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The diagnosis and management of preterm labor with intact membranes
Published in Hung N. Winn, Frank A. Chervenak, Roberto Romero, Clinical Maternal-Fetal Medicine Online, 2021
Roberto Romero, Tinnakorn Chaiworapongsa, Francesca Gotsch, Lami Yeo, Ichchha Madan, Sonia S. Hassan
Recently, amniotic fluid sludge has been demonstrated to represent a biofilm (426,427). A sample of sludge was retrieved by transvaginal amniotomy under ultrasound guidance from a patient at 28 weeks with spontaneous labor and clinical chorioamnionitis. Grossly, the sludge had a “pus-like” appearance and the Gram stain showed gram-positive bacteria. The amniotic fluid culture was positive for Streptococcus mutans, Mycoplasma hominis, and Aspergillus flavus. Of interest, the results of the amniocentesis performed at the time of admission for preterm labor were negative for intraamniotic infection (426,427). The aspirated sludge was then analyzed further. Scanning electron microscopy showed flocs of amniotic fluid sludge that consisted of bacterial cells and the exopolymeric matrix material that are typical of a biofilm (Fig. 8) (427). The evidence that sludge represents a biofilm in this case includes the following: (i) the presence of bacteria detected by fluorescence in situ hybridization, with the use of a probe against the conserved sequence of prokaryotes; (ii)bacterialaggregates were separated bymaterialthatresembled a matrix; and (iii) lectin-based identification of exopolymeric matrix that stained with wheat germ agglutinin (427).
Immunoglobulins
Published in Constantin A. Bona, Francisco A. Bonilla, Textbook of Immunology, 2019
Constantin A. Bona, Francisco A. Bonilla
All genes have a promoter, a recognition site for RNA polymerase. A common motif in eukaryotic genes is an AT-rich group of about seven base pairs called the “TATA box” (Figure 4–6). In addition, the immunoglobulin promoters contain an octamer sequence (OCTA), and other regulatory sequences recognized by DNA-binding proteins. Within the promoters of ϰ and λ light chain genes, the TATA and OCTA sequences have been firmly established as regulatory elements. The role played by the other conserved sequence motifs is still being determined.
The Parasponia-Bradyrhizobium Symbiosis
Published in Peter M. Gresshoff, Molecular Biology of Symbiotic Nitrogen Fixation, 2018
Kieran F. Scott, Gregory L. Bender
The nodD gene product has been shown to bind specifically to a conserved sequence called the "nod box" found preceding all inducible nod operons.53 Since nodD also has some homology to other known regulatory proteins, such as lysR,25 which activate transcription via binding to DNA in the promoter region of an operon, nodD is suggested to activate transcription of nod operons in a similar fashion by binding to the "nod box". This conserved sequence is also found preceding the nodKABC operon in B. parasponia strain ANU289.29 Also, a mutant construct which deletes out half the nod box and a portion of nodK fails to nodulate Parasponia (Table 1, Figure 7). Taken together, these data suggest that the activation of nod gene transcription during Parasponia nodulation occurs in an analogous fashion to activation during legume nodulation.
Current vaccine approaches and emerging strategies against herpes simplex virus (HSV)
Published in Expert Review of Vaccines, 2021
Vindya Nilakshi Wijesinghe, Isra Ahmad Farouk, Nur Zawanah Zabidi, Ashwini Puniyamurti, Wee Sim Choo, Sunil Kumar Lal
Bioinformatic in silico techniques for both novel discovery and development of vaccines has been gaining recognition as a vaccine design approach across diverse viral diseases [135]. In times of urgent requirement for effective vaccines, such as the current SARS-CoV-2 pandemic, bioinformatic approaches may begin to more largely contribute to development as bioinformatic tools can be used to quickly determine conserved sequence regions and meet immunogenicity requirements [136]. This approach, however, requires additional experimental evaluation for designed candidates, as in silico development alone is not enough to consider a particular candidate successful. Ideally, once developed, the candidates require in vitro and in vivo experimentation to evaluate their efficacy and safety before being subjected to clinical trials. Despite these challenges, there remains to be much potential and promise in this approach as bioinformatic tools can identify targets that may take years for standard research alone to determine. Furthermore, bioinformatic approaches for vaccine development promise a more focused search to provide effective candidates in shorter lead times, design antiviral peptides that preclude allergenic reactions and develop more stable targets against mutational changes in viral strains [137]. In this section we describe the overview of the bioinformatic approach and provide some examples of HSV vaccine candidates that have been developed using computational methods.
Technical considerations for circulating tumor DNA detection in oncology
Published in Expert Review of Molecular Diagnostics, 2019
Claire Franczak, Pierre Filhine-Tresarrieu, Pauline Gilson, Jean-Louis Merlin, Lewis Au, Alexandre Harlé
Digital PCR assay was developed in the late 90s by Vogelstein and Kinzler in order to transform the exponential nature of PCR to a linear one, leading to sensitivity improvement [76]. With serial dilutions, a single DNA molecule is isolated in a partition and individual PCR is performed in each partition. Two fluorescent probes are then added. One is specific to the target mutant codon of interest and the other hybridizes with a conserved sequence embedded in the amplicon product. In the final step, fluorescence is analyzed to identify partitions containing wild-type sequence and partitions containing mutant PCR product. Binary results are obtained, thus giving the ‘digital’ term in the name of this approach. Sensitivity of this approach is about 0.1% [76,77] (Table 2). Figure 1 depicts the workflow of a dPCR. KRAS mutations in ctDNA assessment by dPCR yielded 87.2% sensitivity and 99.2% specificity [78]. dPCR has been evaluated in numerous studies. In a large pan-cancer analysis of 640 patients, ctDNA was detected in more than 75% of patients with advanced cancers including CRC, breast cancer and melanoma, but less than 50% of patients with thyroid cancer or glioma [78]. Interestingly, 47% of patients with stage I disease of cancer of all kind had ctDNA detected by dPCR including approximately 75% of patients with localized CRC and almost 50% of patients with breast cancer [78].
Exploring Klebsiella pneumoniae capsule polysaccharide proteins to design multiepitope subunit vaccine to fight against pneumonia
Published in Expert Review of Vaccines, 2022
Jyotirmayee Dey, Soumya Ranjan Mahapatra, S Lata, Shubhransu Patro, Namrata Misra, Mrutyunjay Suar
Genomes of 20 K. pneumonia strains were mined to retrieve corresponding amino acid sequences of the CPS protein (Supplementary Table 6). Consequently, each of the shortlisted CTL, HTL, and B-cell epitopes were analyzed to study the conservancy across all strains using the Conservancy Analysis tool of IEDB (Supplementary Table 6). All selected epitopes demonstrated perfect 100% conservation (Tables 1–3). The results of the MEME tool corroborate the high conservancy of the epitopes as depicted by the sequence logo. The schematic representation of the conserved sequence logos is illustrated in Supplementary Figure 2.