Biomedical subjects

Juan C Salazar

Publications and source records attributed to Juan C Salazar.

14 recordsLinked to original sources

PubMed2025

Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.

Most microbiome studies to date rely on sequencing short amplicons of the 16S rRNA gene on Illumina's platforms. Because of the short read length, sequences often can be identified reliably only to the family or genus levels. Long read sequencing with whole-length 16S rRNA sequencing can improve taxonomic resolution, but often only to the species level. StrainID is an alternative approach that amplifies a large segment of the ribosomal operon, including the entire 16S rRNA gene, internal transcribed spacer, and a portion of the 23S rRNA gene. This longer amplicon is designed to allow ribotype-level classification. Although studies have demonstrated the utility of StrainID for several sample types, it has not yet been validated for saliva. Here, we compared the performance of StrainID to short read amplicons with saliva samples as well as a synthetic mock DNA community and human and mouse fecal samples. Short reads were amplified with primer pairs appropriate for the corresponding sample type, and were classified with two different taxonomic databases. For both saliva and fecal samples, we found that StrainID performed similarly to short reads overall and demonstrated a key benefit with phylogenetic-based beta diversity tests and taxonomic classification. Our results further build on establishing StrainID as a valid method and specifically validate its use with saliva samples.

Journal Article↗

PubMed2007

Shared random effects analysis of multi-state Markov models: application to a longitudinal study of transitions to dementia.

Multi-state models are appealing tools for analysing data about the progression of a disease over time. In this paper, we consider a multi-state Markov chain with two competing absorbing states: dementia and death and three transient non-demented states: cognitively normal, amnestic mild cognitive impairment (amnestic MCI), and non-amnestic mild cognitive impairment (non-amnestic MCI). The likelihood function for the data is derived and estimates for the effects of the covariates on transitions are determined when the process can be viewed as a polytomous logistic regression model with shared random effects. The presence of a shared random effect not only complicates the formulation of the likelihood but also its evaluation and maximization. Three approaches for maximizing the likelihood are compared using a simulation study; the first method is based on the Gauss-quadrature technique, the second method is based on importance sampling ideas, and the third method is based on an expansion by Taylor series. The best approach is illustrated using a longitudinal study on a cohort of cognitively normal subjects, followed annually for conversion to mild cognitive impairment (MCI) and/or dementia, conducted at the Sanders Brown Center on Aging at the University of Kentucky.

Aged↗

PubMed2007

Phagocytosis of Borrelia burgdorferi and Treponema pallidum potentiates innate immune activation and induces gamma interferon production.

We examined the interactions of live and lysed spirochetes with innate immune cells. THP-1 monocytoid cells were activated to comparable extents by live Borrelia burgdorferi and by B. burgdorferi and Treponema pallidum lysates but were poorly activated by live T. pallidum. Because THP-1 cells poorly internalized live spirochetes, we turned to an ex vivo peripheral blood mononuclear cell system that would more closely reflect spirochete-mononuclear phagocyte interactions that occur during actual infection. In this system, B. burgdorferi induced significantly greater monocyte activation and inflammatory cytokine production than did borrelial lysates or T. pallidum, and only B. burgdorferi elicited gamma interferon (IFN-gamma) from NK cells. B. burgdorferi was phagocytosed avidly by monocytes, while T. pallidum was not, suggesting that the enhanced response to live B. burgdorferi was due to phagocytosis of the organism. When cytochalasin D was used to block phagocytosis of live B. burgdorferi, cytokine production decreased to levels comparable to those induced by B. burgdorferi lysates, while the IFN-gamma response was abrogated altogether. In the presence of human syphilitic serum, T. pallidum was efficiently internalized and initiated responses resembling those observed with live B. burgdorferi, including the production of IFN-gamma by NK cells. Depletion of monocytes revealed that they were the primary source of inflammatory cytokines, while dendritic cells (DCs) directed IFN-gamma production from innate lymphocytes. Thus, phagocytosis of live spirochetes initiates cell activation programs in monocytes and DCs that differ qualitatively and quantitatively from those induced at the cell surface by lipoprotein-enriched lysates. The greater stimulatory capacity of B. burgdorferi versus T. pallidum appears to be explained by the successful recognition and phagocytosis of B. burgdorferi by host cells and the ability of T. pallidum to avoid detection and uptake by virtue of its denuded outer membrane rather than by differences in surface lipoprotein expression.

Borrelia burgdorferi↗

PubMed2006

Clostridium septicum infections in children: a case report and review of the literature.

Clostridium myonecrosis is a rare and deadly infection that progresses very rapidly; thus, prompt diagnosis and treatment is vital. In adults, clostridial myonecrosis used to be a well-known complication of war wounds. Today, it is usually seen in settings of trauma, surgery, malignancy, skin infections/burns, and septic abortions. More recently, cases of nontraumatic or spontaneous clostridial myonecrosis have been reported in both adults and children. Clostridium perfringens and Clostridium septicum are responsible for the majority of the clinically relevant infections. Higher mortality rates are seen when C septicum is the causative agent. Here we present a child who survived a severe case of C septicum myonecrosis involving both abdominal and thoracic cavities. This rare infection has a high mortality rate and might be easily misdiagnosed in children, even by experienced clinicians, because of its nonspecific presentation. We also review all reported pediatric cases of C septicum infection and myonecrosis and discuss the surgical and medical interventions associated with improved survival. We identified a total of 47 cases of C septicum infection; of these, 22 (47%) were cases of C septicum associated with myonecrosis. Several factors, if available, were analyzed for each case: age, gender, infection location, previous diagnoses, presenting signs and symptoms, neutropenia, gross pathology of the colon, antibiotic use, surgical intervention, and final outcome. We found that conditions related with C septicum infection in children can be grouped into 3 major categories: patients with neutrophil dysfunction; patients with associated bowel ischemia; and patients with a history of trauma. Malignancies were found in 49% of the cases, cyclic or congenital neutropenia in 21%, hemolytic-uremic syndrome in 11%, structural bowel ischemia in 4%, and local extremity trauma in 6%. In addition, 6% of the cases had no known underlying disorder. Abdominal symptoms including vomiting, diarrhea, blood per rectum, abdominal pain, anorexia, and/or acute abdomen, were reported in 85% of the children. Fever was also a common finding. The mainstay of treatment for C septicum infection was parenteral antibiotics and/or surgical intervention. The mortality rate for children with C septicum infection and myonecrosis was 57% and 59%, respectively. Although 82% of all cases received antibiotics, only 43% underwent therapeutic surgical intervention. Several clinical factors were found to be associated with improved survival. Only 35% of the children with gastrointestinal tract involvement survived, compared with 86% of the children without gastrointestinal tract involvement. The survival rates for other conditions ranged from 0% to 50%. One hundred percent survival was reported in patients with no previously diagnosed conditions and those with infections resulting from trauma to the extremities. All survivors received antibiotic treatment, compared with only 68% of the nonsurvivors. Most survivors (84%) underwent therapeutic surgical intervention, compared with only 12% of nonsurvivors. Other treatments were used adjunctively, including hyperbaric oxygen, granulocyte colony-stimulating factor, granulocyte transfusions, and intravenous immunoglobulin. C septicum infections in children are often fatal; thus, one needs to have a high index of suspicion in at-risk patients. This review describes who these patients are, their clinical presentation, and the therapeutic strategies associated with improved survival.

Abdomen↗

PubMed2006

Long-term cognitive impact of anticholinergic medications in older adults.

OBJECTIVE: The objective of this study was to determine whether chronic use of medications with anticholinergic (AC) properties impact older adults' cognitive functioning. METHODS: Six years of cognitive test data from two groups of older adults (AC and control) were examined retrospectively (N = 592). RESULTS: Declines over time were found for the AC group on parts A and B of the Trail Making Test. CONCLUSION: Physicians prescribing ACs to older adult patients should be aware of their potential effects on psychomotor speed and executive functioning. These cognitive effects may lead to impairments in daily functioning resulting in the need to reevaluate patient medications.

Aged↗

PubMed2005

Lipoprotein-dependent and -independent immune responses to spirochetal infection.

In this study, we used the epidermal suction blister technique, in conjunction with multiparameter flow cytometry, to analyze the cellular and cytokine responses elicited by intradermal injection of human volunteers with synthetic analogs for spirochetal lipoproteins and compared the responses to findings previously reported from patients with erythema migrans (EM). Compared with peripheral blood (PB), lipopeptides derived from the N termini of the Borrelia burgdorferi outer surface protein C and the 17-kDa lipoprotein of Treponema pallidum (OspC-L and 17-L, respectively) elicited infiltrates enriched in monocytes/macrophages and dendritic cells (DCs) but also containing substantial percentages of neutrophils and T cells. Monocytoid (CD11c(+)) and plasmacytoid (CD11c(-)) DCs were selectively recruited to the skin in ratios similar to those in PB, but only the former expressed the activation/maturation surface markers CD80, CD83, and DC-SIGN. Monocytes/macrophages and monocytoid DCs, but not plasmacytoid DCs, displayed significant increases in surface expression of Toll-like receptor 1 (TLR1), TLR2, and TLR4. Staining for CD45RO and CD27 revealed that lipopeptides preferentially recruited antigen-experienced T-cell subsets; despite their lack of antigenicity, these agonists induced marked T-cell activation, as evidenced by surface expression of CD69, CD25, and CD71. Lipopeptides also induced significant increases in interleukin 12 (IL-12), IL-10, gamma interferon, and most notably IL-6 without corresponding increases in serum levels of these cytokines. Although lipopeptides and EM lesional infiltrates shared many similarities, differences were noted in a number of immunologic parameters. These studies have provided in situ evidence for a prominent "lipoprotein effect" during human infection while at the same time helping to pinpoint aspects of the cutaneous response that are uniquely driven by spirochetal pathogens.

Adolescent↗

PubMed2004

A truncated aminoacyl-tRNA synthetase modifies RNA.

Aminoacyl-tRNA synthetases are modular enzymes composed of a central active site domain to which additional functional domains were appended in the course of evolution. Analysis of bacterial genome sequences revealed the presence of many shorter aminoacyl-tRNA synthetase paralogs. Here we report the characterization of a well conserved glutamyl-tRNA synthetase (GluRS) paralog (YadB in Escherichia coli) that is present in the genomes of >40 species of proteobacteria, cyanobacteria, and actinobacteria. The E. coli yadB gene encodes a truncated GluRS that lacks the C-terminal third of the protein and, consequently, the anticodon binding domain. Generation of a yadB disruption showed the gene to be dispensable for E. coli growth in rich and minimal media. Unlike GluRS, the YadB protein was able to activate glutamate in presence of ATP in a tRNA-independent fashion and to transfer glutamate onto tRNA(Asp). Neither tRNA(Glu) nor tRNA(Gln) were substrates. In contrast to canonical aminoacyl-tRNA, glutamate was not esterified to the 3'-terminal adenosine of tRNA(Asp). Instead, it was attached to the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of queuosine, the modified nucleoside occupying the first anticodon position of tRNA(Asp). Glutamyl-queuosine, like canonical Glu-tRNA, was hydrolyzed by mild alkaline treatment. Analysis of tRNA isolated under acidic conditions showed that this novel modification is present in normal E. coli tRNA; presumably it previously escaped detection as the standard conditions of tRNA isolation include an alkaline deacylation step that also causes hydrolysis of glutamyl-queuosine. Thus, this aminoacyl-tRNA synthetase fragment contributes to standard nucleotide modification of tRNA.

Adenosine↗

PubMed2004

Adherence to antiretroviral therapy in HIV-infected pediatric patients improves with home-based intensive nursing intervention.

Adherence to combination antiretroviral therapy (ART) has been shown to be a determining factor in controlling viral replication, maintaining immunologic function and long-term survival in HIV-positive individuals. Little information is available on strategies to improve adherence in pediatric HIV-infected patients. We conducted a randomized, nonblinded, pilot study to determine if a home-based nursing intervention would improve medication adherence. The study was offered to all eligible HIV-positive patients receiving care at Connecticut Children's Medical Center's (CCMC) Pediatric and Youth HIV Program. Sixty-seven percent (37/55) of the patients and their caretakers participated. We randomized participants to either standard of care or the intervention trial. The intervention was designed to improve knowledge and understanding of HIV infection and HIV medications and to resolve or modify barriers to adherence. Both groups completed pre- and post-intervention questionnaires, assessing their knowledge and understanding of HIV, ART, and adherence. Adherence was estimated objectively from medication refill history and subjectively from a self-report score. We also inferred adherence from pre- to post-test plasma viral load and CD4+ T-cell percentages. The knowledge score (p = 0.02) and medication refill history (p = 0.002) improved significantly in the intervention group. The adherence self-report score improved, although not significantly (p = 0.07). We did not observe statistical differences in CD4+ T-cell counts or viral load between groups. We conclude that our home-based nursing intervention helped HIV-positive children and their families in better adhering to prescribed medication regimens.

Adolescent↗

PubMed2003

Coevolution of an aminoacyl-tRNA synthetase with its tRNA substrates.

Glutamyl-tRNA synthetases (GluRSs) occur in two types, the discriminating and the nondiscriminating enzymes. They differ in their choice of substrates and use either tRNAGlu or both tRNAGlu and tRNAGln. Although most organisms encode only one GluRS, a number of bacteria encode two different GluRS proteins; yet, the tRNA specificity of these enzymes and the reason for such gene duplications are unknown. A database search revealed duplicated GluRS genes in >20 bacterial species, suggesting that this phenomenon is not unusual in the bacterial domain. To determine the tRNA preferences of GluRS, we chose the duplicated enzyme sets from Helicobacter pylori and Acidithiobacillus ferrooxidans. H. pylori contains one tRNAGlu and one tRNAGln species, whereas A. ferrooxidans possesses two of each. We show that the duplicated GluRS proteins are enzyme pairs with complementary tRNA specificities. The H. pylori GluRS1 acylated only tRNAGlu, whereas GluRS2 was specific solely for tRNAGln. The A. ferrooxidans GluRS2 preferentially charged tRNA(UUG)(Gln). Conversely, A. ferrooxidans GluRS1 glutamylated both tRNAGlu isoacceptors and the tRNA(CUG)(Gln) species. These three tRNA species have two structural elements in common, the augmented D-helix and a deletion of nucleotide 47. It appears that the discriminating or nondiscriminating natures of different GluRS enzymes have been derived by the coevolution of protein and tRNA structure. The coexistence of the two GluRS enzymes in one organism may lay the groundwork for the acquisition of the canonical glutaminyl-tRNA synthetase by lateral gene transfer from eukaryotes.

Acidithiobacillus↗

PubMed2003

Coevolution of markers of innate and adaptive immunity in skin and peripheral blood of patients with erythema migrans.

We used multiparameter flow cytometry to characterize leukocyte immunophenotypes and cytokines in skin and peripheral blood of patients with erythema migrans (EM). Dermal leukocytes and cytokines were assessed in fluids aspirated from epidermal suction blisters raised over EM lesions and skin of uninfected controls. Compared with corresponding peripheral blood, EM infiltrates were enriched for T cells, monocytes/macrophages, and dendritic cells (DCs), contained lower proportions of neutrophils, and were virtually devoid of B cells. Enhanced expression of CD14 and HLA-DR by lesional neutrophils and macrophages indicated that these innate effector cells were highly activated. Staining for CD45RO and CD27 revealed that lesional T lymphocytes were predominantly Ag-experienced cells; furthermore, a subset of circulating T cells also appeared to be neosensitized. Lesional DC subsets, CD11c(+) (monocytoid) and CD11c(-) (plasmacytoid), expressed activation/maturation surface markers. Patients with multiple EM lesions had greater symptom scores and higher serum levels of IFN-alpha, TNF-alpha, and IL-2 than patients with solitary EM. IL-6 and IFN-gamma were the predominant cytokines in EM lesions; however, greater levels of both mediators were detected in blister fluids from patients with isolated EM. Circulating monocytes displayed significant increases in surface expression of Toll-like receptor (TLR)1 and TLR2, while CD11c(+) DCs showed increased expression of TLR2 and TLR4; lesional macrophages and CD11c(+) and CD11c(-) DCs exhibited increases in expression of all three TLRs. These results demonstrate that Borrelia burgdorferi triggers innate and adaptive responses during early Lyme disease and emphasize the interdependence of these two arms of the immune response in the efforts of the host to contain spirochetal infection.

Adult↗

PubMed2003

HACEK endocarditis in infants and children: two cases and a literature review.

We report 2 cases of Haemophilus parainfluenzae endocarditis and review 34 cases of HACEK endocarditis from the literature. HACEK organisms are the most common cause of Gram-negative endocarditis in children. They have a propensity to form friable vegetations (especially H. parainfluenzae) that break off and cause symptomatic emboli. HACEK endocarditis (from a review of the 36 published cases) may involve previously normal hearts (33%), may be complicated by embolization (31%) and may require vegetectomy or other surgery (31%). Mortality with HACEK endocarditis was 14%. HACEK organisms may be resistant to penicillins but are susceptible to third generation cephalosporins.

Ceftriaxone↗

PubMed2003

Pediatric clinical trial experience: government, child, parent and physician's perspective.

In contrast to investigations in adults, investigation of drugs via clinical trials has been lacking in the pediatric population. Until recently there was little incentive on the part of the pharmaceutical industry to conduct clinical trials of new drugs in children. However, government legislation approved in the late 1990s has promoted efforts to investigate the effects of drugs in the treatment of a variety of children's diseases. Such data provide important and needed information on appropriate dosing, rates and types of adverse reactions and efficacy for treatment of pediatric illnesses. The conduct of clinical trials in children is dependent on a careful dialogue between the investigator, child and guardians wherein a detailed description of benefits vs. risks is conveyed. The focus of this paper is to summarize various perspectives on conducting clinical trials in children, including those of the government, the child, the parents or guardians and the investigator. Although children now have access to new medicines during the development process, their participation in clinical trials must still protect them from undue risk and secure their well being.

Child↗

PubMed2002

The immune response to infection with Treponema pallidum, the stealth pathogen.

Cutaneous immunobiology and spirochetal molecular biology have allowed investigators to propose a conceptual framework for the development of both the innate and adaptive immune response to Treponema pallidum infection. While some clinical manifestations can be attributed to humoral responses, most can be attributed to a combination of local innate and adaptive cellular immunity.

Antibody Formation↗

PubMed2002

Streptococcus pyogenes pyomyositis.

Group A beta-hemolytic Streptococcus pyomyositis continues to be an uncommon disease. We present a case of a 7-year-old boy with an M protein type 1, streptococcal pyrogenic exotoxin A and B, Streptococcus pyogenes pyomyositis and streptococcal toxic shock syndrome.

Antibodies↗