help motivate the use of face covers, now and in future pandemics, could be the voluntary and synchronized use of door signs which may serve as gentle reminders to promote droplet public safety among the public, in both public and private locales. Because a 'scarf' is not a mask, but could serve for 'droplet control', it is advisable to use more inclusive expressions or terms, such as Facecovers, to improve their adoption and increase the cleanliness of our environment. To avo...

Free Radical Biology and Medicine, 2021

Reactive oxygen species play a major role in the induction of programmed cell death and numerous ... more Reactive oxygen species play a major role in the induction of programmed cell death and numerous diseases. Production of reactive oxygen species is ubiquitous in biological systems such as humans, bacteria, fungi/yeasts, and plants. Although reactive oxygen species are known to cause diseases, little is known about the importance of the combined oxidative stress burden in the gut. Understanding the dynamics and the level of oxidative stress 'reactivity' across kingdoms could help ascertain the combined consequences of free radical accumulation in the gut lumen. Here, we present fundamental similarities of oxidative stress derived from the host immune cells, bacteria, yeasts, plants, and the therein-derived diets, which often accentuate the burden of free radicals by accumulation during storage and cooking conditions. Given the described similarities, oxidative stress could be better understood and minimized by monitoring the levels of oxidative stress in the feces to identify pro-inflammatory factors. However, we illustrate that dietary studies rarely monitor oxidative stress markers in the feces, and therefore our knowledge on fecal oxidative stress monitoring is limited. A more holistic approach to understanding oxidative stress 'reactivity' in the gut could help improve strategies to use diet and microbiota to prevent intestinal diseases.

bioRxiv, 2020

Bile acids (BAs) are fundamental lipid emulsifying metabolites synthesized in hepatocytes and mai... more Bile acids (BAs) are fundamental lipid emulsifying metabolites synthesized in hepatocytes and maintained in vivo through enterohepatic circulation between the liver and small intestine1. As detergents, BAs can cause toxicity and inflammation in enterohepatic tissues2, and several nuclear receptors have evolved to detoxify BAs in hepatocytes and enterocytes3. By contrast, it is unclear how mucosal immune cells protect themselves from high BA concentrations in the small intestine. We previously reported that CD4+ T effector (Teff) cells upregulate expression of the xenobiotic transporter MDR1 in the ileum to prevent BA toxicity and suppress Crohn’s disease-like small bowel inflammation4. Here, we identify the nuclear xenobiotic receptor, constitutive androstane receptor (CAR/NR1I3), as a transcriptional regulator of MDR1 expression in mucosal T cells. CAR promoted large-scale transcriptional reprogramming in Teff cells infiltrating the small intestine lamina propria (siLP), but not th...

Frontiers in Immunology, 2021

With the epidemic of human obesity, dietary fats have increasingly become a focal point of biomed... more With the epidemic of human obesity, dietary fats have increasingly become a focal point of biomedical research. Epidemiological studies indicate that high-fat diets (HFDs), especially those rich in long-chain saturated fatty acids (e.g., Western Diet, National Health Examination survey; NHANES ‘What We Eat in America’ report) have multi-organ pro-inflammatory effects. Experimental studies have confirmed some of these disease associations, and have begun to elaborate mechanisms of disease induction. However, many of the observed effects from epidemiological studies appear to be an over-simplification of the mechanistic complexity that depends on dynamic interactions between the host, the particular fatty acid, and the rather personalized genetics and variability of the gut microbiota. Of interest, experimental studies have shown that certain saturated fats (e.g., lauric and myristic fatty acid-rich coconut oil) could exert the opposite effect; that is, desirable anti-inflammatory and...

Frontiers in Immunology, 2020

Alistipes is a relatively new genus of bacteria isolated primarily from medical clinical samples,... more Alistipes is a relatively new genus of bacteria isolated primarily from medical clinical samples, although at a low rate compared to other genus members of the Bacteroidetes phylum, which are highly relevant in dysbiosis and disease. According to the taxonomy database at The National Center for Biotechnology Information, the genus consists of 13 species: Alistipes finegoldii, Alistipes putredinis, Alistipes onderdonkii, Alistipes shahii, Alistipes indistinctus, Alistipes senegalensis, Alistipes timonensis, Alistipes obesi, Alistipes ihumii, Alistipes inops, Alistipes megaguti, Alistipes provencensis, and Alistipes massiliensis. Alistipes communis and A. dispar, and the subspecies A. Onderdonkii subspecies vulgaris (vs. onderdonkii subsp.) are the newest strains featured outside that list. Although typically isolated from the human gut microbiome various species of this genus have been isolated from patients suffering from appendicitis, and abdominal and rectal abscess. It is possible that as Alistipes spp. emerge, their identification in clinical samples may be underrepresented as novel MS-TOF methods may not be fully capable to discriminate distinct species as separate since it will require the upgrading of MS-TOF identification databases. In terms of pathogenicity, there is contrasting evidence indicating that Alistipes may have protective effects against some diseases, including liver fibrosis, colitis, cancer immunotherapy, and cardiovascular disease. In contrast, other studies indicate Alistipes is pathogenic in colorectal cancer and is associated with mental signs of depression. Gut dysbiosis seems to play a role in determining the compositional abundance of Alistipes in the feces (e.g., in non-alcoholic steatohepatitis, hepatic encephalopathy, and liver fibrosis). Since Alistipes is a relatively recent sub-branch genus of the Bacteroidetes phylum, and since Bacteroidetes are commonly associated with chronic intestinal inflammation, this narrative review illustrates emerging immunological and mechanistic implications by which Alistipes spp. correlate with human health.

Frontiers in Medicine, 2020

The main form of COVID-19 transmission is via "oral-respiratory droplet contamination" (droplet: ... more The main form of COVID-19 transmission is via "oral-respiratory droplet contamination" (droplet: very small drop of liquid) produced when individuals talk, sneeze, or cough. In hospitals, health-care workers wear facemasks as a minimum medical "droplet precaution" to protect themselves. Due to the shortage of masks during the pandemic, priority is given to hospitals for their distribution. As a result, the availability/use of medical masks is discouraged for the public. However, for asymptomatic individuals, not wearing masks in public could easily cause the spread of COVID-19. The prevention of "environmental droplet contamination" (EnvDC) from coughing/sneezing/speech is fundamental to reducing transmission. As an immediate solution to promote "public droplet safety," we assessed household textiles to quantify their potential as effective environmental droplet barriers (EDBs). The synchronized implementation of a universal "community droplet reduction solution" is discussed as a model against COVID-19. Using a bacterial-suspension spray simulation model of droplet ejection (mimicking a sneeze), we quantified the extent by which widely available clothing fabrics reduce the dispersion of droplets onto surfaces within 1.8 m, the minimum distance recommended for COVID-19 "social distancing." All textiles reduced the number of droplets reaching surfaces, restricting their dispersion to <30 cm, when used as single layers. When used as double-layers, textiles were as effective as medical mask/surgical-cloth materials, reducing droplet dispersion to <10 cm, and the area of circumferential contamination to ∼0.3%. The synchronized implementation of EDBs as a "community droplet reduction solution" (i.e., face covers/scarfs/masks and surface covers) will reduce COVID-19 EnvDC and thus the risk of transmitting/acquiring COVID-19.

ABSTRACTDue to the shortage of masks during the pandemic, we recently demonstrated that household... more ABSTRACTDue to the shortage of masks during the pandemic, we recently demonstrated that household textiles are effective environmental droplet barriers (EDBs) with identical droplet retention potential as medical masks. To further promote the implementation of a universal community droplet reduction solution based on a synchronized encouragement/enforcement of mask utilization by the public based on widely available textiles (mask fabrication without the need for sewing machines), here we conducted a study using germ-free mice to determine to what extent textiles were effective in vivo. Using a bacterial-suspension spray simulation model of droplet ejection (mimicking a sneeze), we quantified the extent by which 100% cotton textile prevented the contamination of germ-free animals on the other side of the textile-barrier (simulating a properly worn mask). Of relevance, all mice protected with textiles remained germ-free after two sprays (inoculation dose: >600 bacterial droplet un...

Inflammatory Bowel Diseases, 2018

Background: TNF-like cytokine 1A (TL1A) and its functional receptor, death-domain-receptor-3 (DR3... more Background: TNF-like cytokine 1A (TL1A) and its functional receptor, death-domain-receptor-3 (DR3), are multifunctional mediators of effector and regulatory immunity. We aimed to evaluate the functional role and therapeutic potential of TL1A/DR3 signaling in Crohn's disease-like ileitis. Methods: Ileitis-prone SAMP1/YitFc (SAMP) and TNF ΔARE/+ mice were rendered deficient for DR3 or TL1A by microsatellite marker-assisted backcrossing. Pathological and immunological characteristics were compared between control and knockout mice, and mucosal immunophenotype was analyzed by Nanostring microarray assay. The therapeutic effect of pharmacological TL1A neutralization was also investigated. Results: DR3 deficiency was associated with restoration of a homeostatic mucosal immunostat in SAMP mice through the regulation of several pro-and anti-inflammatory genes. This led to suppression of effector immunity, amelioration of ileitis severity, and compromised ability of either unfractionated CD4 + or CD4 + CD45RB hi mucosal lymphocytes to transfer ileitis to severe combined immunodeficient mice recipients. TNF-driven ileitis was also prevented in TNF ΔARE/+ xDR3-/mice, in association with decreased expression of the pro-inflammatory cytokines TNF and IFN-γ. In contrast to DR3, TL1A was dispensable for the development of ileitis although it affected the kinetics of inflammation, as TNF ΔARE/+ xTL1A-/demonstrated delayed onset of inflammation, whereas administration of a neutralizing, anti-TL1A antibody ameliorated early but not late TNFΔARE/+ ileitis. Conclusion: We found a prominent pro-inflammatory role of DR3 in chronic ileitis, which is only partially mediated via interaction with TL1A, raising the possibility for additional DR3 ligands. Death-domain-receptor-3 appears to be a master regulator of mucosal homeostasis and inflammation and may represent a candidate therapeutic target for chronic inflammatory conditions of the bowel.

Frontiers in Immunology, 2016

Numerous reviews have discussed gut microbiota composition changes during inflammatory bowel dise... more Numerous reviews have discussed gut microbiota composition changes during inflammatory bowel diseases (IBD), particularly Crohn's disease (CD). However, most studies address the observed effects by focusing on studying the univariate connection between disease and dietary-induced alterations to gut microbiota composition. The possibility that these effects may reflect a number of other interconnected (i.e., pantropic) mechanisms, activated in parallel, particularly concerning various bacterial metabolites, is in the process of being elucidated. Progress seems, however, hampered by various difficult-to-study factors interacting at the mucosal level. Here, we highlight some of such factors that merit consideration, namely: (1) the contribution of host genetics and diet in altering gut microbiome, and in turn, the crosstalk among secondary metabolic pathways; (2) the interdependence between the amount of dietary fat, the fatty acid composition, the effects of timing and route of administration on gut microbiota community, and the impact of microbiota-derived fatty acids; (3) the effect of diet on bile acid composition, and the modulator role of bile acids on the gut microbiota; (4) the impact of endogenous and exogenous intestinal micronutrients and metabolites; and (5) the need to consider food associated toxins and chemicals, which can introduce confounding immune modulating elements (e.g., antioxidant and phytochemicals in oils and proteins). These concepts, which are not mutually exclusive, are herein illustrated paying special emphasis on physiologically interrelated processes.

The American journal of pathology, Jan 20, 2016

Although a clear association has been established between IL-33 and inflammatory bowel disease, m... more Although a clear association has been established between IL-33 and inflammatory bowel disease, mechanistic studies to date, primarily using acute murine models of colitis, have yielded contradicting results, demonstrating both pathogenic and protective roles. We used a well-characterized, spontaneous model of inflammatory bowel disease [ie, SAMP1/YitFc (SAMP) mice] to investigate the role of IL-33 during chronic intestinal inflammation. Our results showed marked eosinophil infiltration into the gut mucosa with increased levels of eotaxins and type 2 helper T-cell (Th2) cytokines as disease progressed and became more severe, which could be reversed on either eosinophil depletion or blockade of IL-33 signaling. Exogenous IL-33 administration recapitulated these effects in ilea of uninflamed (parental) control AKR/J mice. Human data supported these findings, showing colocalization and up-regulation of IL-33 and eosinophil in the colonic mucosa of inflammatory bowel disease patients ve...

Nature communications, Jan 8, 2015

Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory... more Histology is fundamental to assess two-dimensional intestinal inflammation; however, inflammatory bowel diseases (IBDs) are often indistinguishable microscopically on the basis of mucosal biopsies. Here, we use stereomicroscopy (SM) to rapidly profile the entire intestinal topography and assess inflammation. We examine the mucosal surface of >700 mice (encompassing >16 strains and various IBD-models), create a profiling catalogue of 3D-stereomicroscopic abnormalities and demonstrate that mice with comparable histological scores display unique sub-clusters of 3D-structure-patterns of IBD pathology, which we call 3D-stereoenterotypes, and which are otherwise indiscernible histologically. We show that two ileal IBD-stereoenterotypes ('cobblestones' versus 'villous mini-aggregation') cluster separately within two distinct mouse lines of spontaneous ileitis, suggesting that host genetics drive unique and divergent inflammatory 3D-structural patterns in the gut. In h...

Journal of Pathogens, 2014

We (i) determined the prevalence ofClostridium difficileand their antimicrobial resistance to six... more We (i) determined the prevalence ofClostridium difficileand their antimicrobial resistance to six antimicrobial classes, in a variety of fresh vegetables sold in retail in Ohio, USA, and (ii) conducted cumulative meta-analysis of reported prevalence in vegetables since the 1990s. Six antimicrobial classes were tested for their relevance as risk factors forC. difficileinfections (CDIs) (clindamycin, moxifloxacin) or their clinical priority as exhaustive therapeutic options (metronidazole, vancomycin, linezolid, and tigecycline). By using an enrichment protocol we isolatedC. difficilefrom three of 125 vegetable products (2.4%). All isolates were toxigenic, and originated from 4.6% of 65 vegetables cultivated above the ground (n=3; outer leaves of iceberg lettuce, green pepper, and eggplant). Root vegetables yielded noC. difficile. TheC. difficileisolates belonged to two PCR ribotypes, one with an unusual antimicrobial resistance for moxifloxacin and clindamycin (lettuce and pepper; 02...

Veterinary Microbiology, 2007

Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on ... more Elsevier has created a COVID-19 resource centre with free information in English and Mandarin on the novel coronavirus COVID-19. The COVID-19 resource centre is hosted on Elsevier Connect, the company's public news and information website. Elsevier hereby grants permission to make all its COVID-19-related research that is available on the COVID-19 resource centre-including this research content-immediately available in PubMed Central and other publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active.

Animal Health Research Reviews, 2013

Many articles have summarized the changing epidemiology ofClostridium difficileinfections (CDI) i... more Many articles have summarized the changing epidemiology ofClostridium difficileinfections (CDI) in humans, but the emerging presence ofC. difficilein foods and animals and possible measures to reduce human exposure to this important pathogen have been infrequently addressed. CDIs have traditionally been assumed to be restricted to health-care settings. However, recent molecular studies indicate that this is no longer the case; animals and foods might be involved in the changing epidemiology of CDIs in humans; and genome sequencing is disproving person-to-person transmission in hospitals. Although zoonotic and foodborne transmission have not been confirmed, it is evident that susceptible people can be inadvertently exposed toC. difficilefrom foods, animals, or their environment. Strains of epidemic clones present in humans are common in companion and food animals, raw meats, poultry products, vegetables, and ready-to-eat foods, including salads. In order to develop science-based prev...

Journal of Visualized Experiments, 2013

Journal of Veterinary Medical Science, 2014

A real-time PCR for detection and quantification of M. ovipneumoniae was developed using 9 recent... more A real-time PCR for detection and quantification of M. ovipneumoniae was developed using 9 recently sequenced M. ovipneumoniae genomes and primers targeting a putative adhesin gene p113. The assay proved to be specific and sensitive (with a detection limit of 22 genomic DNA) and could quantify M. ovipneumoniae DNA over a wide linear range, from 2.2 × 10 2 to 2.2 × 10 7 genomes.