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The Vaginal Microbiome
Published in Carlos Simón, Carmen Rubio, Handbook of Genetic Diagnostic Technologies in Reproductive Medicine, 2022
Shahriar Mowla, Phillip R. Bennett, David A. MacIntyre
Culture and microscopy continue to be mainstay techniques for clinical diagnosis of abnormal vaginal microbiota, particularly in the case of bacterial vaginosis (BV). The Amsel Criteria, first described in 1983, is based upon a combined assessment of both clinical symptoms (e.g., fishy odor, pH, white discharge) and microscopic features of vaginal secretions that include presence of vaginal epithelial cells coated by gram-variable bacteria referred to as Clue cells (14). The Nugent Criteria is often used for diagnosis of BV in research settings and relies upon microscopic evaluation and grading for the presence or absence of three key bacterial morphotypes; i) large gram-positive rods, ii) small gram-variable rods and iii) curved gram-variable rods (15). These morphotypes were thought to correspond to the genera Lactobacillus, Gardnerella, and Mobiluncus respectively, although recent molecular analyses of the Mobiluncus morphotypes indicates that they are more likely to be other BV-associated bacteria such as BV-associated bacterium-1 (BVAB1) (16), now referred to as Candidatus Lachnocurva vaginae (17).
Candidiasis
Published in Rebecca A. Cox, Immunology of the Fungal Diseases, 2020
Judith E. Domer, Emily W. Carrow
Several investigators have attempted immunotherapy in experimental animal models using both thymosin factor 5, a product of the thymus gland known to stimulate T cell development,295 and TF.296 Most recently, Salvin and Tanner297 reported that thymosin treatment of alloxan-diabetic mice restored most of the cell-mediated functions lost as a consequence of alloxan-induced hypoglycemia, i.e., DTH to C. albicans antigens and in vivo MIF production. Bistoni et al.298 and Ishitsuka et al.299 also treated mice with thymosin and reported favorable results if the timing of thymosin administration was appropriate, i.e., just prior to or concomitant with inoculation with Candida, but not after the administration of Candida. Ishitsuka et al.299 arbitrarily administered the thymosin daily for 8 to 10 days prior to infection and then introduced the cytotoxic drug 5-fluorouracil and the macrophage- depressant, carrageenan, into their experimental protocol. Here again, however, the experimental variables were such that innate resistance was being measured; thus, the data could have been explained on the basis of PMNL activity. Since the thymosin appeared to be effective only as a prophylactic, it would not seem to be a suitable candidate for immunotherapy of candidiasis. Akhter et al.300 used thymosin in vitro with lymphocytes from a patient with CMCC, also, but it did not restore the in vitro unresponsiveness.
Strategies for Gene Discovery
Published in Thomas R. O’Brien, Chemokine Receptors and AIDS, 2019
Direct gene analysis can be considered an extension of the standard approach for identifying genes involved in mendelian disorders (Figure 2A). For simple inherited diseases, linkage analysis is used to identify a region of the genome linked to the disease locus. That region of the genome is cloned, and genes in the area become candidate genes. The candidate genes are scanned for mutations by a series of methods and the alterations identified are tested for association with the disease. In contrast, direct gene analysis (Figure 2B) begins with a candidate gene that is selected based on its potential functional relevance to the disease. Direct gene analysis is complicated by the many genes and alleles that can be tested for a given disease. One must be concerned with interpreting the statistical significance of results if multiple comparisons have been made. In addition, because human populations are sometimes complex mixtures of many subpopulations, unrecognized population differences between cases and controls that can lead to spurious associations.
Complete Androgen Insensitivity in Girls with Inguinal Hernias: A Serendipity Opportunity for Early Diagnosis
Published in Journal of Investigative Surgery, 2021
In several cases, the diagnosis of 46,XY DSD is a challenge. It is usually necessary karyotype analysis, image studies, and a combination of hormonal dosages either at basal or after gonadal stimulation. After that, molecular diagnosis is recommended through several strategies: parallel sequencing, next generation sequencing, or candidate gene sequencing. Despite this, the molecular etiology of most 46,XY DSD will remain unknown, which made the genetic diagnosis of 46,XY difficult and expansive. CAIS is an important exception. As mentioned above, allelic variants in the AR gene are found in an expressive percentage of CAIS patients. It made AR sequencing enough for CAIS diagnosis. For CAIS, a Sanger sequencing of the AR gene is more helpful than karyotype analysis. While the karyotype analysis is able to show the presence of Y chromosome, Sanger sequencing of the AR gene is able either to show the AR allelic variant and to suggest a XY karyotype (due to hemozigosity).
Analysis of oral microbiome in glaucoma patients using machine learning prediction models
Published in Journal of Oral Microbiology, 2021
Byung Woo Yoon, Su-Ho Lim, Jong Hoon Shin, Ji-Woong Lee, Young Lee, Je Hyun Seo
In patients with POAG aged <60 years, Lactococcus was the significant taxon, whereas Lactococcus, Candidatus Pelagibacter, and Atopobium were the significant taxa in patients with POAG aged ≥60 years (Table 5). In the POAG group with baseline IOP <20 mmHg, Lactococcus, Candidatus Pelagibacter, and Atopobium were the significant taxa, whereas Lactococcus and Atopobium were the significant taxa in the POAG group with baseline IOP≥20 mmHg (Table 5). According to glaucoma severity based on RNFL thickness and visual field index in the POAG group, Lactococcus, Candidatus Pelagibacter, and Atopobium were the significant taxa. CPAR-derived association rule shows one ‘POAG’ rule and four ‘normal’ rules derived with high accuracy (Table 6). The ‘POAG’ rule 1 states that if the composition is Atopobium, ≤0.433; Candidatus Pelagibacter, ≤0.001; Endobacter, ≤0.015; and Lactococcus, ≤0.015, the patient has POAG (accuracy, 93.0%). The ‘normal’ rule 1 states that if the composition is Candidatus Pelagibacter, 0.001–0.014, the patients is ‘normal’ (accuracy, 93.0%).
Isolation and cultivation of candidate phyla radiation Saccharibacteria (TM7) bacteria in coculture with bacterial hosts
Published in Journal of Oral Microbiology, 2020
Pallavi P. Murugkar, Andrew J. Collins, Tsute Chen, Floyd E. Dewhirst
Banfield’s group studying the microbes in acid mine drainage was the first to show that genomic sequencing could be applied to bacterial communities [12,13]. From the early efforts in community genomics, now more commonly called metagenomics, began our understanding of microbial metabolic potential of the uncultured world. Marcy et al. were among the first to use the term ‘dark matter’ to refer to microbes from uncultivated linages in a landmark paper on genetic analysis of TM7 bacteria from the human mouth by single-cell manipulation and subsequent sequencing [14]. The term ‘microbial dark matter’ was introduced by Rinke et al. in one of the first major papers describing the phylogeny and coding potential of bacterial taxa from 29 uncultivated phyla using single-cell sequencing [15]. Several major papers describing genomes of uncultured organisms were published around 2013 [15–19] providing an initial glimpse of the breadth of microbial genomic potential. With the ability to obtain complete genome sequences for uncultured organisms, investigators began giving ‘Candidatus’ names to the uncultured phyla. The TM7 phylum was named ‘Candidatus Saccharibacteria’ based on the complete genome sequence of ‘Candidatus Saccharimonas aalborgensis’ by Albertsen et al. [19]. With the initiation of Candidatus naming, the ‘uncultured phyla’ became the ‘candidate phyla’. Twenty-six phyla were given names by Brown et al. [20].