Fungal load quantification is a critical component of fungal community analyses. Limitation of current approaches for quantifying the fungal component in the human microbiome suggests the need for ...new broad-coverage techniques.
We analyzed 2,085 18S rRNA gene sequences from the SILVA database for assay design. We generated and quantified plasmid standards using a qPCR-based approach. We evaluated assay coverage against 4,968 sequences and performed assay validation following the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines.
We designed FungiQuant, a TaqMan® qPCR assay targeting a 351 bp region in the fungal 18S rRNA gene. Our in silico analysis showed that FungiQuant is a perfect sequence match to 90.0% of the 2,617 fungal species analyzed. We showed that FungiQuant's is 100% sensitive and its amplification efficiencies ranged from 76.3% to 114.5%, with r(2)-values of >0.99 against the 69 fungal species tested. Additionally, FungiQuant inter- and intra-run coefficients of variance ranged from <10% and <20%, respectively. We further showed that FungiQuant has a limit of quantification 25 copies and a limit of detection at 5 copies. Lastly, by comparing results from human-only background DNA with low-level fungal DNA, we showed that amplification in two or three of a FungiQuant performed in triplicate is statistically significant for true positive fungal detection.
FungiQuant has comprehensive coverage against diverse fungi and is a robust quantification and detection tool for delineating between true fungal detection and non-target human DNA.
Sugammadex binds progesterone with high affinity and may interfere with hormonal contraceptive effectiveness. The clinical, economical, and ethical implications of unintended pregnancy should prompt ...anesthesiologists to actively consider and manage this pharmacologic interaction. We surveyed anesthesiology providers at our institution about knowledge of this potential adverse drug interaction, how they manage it clinically, and the extent to which they involve patients in shared decision-making regarding choice of neuromuscular blocker antagonist.
A survey instrument was distributed to anesthesiology providers at a large, tertiary-care medical center. The survey explored prior experience using neostigmine and sugammadex, knowledge about potential sugammadex interference with hormonal contraception, pre-/postoperative counseling practices, clinical management, and shared decision-making regarding potential use of neostigmine in lieu of sugammadex to avoid this drug-drug interaction.
Of 259 surveys distributed, 155 were fully completed, and 10 were partially completed. Overall response rate was 60% (residents 85%, student nurse anesthetists 53%, certified registered nurse anesthetists 58%, attendings 48%). All but 1 respondent recognized the potential for sugammadex interference with oral hormonal contraception. Far fewer accurately identified potential interference with hormonal intrauterine devices (44%) and hormonal contraceptive implants (55%). The manufacturer's recommended 7-day duration of alternative contraception was correctly identified by 72% of respondents; others (22%) reported longer durations (range 10-30 days). Most (78% overall) agreed/strongly agreed that potential interference with contraceptive effectiveness should be discussed with patients preoperatively. Despite the majority (86% overall) that endorsed shared decision-making and inviting patient input regarding choice between sugammadex and neostigmine, many respondents reported "rarely/never" having discussed this drug interaction with patients in actual clinical practice, either preoperatively (67%) or postoperatively (80%). Furthermore, most respondents (79%) reported "rarely/never" administering neostigmine to intentionally avoid this drug interaction.
Two years after designating sugammadex as antagonist of choice, physician and nurse anesthesia providers reported seldom inquiring about contraceptive use among women of childbearing potential and rarely discussing potential risk of contraceptive failure from sugammadex exposure. Most lack accurate knowledge of sugammadex interference with hormonal intrauterine and subcutaneous contraceptive devices. Although most endorse preoperative counseling and support patient autonomy or shared decision-making regarding choice of reversal agent, the same respondents report rarely, if ever, actualizing these positions in clinical practice. These conflicting findings highlight the need for education regarding residual neuromuscular block versus adverse drug interactions, collaboration among providers involved in patient counseling, and intentional mindfulness of reproductive justice when caring for women of childbearing potential.
Semen is a major vector for HIV transmission, but the semen HIV RNA viral load (VL) only correlates moderately with the blood VL. Viral shedding can be enhanced by genital infections and associated ...inflammation, but it can also occur in the absence of classical pathogens. Thus, we hypothesized that a dysregulated semen microbiome correlates with local HIV shedding. We analyzed semen samples from 49 men who have sex with men (MSM), including 22 HIV-uninfected and 27 HIV-infected men, at baseline and after starting antiretroviral therapy (ART) using 16S rRNA gene-based pyrosequencing and quantitative PCR. We studied the relationship of semen bacteria with HIV infection, semen cytokine levels, and semen VL by linear regression, non-metric multidimensional scaling, and goodness-of-fit test. Streptococcus, Corynebacterium, and Staphylococcus were common semen bacteria, irrespective of HIV status. While Ureaplasma was the more abundant Mollicutes in HIV-uninfected men, Mycoplasma dominated after HIV infection. HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART. In HIV-infected men, semen bacterial load correlated with seven pro-inflammatory semen cytokines, including IL-6 (p = 0.024), TNF-α (p = 0.009), and IL-1b (p = 0.002). IL-1b in particular was associated with semen VL (r(2) = 0.18, p = 0.02). Semen bacterial load was also directly linked to the semen HIV VL (r(2) = 0.15, p = 0.02). HIV infection reshapes the relationship between semen bacteria and pro-inflammatory cytokines, and both are linked to semen VL, which supports a role of the semen microbiome in HIV sexual transmission.
Background
Topical treatments with nasal saline irrigation, topical steroid sprays, or corticosteroid rinses can improve sinonasal symptoms in chronic rhinosinusitis (CRS). However, the impact of ...these therapies on commensals (Corynebacterium) and on biofilm pathogens associated with CRS (Staphylococcus aureus and Pseudomonas) is not well characterized.
Methods
Paired nasal and sinus swabs were collected endoscopically from 28 controls and 14 CRS patients with nasal polyposis (CRSwNP) who had not received systemic antibiotics or corticosteroids in the previous 8 weeks. Total DNA from swab eluents were extracted and analyzed by 16S rRNA gene‐based pyrosequencing. A total of 359,077 reads were obtained and classified taxonomically. The association of use of topical therapies with sinonasal microbiota composition was assessed by factor/vector‐fitting. The proportional abundances of sinonasal bacteria between topical therapy users and nonusers were further compared by 2‐tailed Kolmogorov‐Smirnov test among controls and among CRSwNP participants.
Results
Nasal saline irrigation, with or without added budesonide, was not associated with significantly distinct sinonasal microbiota composition or significantly decreased Pseudomonas or S. aureus abundances among either controls or CRSwNP participants. Corynebacterium was slightly lower in controls that reported using saline irrigation than those who did not. No significant association was found between nasal saline irrigation and the proportional abundances of Pseudomonas, S. aureus, and Corynebacterium in CRSwNP participants. However, male CRSwNP patients were noted to have significantly higher Corynebacterium proportional abundances than their female counterparts. The use of topical steroid sprays was associated with a distinct microbiota in control subjects, characterized by higher proportional abundances of Dolosigranulum and Simonsiella and a lower proportional abundance of Campylobacter.
Conclusion
Nasal saline irrigation is not associated with a distinct alteration in the proportional abundance of commensal bacteria or biofilm‐forming pathogens in CRSwNP patients. However, use of topical intranasal corticosteroid sprays in control subjects is associated with a distinct sinonasal microbiota.
Background
Chronic rhinosinusitis (CRS) is a highly prevalent and heterogeneous condition frequently treated with antibiotics and corticosteroid therapy. However, the effect of medical therapy on ...sinus microbiota remains unknown.
Methods
We enrolled CRS patients (n = 6) with patent maxillary antrostomies and active mucosal inflammation, who had not received antibiotics or corticosteroids in the previous 8 weeks. A pretreatment and posttreatment maxillary sinus swab was collected, from which DNA was extracted, pyrosequenced, and analyzed using a naïve Bayesian classifier and ecological analyses.
Results
Four patients showed significant improvement in endoscopic appearance. The shifts in microbiota in response to therapy were highly individualized. There was no single common microbiota profile among patients with similar clinical outcomes, but overall there was significant decrease in microbiota diversity (t(5) = 2.05, p = 0.10) and evenness (t(5) = 2.28, p = 0.07) after treatment.
Conclusion
Our findings strongly correlate with earlier studies that examined the impact of antibiotics on human microbiota. We observed that posttreatment, patients frequently became colonized by taxa that are less susceptible to the prescribed antibiotics. Our findings highlight the challenge in seeking generalizable diagnostic and therapeutic options in CRS, particularly regarding microbiological response and outcomes.
Semen is a major vector for HIV transmission, but the semen HIV RNA viral load (VL) only correlates moderately with the blood VL. Viral shedding can be enhanced by genital infections and associated ...inflammation, but it can also occur in the absence of classical pathogens. Thus, we hypothesized that a dysregulated semen microbiome correlates with local HIV shedding. We analyzed semen samples from 49 men who have sex with men (MSM), including 22 HIV-uninfected and 27 HIV-infected men, at baseline and after starting antiretroviral therapy (ART) using 16S rRNA gene-based pyrosequencing and quantitative PCR. We studied the relationship of semen bacteria with HIV infection, semen cytokine levels, and semen VL by linear regression, non-metric multidimensional scaling, and goodness-of-fit test. Streptococcus, Corynebacterium, and Staphylococcus were common semen bacteria, irrespective of HIV status. While Ureaplasma was the more abundant Mollicutes in HIV-uninfected men, Mycoplasma dominated after HIV infection. HIV infection was associated with decreased semen microbiome diversity and richness, which were restored after six months of ART. In HIV-infected men, semen bacterial load correlated with seven pro-inflammatory semen cytokines, including IL-6 (p = 0.024), TNF-α (p = 0.009), and IL-1b (p = 0.002). IL-1b in particular was associated with semen VL (r2 = 0.18, p = 0.02). Semen bacterial load was also directly linked to the semen HIV VL (r2 = 0.15, p = 0.02). HIV infection reshapes the relationship between semen bacteria and pro-inflammatory cytokines, and both are linked to semen VL, which supports a role of the semen microbiome in HIV sexual transmission.
An international consortium is sequencing the euchromatic genespace of Medicago truncatula. Extensive bioinformatic and database resources support the marker-anchored bacterial artificial chromosome ...(BAC) sequencing strategy. Existing physical and genetic maps and deep BAC-end sequencing help to guide the sequencing effort, while EST databases provide essential resources for genome annotation as well as transcriptome characterization and microarray design. Finished BAC sequences are joined into overlapping sequence assemblies and undergo an automated annotation process that integrates ab initio predictions with EST, protein, and other recognizable features. Because of the sequencing project's international and collaborative nature, data production, storage, and visualization tools are broadly distributed. This paper describes databases and Web resources for the project, which provide support for physical and genetic maps, genome sequence assembly, gene prediction, and integration of EST data. A central project Web site at medicago.org/genome provides access to genome viewers and other resources project-wide, including an Ensembl implementation at medicago.org, physical map and marker resources at mtgenome.ucdavis.edu, and genome viewers at the University of Oklahoma (www.genome.ou.edu), the Institute for Genomic Research (www.tigr.org), and Munich Information for Protein Sequences Center (mips.gsf.de).
Activation of members of the mitogen-activated protein (MAP) kinase family and their downstream effectors has been proposed to play a key role in the pathogenesis of cell survival, ischaemic ...preconditioning, cardiac hypertrophy and heart failure. This study investigated the responses of Src kinase and multiple MAP kinases during the transition from compensated pressure-overload hypertrophy to decompensated congestive heart failure. Extracellular signal-regulated protein kinase (ERK) 1/2, p38, and Src were activated by chronic pressure-overload and their activity was sustained for 8 weeks after aortic banding. In contrast, while p90 ribosomal S6 kinase (90RSK) and big MAP kinase 1 (BMK1) were activated in compensated hypertrophy, their activities were significantly decreased in hearts with heart failure. No changes were found in C-Jun NH2terminal kinase (JNK) activity after aortic banding. These data suggest that differential activation of MAP kinase family members may contribute to the transition from compensated to decompensated hypertrophy. We also examined acute effects of mechanical stretch on the activation of these kinases in normal and hypertrophied hearts. In the isolated coronary-perfused heart, a balloon in the left ventricle was inflated to achieve minimum end-diastolic pressure of 25 mmHg for 10–20 min. In normal guinea pig hearts, stretch activated ERK1/2, p90RSK, p38, Src, and BMK1 but not JNK. However in hypertrophied hearts, further activation of these kinases was not observed by acute mechanical stretch. Mechanical stretch-induced activation of ERK1/2 and p38 kinase in normal hearts was attenuated significantly by a protein kinase C inhibitor, chelerythrine. We demonstrate that ERK1/2, p90RSK, p38, Src, and BMK1 are activated by chronic pressure-overload and by acute mechanical stretch. These data suggest that Src, BMK1 and p90RSK play a role as novel signal transduction pathways leading to cardiac hypertrophy. In addition, the differential inhibition of p90RSK and BMK1 in hearts with congestive heart failure suggests the specific role of these two kinases to maintain cardiac function under chronic pressure-overload.
PDF
