A5088669922- Genomics and Phylogenetic Studies
- Urinary Tract Infections Management
- Gut microbiota and health
- Pelvic floor disorders treatments
- Network Security and Intrusion Detection
- Network Packet Processing and Optimization
- Microbial Community Ecology and Physiology
- Urinary Bladder and Prostate Research
- Reproductive tract infections research
- Algorithms and Data Compression
- Chromosomal and Genetic Variations
- Internet Traffic Analysis and Secure E-voting
- Syphilis Diagnosis and Treatment
- Gene expression and cancer classification
- Mobile Ad Hoc Networks
- Cooperative Communication and Network Coding
- COVID-19 epidemiological studies
- Diet and metabolism studies
- Burn Injury Management and Outcomes
- SARS-CoV-2 and COVID-19 Research
- Gastrointestinal motility and disorders
- RNA and protein synthesis mechanisms
- Pneumocystis jirovecii pneumonia detection and treatment
- COVID-19 and healthcare impacts
- Vector-borne infectious diseases
Loyola University Chicago
2015-2024
Loyola University Medical Center
2021-2024
University of Chicago
2015-2022
Harvard University
2021
Indiana Clinical and Translational Sciences Institute
2021
Indiana University – Purdue University Indianapolis
2021
Massachusetts General Hospital
2021
University of California, San Diego
2021
Stanford University
2021
University of California, Los Angeles
2021
We describe the draft genome of microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count a consequence an elevated rate duplication resulting in tandem clusters. More than third Daphnia's genes have no detectable homologs any other available proteome, most amplified families are specific to lineage. coexpansion interacting within metabolic pathways suggests that maintenance duplicated not random, analysis expression under different...
ABSTRACT Clinical urine specimens are usually considered to be sterile when they do not yield uropathogens using standard clinical cultivation procedures. Our aim was test if the adult female bladder might contain bacteria that identified by these routine An additional identify and recommend appropriate collection method for study of bacterial communities in bladder. Consenting participants who were free known urinary tract infection provided samples voided, transurethral, and/or suprapubic...
Purpose.: Ocular surface (OS) microbiota contributes to infectious and autoimmune diseases of the eye. Comprehensive analysis microbial diversity at OS has been impossible because limitations conventional cultivation techniques. This pilot study aimed explore true human using DNA sequencing-based detection identification bacteria. Methods.: Composition bacterial community was characterized deep sequencing 16S rRNA gene amplicon libraries generated from total conjunctival swab DNA. The...
Background The microbiome of the male urogenital tract is poorly described but it has been suggested that bacterial colonization urethra might impact risk sexually transmitted infection (STI). Previous cultivation-dependent studies showed a variety non-pathogenic bacteria colonize did not thoroughly characterize these microbiomes or establish links between compositions urethral and STI. Methodology/Findings Here, we used 16S rRNA PCR sequencing to identify in urine specimens collected from...
Lactobacillus-dominated vaginal microbiotas are associated with reproductive health and STI resistance in women, whereas altered bacterial vaginosis (BV), risk poor outcomes. Putative taxa have been observed male first-catch urine, urethral swab coronal sulcus (CS) specimens but the significance of these observations is unclear. We used 16 S rRNA sequencing to characterize microbiota CS urine collected from 18 adolescent men over three consecutive months. most participants were more stable...
Degrees of Separation Proteins embedded in membranes represent an interesting point communication between the cell and its environment, but their localization to can make them difficult study. Jones et al. (p. 711 ) found approach catalog thousands interactions involving membrane proteins membrane-associated signaling machinery—including many previously uncharacterized proteins. With a focus on model plant Arabidopsis , several identified fill gaps important signal transduction chains, while...
Species-level classification for 16S rRNA gene sequences remains a serious challenge microbiome researchers, because existing taxonomic tools either do not provide species-level classification, or their results are unreliable. The unreliable due to the limitations in methods which lack solid probabilistic-based criteria evaluate confidence of assignments, use nucleotide k-mer frequency as proxy sequence similarity measurement.We have developed method that shows significantly improved over...
PlantGDB ( http://www.plantgdb.org/ ) is a database of molecular sequence data for all plant species with significant sequencing efforts. The organizes EST sequences into contigs that represent tentative unique genes. Contigs are annotated and, whenever possible, linked to their respective genomic DNA. Genome fragments assembled similarly. goal the web site establish basis identifying sets genes common plants or specific particular by integrating number bioinformatics tools facilitate gene...
Urine is the CDC-recommended specimen for STI testing. It was unknown if bacterial communities (microbiomes) in urine reflected those distal male urethra. We compared microbiomes of 32 paired and urethral swab specimens obtained from adult men attending an STD clinic, by 16S rRNA PCR deep pyrosequencing. Microbiomes swabs were remarkably similar, regardless status subjects. Thus, can be used to characterize when are undesirable, such as population-based studies microbiome or where multiple...
Inflammation and infection of bovine mammary glands, commonly known as mastitis, imposes significant losses each year in the dairy industry worldwide. While several different bacterial species have been identified causative agents many clinical mastitis cases remain culture negative, even after enrichment for growth. To understand basis this increasingly common phenomenon, composition communities from milk samples was analyzed using independent pyrosequencing amplicons 16S ribosomal RNA...
Diabetes mellitus is a major risk factor for chronic periodontitis. We investigated the effects of type 2 diabetes on subgingival plaque bacterial composition by applying culture-independent 16S rDNA sequencing to periodontal bacteria isolated from four groups volunteers: non-diabetic subjects without periodontitis, with diabetic patients and A total 71,373 high-quality sequences were produced V1-V3 region genes 454 pyrosequencing. Those classified into 16 phyla, 27 classes, 48 orders, 85...
ABSTRACT The influence of the skin microbiota on host susceptibility to infectious agents is largely unexplored. harbors diverse bacterial species that may promote or antagonize growth an invading pathogen. We developed a human infection model for Haemophilus ducreyi in which volunteers are inoculated upper arm. After inoculation, papules form and either spontaneously resolve progress pustules. To examine role outcome H. infection, we analyzed microbiomes four dose-matched pairs “resolvers”...
Resident bacterial communities (microbiota) and host antimicrobial peptides (AMPs) are both essential components of normal innate immune responses that limit infection pathogen induced inflammation. However, their interdependence has not been investigated in the context urinary tract (UTI) susceptibility. Here, we explored interrelationship between microbiota AMP as mechanisms for UTI risk. Using prospectively collected day surgery (DOS) urine specimens from female pelvic floor participants,...
Rationale: Previous work found the lung microbiome in healthy subjects infected with HIV was similar to that uninfected subjects. We hypothesized from more advanced disease would differ of an control population.Objectives: To measure HIV-infected population disease.Methods: 16s RNA gene sequencing performed on acellular bronchoalveolar lavage (BAL) fluid 30 (baseline mean CD4 count, 262 cells/mm3) before and up 3 years after starting highly active antiretroviral therapy (HAART) compared 22...
Urobiome research has the potential to advance understanding of a wide range diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early method consensus facilitate greater, common good. This document, developed by group expert investigators currently engaged in urobiome (UROBIOME 2020 conference participants), aims promote standardization advances this field adoption core practices. We propose standardized nomenclature as well...
We address the problem of energy-efficient reliable wireless communication in presence unreliable or lossy link layers multi-hop networks. Prior work [1] has provided an optimal energy efficient solution to this for case where implement perfect reliability. However, a more common scenario --- layer that is not perfectly reliable, was left as open problem. In paper we first present two centralized algorithms, BAMER and GAMER, optimally solve minimum links. Subsequently distributed algorithm,...
Abstract Summary: Ergatis is a flexible workflow management system for designing and executing complex bioinformatics pipelines. However, its complexity restricts usage to only highly skilled bioinformaticians. We have developed web-based prokaryotic genome annotation server, Integrative Services Genomics Analysis (ISGA), which builds upon the system, integrates other dynamic analysis tools provides intuitive web interfaces biologists customize execute their own ISGA designed be installed at...
The RDP Classifier is a widely used bioinformatic program that performs taxonomic classification of 16S rRNA gene sequences.However, the accuracy not clear when it applied to common PCR products variable regions, which are heavily in microbiome projects.In this study, fulllength alignments from SILVA database were simulate combined regions (i.e., V1-V3, V3-V5, and V6-V9).The accuracies obtained evaluated for each simulated at different confidence score thresholds.Although minor bias was...
Domestic combustion of biomass fuels, such as wood, charcoal, crop residue and dung causes Household Air Pollution (HAP). These inhaled particulates affect more than half the world's population, causing respiratory problems infection inflammatory lung disease. We examined whether presence black carbon in alveolar macrophages was associated with alterations microbiome a Malawi population. Bronchoalveolar lavage samples from 44 healthy adults were sequenced using 16S rDNA amplification to...
Temporal dynamics of certain human microbiotas have been described in longitudinal studies; variability often relates to modifiable factors or behaviors. Early studies the urinary microbiota preferentially used samples obtained by transurethral catheterization minimize vulvovaginal microbial contributions. Whereas voided specimens are preferred for studies, few that reported data were limited women with lower tract (LUT) symptoms, due ease accessing a clinical population sampling and...
Monkeypox (now Mpox), a zoonotic disease caused by the monkeypox virus (MPXV) is an emerging threat to global health. In time span of only six months, from May October 2022, number MPXV cases breached 80,000 and many outbreaks occurred in locations that had never previously reported MPXV. Currently there are no FDA-approved MPXV-specific vaccines or treatments, therefore, finding drugs combat utmost importance. The A42R profilin-like protein involved cell development motility making it...