BRD2 promotes antibody class switch recombination by facilitating DNA repair in collaboration with NIPBL.

Efficient repair of DNA double-strand breaks in the Ig heavy chain gene locus is crucial for B-cell antibody class switch recombination (CSR). The regulatory dynamics of the repair pathway direct CSR preferentially through nonhomologous end joining (NHEJ) over alternative end joining (AEJ). Here, we demonstrate that the histone acetyl reader BRD2 suppresses AEJ and aberrant recombination as well as random genomic sequence capture at the CSR junctions. BRD2 deficiency impairs switch (S) region synapse, optimal DNA damage response (DDR), and increases DNA break end resection. Unlike BRD4, a similar bromodomain protein involved in NHEJ and CSR, BRD2 loss does not elevate RPA phosphorylation and R-loop formation in the S region. As BRD2 stabilizes the cohesion loader protein NIPBL in the S regions, the loss of BRD2 or NIPBL shows comparable deregulation of S-S synapsis, DDR, and DNA repair pathway choice during CSR. This finding extends beyond CSR, as NIPBL and BRD4 have been linked to Cornelia de Lange syndrome, a developmental disorder exhibiting defective NHEJ and Ig isotype switching. The interplay between these proteins sheds light on the intricate mechanisms governing DNA repair and immune system functionality.

A comparative evaluation of the sniffing, the simple head extension and the head hyperextension positions for laryngoscopic view and intubation difficulty in adults undergoing direct laryngoscopy.

OBJECTIVE: This work aimed to compare between the laryngoscopy positions; sniffing, simple head extension and head hyperextension positions to assess whether the laryngeal view, intubation time and intubation difficulty could improve with one of these positions than the others. DESIGN: Prospective randomized three arms clinical trial. SETTING: Operation room, the phoniatrics unit [removed for blind peer review]. PARTICIPANTS: The study included 75 cases with 25 cases in each group. Group "A" with head in the sniffing position, Group "B" with the head in simple extension position, Group "C" with head in hyperextension position. RESULTS: The three groups were compared regarding intubation time and laryngoscopic view time. Intubation time showed statistically significant difference between the three groups. Mean of sniffing group (No. = 25) was 13.19 s (± 3.35). Mean of simple extension group (No. = 25) was 11.29 s (± 3.14). Mean of Hyperextension group (No. = 25) was 14.39 s (± 4.14). Laryngoscopic view time showed statistically highly significant difference between the three groups. Mean of sniffing group (No. = 25) was 17.19 s (± 7.27). Mean of simple group (No. = 25) was 12.18 s (± 4.46). Mean of hyperextension group (No. = 25) was 17.08 s (± 6.51). CONCLUSION: Comparing the sniffing, the simple extension and the hyperextension positions, the simple extension position showed the best time regarding intubation time and laryngoscopic view time.

HNRNPU facilitates antibody class-switch recombination through C-NHEJ promotion and R-loop suppression.

B cells generate functionally different classes of antibodies through class-switch recombination (CSR), which requires classical non-homologous end joining (C-NHEJ) to join the DNA breaks at the donor and acceptor switch (S) regions. We show that the RNA-binding protein HNRNPU promotes C-NHEJ-mediated S-S joining through the 53BP1-shieldin DNA-repair complex. Notably, HNRNPU binds to the S region RNA/DNA G-quadruplexes, contributing to regulating R-loop and single-stranded DNA (ssDNA) accumulation. HNRNPU is an intrinsically disordered protein that interacts with both C-NHEJ and R-loop complexes in an RNA-dependent manner. Strikingly, recruitment of HNRNPU and the C-NHEJ factors is highly sensitive to liquid-liquid phase separation inhibitors, suggestive of DNA-repair condensate formation. We propose that HNRNPU facilitates CSR by forming and stabilizing the C-NHEJ ribonucleoprotein complex and preventing excessive R-loop accumulation, which otherwise would cause persistent DNA breaks and aberrant DNA repair, leading to genomic instability.

Computational Analysis of Deleterious SNPs in NRAS to Assess Their Potential Correlation With Carcinogenesis.

The NRAS gene is a well-known oncogene that acts as a major player in carcinogenesis. Mutations in the NRAS gene have been linked to multiple types of human tumors. Therefore, the identification of the most deleterious single nucleotide polymorphisms (SNPs) in the NRAS gene is necessary to understand the key factors of tumor pathogenesis and therapy. We aimed to retrieve NRAS missense SNPs and analyze them comprehensively using sequence and structure approaches to determine the most deleterious SNPs that could increase the risk of carcinogenesis. We also adopted structural biology methods and docking tools to investigate the behavior of the filtered SNPs. After retrieving missense SNPs and analyzing them using six in silico tools, 17 mutations were found to be the most deleterious mutations in NRAS. All SNPs except S145L were found to decrease NRAS stability, and all SNPs were found on highly conserved residues and important functional domains, except R164C. In addition, all mutations except G60E and S145L showed a higher binding affinity to GTP, implicating an increase in malignancy tendency. As a consequence, all other 14 mutations were expected to increase the risk of carcinogenesis, with 5 mutations (G13R, G13C, G13V, P34R, and V152F) expected to have the highest risk. Thermodynamic stability was ensured for these SNP models through molecular dynamics simulation based on trajectory analysis. Free binding affinity toward the natural substrate, GTP, was higher for these models as compared to the native NRAS protein. The Gly13 SNP proteins depict a differential conformational state that could favor nucleotide exchange and catalytic potentiality. A further application of experimental methods with all these 14 mutations could reveal new insights into the pathogenesis and management of different types of tumors.

Mining of Marburg Virus Proteome for Designing an Epitope-Based Vaccine.

Marburg virus (MARV) is one of the most harmful zoonotic viruses with deadly effects on both humans and nonhuman primates. Because of its severe outbreaks with a high rate of fatality, the world health organization put it as a risk group 4 pathogen and focused on the urgent need for the development of effective solutions against that virus. However, up to date, there is no effective vaccine against MARV in the market. In the current study, the complete proteome of MARV (seven proteins) was analyzed for the antigenicity score and the virulence or physiological role of each protein where we nominated envelope glycoprotein (Gp), Transcriptional activator (VP30), and membrane-associated protein (VP24) as the candidates for epitope prediction. Following that, a vaccine construct was designed based on CTL, HTL, and BCL epitopes of the selected protein candidates and to finalize the vaccine construct, several amino acid linkers, ß-defensin adjuvant, and PADRE peptides were incorporated. The generated potential vaccine was assessed computationally for several properties such as antigenicity, allergenicity, stability, and other structural features where the outcomes of these assessments nominated this potential vaccine to be validated for its binding affinity with two molecular targets TLR-8 and TLR-4. The binding score and the stability of the vaccine-receptor complex, which was deeply studied through molecular docking-coupled dynamics simulation, supported the selection of our designed vaccine as a putative solution for MARV that should be validated through future wet-lab experiments. Here, we describe the computational approach for designing and analysis of this potential vaccine.

Transoral Versus Transnasal Approaches in Office-Based Laryngeal Biopsy: A Cohort-Selection Cross-Sectional Diagnostic Accuracy Study.

OBJECTIVE: The aim of this study is to explore the accuracy of two different approaches: transoral versus transnasal office-based laryngeal biopsy. DESIGN: Cohort-selection cross-sectional study. SETTING: Outpatient clinic of Phoniatrics in El Demerdash Hospital, faculty of medicine, Ain Sham University, Cairo, Egypt). PARTICIPANTS: The study included all patients aged 18 years or more with suspicious lesions of the larynx or the oropharynx who are eligible for biopsy who came to the outpatient clinic due to different reasons during the period of March 2017 and March 2020. MAIN OUTCOME MEASURES: Patients with suspicious lesions were referred for office-based-based biopsy-either transnasal biopsy or transoral biopsy. All patients were referred for subsequent direct laryngoscopy for definitive diagnosis. RESULTS: The overall sample was 60 cases with 30 in each group. The majority of both groups were smokers. The most frequent cause of referral for biopsy was suspicious laryngeal mass. The number of biopsies obtained was significantly higher in the transoral group. Both approaches were tolerated by all patients with few limited aspiration or epistaxis. The sensitivity of the transoral approach was compared with that of direct laryngoscopy and was 95.8% with a specificity of 83.3%. The sensitivity of the transnasal approach was compared with that of direct laryngoscopy and was 26.3%; the specificity was 90.9%. CONCLUSION: The transoral approach to obtaining a biopsy from the upper aero-digestive tract has better diagnostic accuracy than the transnasal approach when combined with transnasal visualization and transcricothyroid anesthesia.

Impact of smoking on heavy metal contamination and DNA fragmentation.

Tobacco is smoked by different techniques through cigarette and shisha smoking. The prevalence of tobacco is considered one of the major threats to public health. This study aims to assess the effect of cigarette, shisha, and mixed (cigarette/shisha) smoking on heavy metal contamination in hair samples, hair loss, and DNA fragmentation, to correlate age, incidence of hair loss, and smoking duration with the amount of accumulated metals and the DNA fragmentation, and to correlate the level of heavy metal contamination with DNA fragmentation. This study was implemented in Saudi Arabia among sixty males divided into four groups (15/group): control and cigarette, shisha, and mixed smokers. Heavy metal contamination in hair samples and urinary DNA levels were assayed. All metal and urinary DNA levels were significantly elevated in cigarette, shisha, and mixed smokers compared to non-smokers. Hair loss was also higher among smokers especially among participants with high DNA concentrations. There were positive significant correlations of age and incidence of hair loss with urinary DNA concentration. There were positive significant correlations between urinary DNA concentration and all heavy metal levels. Cigarette, shisha, and mixed smoking trigger metal contamination, DNA fragmentation, and hair loss. Moreover, hair loss was observed to be associated with Sb, Cd, and Ni as well as urinary DNA level, while age was associated only with lead and urinary DNA levels. The duration of smoking had a major impact on Pb and Sb levels. Finally, contamination with all six metals was significantly associated with DNA fragmentation.

Pharyngo-esophageal complications of Ryle tube insertion in neonates: management and fate.

INTRODUCTION: The following provides clinical reporting of seven neonates with iatrogenic pharyngeal trauma due to forceful untrained use of nasogastric feeding tube. A range of symptoms were observed beginning with excessive frothy secretions culminating in more severe pneumothorax in some. These cases are presented in the context of an exhaustive literature review producing only 50 similar cases worldwide. Special attention is paid toward accurate diagnosis, prognosis, and guidance on most effective modes of treatment. PATIENTS AND METHODS: Using Medtronic flexible nasopharyngolaryngeal endoscope, examination of the presented neonates was done in the neonatal care unit. Some neonates underwent videofluroscopic study. CONCLUSION: Ryle tube insertion in neonates could result in range of complications that could be easily avoided and managed.

Evaluation of Skin Surface as an Alternative Source of Reference DNA Samples: A Pilot Study.

An acceptable area for collecting DNA reference sample is a part of the forensic DNA analysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of reference DNA sample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. Genomic DNA was extracted and quantified then genotyped using standard techniques. The highest DNA concentration of SSC samples was collected using the tape/forearm method of collection (2.1 ng/µL). Cotton swabs moistened with ethanol yielded higher quantities of DNA than swabs moistened with salicylic acid, and it gave the highest percentage of full STR profiles (97%). This study supports the use of SSC as a noninvasive sampling technique and as a extremely useful source of DNA reference samples among certain cultures where the use of buccal swabs can be considered socially unacceptable.