Structural Biology of RNA Polymerase II Transcription: 20 Years On.

Gene transcription by RNA polymerase II (Pol II) is the first step in the expression of the eukaryotic genome and a focal point for cellular regulation during development, differentiation, and responses to the environment. Two decades after the determination of the structure of Pol II, the mechanisms of transcription have been elucidated with studies of Pol II complexes with nucleic acids and associated proteins. Here we provide an overview of the nearly 200 available Pol II complex structures and summarize how these structures have elucidated promoter-dependent transcription initiation, promoter-proximal pausing and release of Pol II into active elongation, and the mechanisms that Pol II uses to navigate obstacles such as nucleosomes and DNA lesions. We predict that future studies will focus on how Pol II transcription is interconnected with chromatin transitions, RNA processing, and DNA repair.

The Cdk8 kinase module regulates interaction of the mediator complex with RNA polymerase II.

The Cdk8 kinase module (CKM) is a dissociable part of the coactivator complex mediator, which regulates gene transcription by RNA polymerase II. The CKM has both negative and positive functions in gene transcription that remain poorly understood at the mechanistic level. In order to reconstitute the role of the CKM in transcription initiation, we prepared recombinant CKM from the yeast Saccharomyces cerevisiae. We showed that CKM bound to the core mediator (cMed) complex, sterically inhibiting cMed from binding to the polymerase II preinitiation complex (PIC) in vitro. We further showed that the Cdk8 kinase activity of the CKM weakened CKM-cMed interaction, thereby facilitating dissociation of the CKM and enabling mediator to bind the PIC in order to stimulate transcription initiation. Finally, we report that the kinase activity of Cdk8 is required for gene activation during the stressful condition of heat shock in vivo but not under steady-state growth conditions. Based on these results, we propose a model in which the CKM negatively regulates mediator function at upstream-activating sequences by preventing mediator binding to the PIC at the gene promoter. However, during gene activation in response to stress, the Cdk8 kinase activity of the CKM may release mediator and allow its binding to the PIC, thereby accounting for the positive function of CKM. This may impart improved adaptability to stress by allowing a rapid transcriptional response to environmental changes, and we speculate that a similar mechanism in metazoans may allow the precise timing of developmental transcription programs.

Epidemiology of pediatric sepsis in the pediatric intensive care unit of king Abdulaziz Medical City, Jeddah, Saudi Arabia.

BACKGROUND: Pediatric sepsis remains a significant cause of morbidity and mortality worldwide. This study aimed to identify the incidence of sepsis and septic shock among patients admitted to the pediatric intensive care unit (PICU) of a tertiary center in Saudi Arabia.  Patients' demographics and risk factors associated with sepsis-related mortality were also investigated. METHODS: A retrospective cohort study was conducted in the PICU of King Abdulaziz Medical City, Jeddah (KAMC-J). KAMC-J is a tertiary care hospital in the western region of Saudi Arabia. A total of 2389 patients admitted to the PICU of KAMC-J between January 1, 2013 and December 31, 2017 were screened and evaluated for sepsis using The Third International Consensus Definitions for Sepsis and Septic Shock (Sepsis-3). RESULTS: Of the 2389 total admissions to the PICU, 113 patients (4.9%) met the definition of Sepsis-3; 50.4% of the 113 patients met the definition of septic shock. Most patients (66.3%) were less than 6 years old, and 52.2% were male. Eight-five patients (75.2%) had underlying comorbidities. The respiratory system was the most common primary site of infection (57.5%). Bacterial and viral infections were the most common infectious etiology with reported rates of 29.2 and 21.2%, respectively. The median duration of PICU stay was 8 days and the 28-day PICU mortality rate was 23.9%. A Pediatric Sequential Organ Failure Assessment (pSOFA) Score greater than four and a pre-existing percutaneous central venous catheter were associated with a significant increase in mortality, with adjusted odds ratios of 3.6 (95% confidence interval: 1.30-9.93) and 9.27 (95% confidence interval: 1.28-67.29), respectively. CONCLUSIONS: The incidence of sepsis in our institution is comparable to that reported internationally; however, the mortality rate is higher than that of developed countries. Nationwide studies identifying sepsis epidemiology are needed to improve the outcome of pediatric sepsis. Following international guidelines for central-line insertion and maintenance is of paramount importance.

Incidence of Low Seroimmunity to Hepatitis B Virus in Children with Inflammatory Bowel Disease: A Single Center Experience.

Purpose: Immunosuppressive therapy is frequently administered to patients with inflammatory bowel disease (IBD), which may make them more susceptible to infections like hepatitis B. Methods: A cross-sectional study was conducted on patients aged 5-18 years diagnosed with IBD who visited a gastroenterology clinic along with controls who were the same age as the patients with IBD and were healthy overall. A logistic regression analysis using the independent variables of age, sex, race, disease phenotype, surgery, and medications and the dependent variable of adequate hepatitis B surface antibody (HBsAb) titers (>10 mIU/mL) was performed on quantitative serum HBsAb titers. Results: The study enrolled 62 patients, including 37 males and 25 females. Crohn's disease, ulcerative colitis, and indeterminate colitis were diagnosed in 16, 22, and 24 patients, respectively. Thirty-nine patients were taking corticosteroids at the time of the study, 42 were taking immunomodulators, and four were taking biologics. Compared to 44.7% of the control group, 9.3% of the patients had protective titers. Only 12 out of 62 patients had HBsAb titers greater than 10 million IU/mL. None of the patients who received biologics or corticosteroids and 3.2% of those who received immunomodulators were found to be seroimmuned. Conclusion: The younger patients had the highest titers. Patient-specific factors that may impact these low titers include the length of the patient's illness and the use of immunosuppressants.

Disseminated Melioidosis Presenting as Sepsis, Neurological Melioidosis, Liver and Prostate Abscess in United Arab Emirates.

Background: Melioidosis is an infection caused by Burkholderia pseudomallei, a Gram-negative bacterium. It is a disease endemic to Southeast Asia and northern Australia although its global incidence has been rising. It most commonly infects people with certain identified risk factors such as diabetes, alcoholism, thalassemia, and underlying chronic disease involving lungs, kidney and liver. This bacterium is capable of producing a wide array of clinical manifestations ranging from asymptomatic disease to localised infections such as in the lung, bone or skin to disseminated infection. Case description: This is a case, from United Arab Emirates, of a 40-year-old male recently diagnosed with diabetes who presented with multiple abscesses and was eventually diagnosed with disseminated melioidosis. He was treated successfully with antibiotics and drainage of abscesses. Conclusion: In non-endemic regions, melioidosis can be easily missed in common diagnostic approaches. This gap of awareness could delay the diagnosis and allow further deterioration of the patient due to complications. Thus, case reports like this can enlighten internists about changing incidences and complexity of clinical presentations, thus preparing them to better handle such patients in the future. LEARNING POINTS: Owing to its considerably rare incidence in non-endemic regions including the United Arab Emirates, melioidosis can easily be overlooked or misdiagnosed.Moreover, due to similarity with multiple other diseases and infections as well as significant absence from standard medical curricula, melioidosis is rarely on the differential list of an internist.This report aims to enhance awareness and alertness to aid earlier detection and avoid severe complications.

The Effect of Ventilator-Associated Pneumonia on the Time-to-Extubation in Adult and Pediatric Intensive Care Unit Patients Requiring Mechanical Ventilation: A Retrospective Cohort Study.

INTRODUCTION: Ventilator-associated pneumonia (VAP) ranks as a prominent hospital-acquired infection. VAP has been shown to have a detrimental impact on patients and healthcare facilities, leading to extended hospital stays, increased demands on medical resources, and higher financial expenses. This study aims to assess the influence of VAP on time-to-extubation and length of hospital stay (LOS) in patients requiring mechanical ventilation for more than 48 hours in pediatric and adult intensive care units (ICU). METHODS: This retrospective cohort study included adult and pediatric ICU patients admitted to King Abdul-Aziz Medical City in Jeddah, Saudi Arabia, from June 2016 to May 2020. The study encompassed ICU patients who required mechanical ventilation for more than 48 hours. Time-to-extubation and LOS were measured in days and compared between those who developed VAP and those who did not. A Kaplan-Meier curve was employed to estimate and compare both groups' survival functions (time-to-event). RESULTS: The study involved 367 subjects, with 226 adults and 141 pediatric patients. Among the 367 mechanically ventilated patients, 33 (8.99%) developed VAP during their ICU stay, with 9 of them being children. VAP patients experienced a significantly longer time to extubation than non-VAP patients (13.5 vs. six days, p<0.0001). Likewise, ICU stays for VAP patients were significantly longer than those for non-VAP patients (19.5 vs. 13 days, p<0.002). However, the mortality rate at 28 days from intubation did not exhibit significant differences between the VAP and non-VAP groups (36.36% vs. 27.54%, p=0.283). CONCLUSION: This study underscores that VAP patients face a substantial delay in time-to-extubation and an increased length of ICU stay compared to non-VAP patients. Such findings substantially impact the cost of hospital care and the risk of exposure to other infection-related complications while under mechanical ventilation. Enhanced preventive measures are warranted to reduce the occurrence and consequences of VAP.

Epidemiology and Risk Factor Analysis of Children with Bronchiolitis Admitted to the Intensive Care Unit at a Tertiary Care Center in Saudi Arabia.

Bronchiolitis is a leading cause of hospitalization worldwide for children aged ≤2 years. Few studies have compared general ward and pediatric intensive care unit (PICU) admissions, particularly in Saudi Arabia. This retrospective cohort study aimed to compare the demographic and clinical characteristics of children with bronchiolitis admitted to the general ward with those admitted to the PICU. Children (≤6 years) previously diagnosed with bronchiolitis and admitted to the PICU or general ward at a tertiary center in Saudi Arabia between May 2016 and May 2021 were included. Multiplex polymerase chain reaction was used to identify respiratory viruses. Of the 417 patients enrolled, 67 (16.06%) were admitted to the PICU. The PICU group was younger (median, 2 months; interquartile range [IQR], 1-5 months) vs. (6 months; IQR, 2.65-13.25 months). There was a dramatic reduction in bronchiolitis admissions during the COVID-19 pandemic. The most common causative virus was respiratory syncytial virus (RSV) (54.9%). In the multivariate regression analysis, hypoxia, hyperinflation on X-ray, and non-RSV bronchiolitis were independently associated with PICU admission. However, a higher chronological age and cough were protective. Children with Down syndrome, immunodeficiency, or neuromuscular disorders, and intermediate preterm infants (29-33 weeks of gestation) are at a high risk of PICU admission (adjusted odds ratio: 2.4, 7.1, 2.9, and 2.9; p = 0.037, 0.046, 0.033, and 0.029, respectively). Bronchiolitis is still one of the leading causes of PICU admission. Particular attention should be paid to preventive measures, especially in the post-COVID-19 era, targeting high-risk groups.

Healthcare Professionals' Experiences During the COVID-19 Pandemic in Sudan: A Cross-Sectional Survey Assessing Quality of Life, Mental Health, and Work-Life-Balance.

Objectives: The main objective of this research was to investigate the Work-life balance (WLB), mental health, and quality of life and their associated factors among Healthcare Professionals (HCPs) in Sudan during the peak of the COVID-19 pandemic during 2021. Methods: An observational cross-sectional web-based survey was conducted during August-December 2021 among a sample of 430 HCPs working in the hospitals of four Sudanese states. The study used the WHOQoLBREF scale, Work-Life Balance Scale, and General Anxiety Disorder (GAD-7). Results: HCPs reporting a poor quality of life made up 33.5% (95% CI 29.1-38.0), while those reporting worse WLB made up 52.6% (95% CI 47.8-57.2). HCPs reporting moderate to severe anxiety symptoms accounted for 35.8% (95% CI 31.4-40.5). The Multiple Regression model indicated that an increase in the anxiety scores is associated with a decrease in Health-related Quality of Life (HRQoL) (ß= 0.831, p < 0.05). Female HCPs exhibited 4.53-fold lower HRQoL scores than their male colleagues (p < 0.05). Conclusion: Approximately one-third of the HCPs in Sudan reported low HRQoL and suffered from moderate to severe anxiety, while a large portion of them had an unequal work-life balance during COVID-19. Health policies addressing these factors are needed to improve the quality of health of HCPs.

Selective COVID-19 Coinfections in Diabetic Patients with Concomitant Cardiovascular Comorbidities Are Associated with Increased Mortality.

Coinfections and comorbidities add additional layers of difficulties into the challenges of COVID-19 patient management strategies. However, studies examining these clinical conditions are limited. We have independently investigated the significance of associations of specific bacterial species and different comorbidities in the outcome and case fatality rates among 129 hospitalized comorbid COVID-19 patients. For the first time, to best of our knowledge, we report on the predominance of Klebsiella pneumoniae and Acinetobacter baumannii in COVID-19 non-survival diabetic patients The two species were significantly associated to COVID-19 case fatality rates (p-value = 0.02186). Coinfection rates of Klebsiella pneumoniae and Acinetobacter baumannii in non-survivors were 93% and 73%, respectively. Based on standard definitions for antimicrobial resistance, Klebsiella pneumoniae and Acinetobacter baumannii were classified as multidrug resistant and extremely drug resistant, respectively. All patients died at ICU with similar clinical characterisitics. Of the 28 major coinfections, 24 (85.7%) were in non-survivor diabetic patients, implying aggravating and worsening the course of COVID-19. The rates of other comorbidities varied: asthma (47%), hypertension (79.4%), ischemic heart disease (71%), chronic kidney disease (35%), and chronic liver disease (32%); however, the rates were higher in K. pneumoniae and were all concomitantly associated to diabetes. Other bacterial species and comorbidities did not have significant correlation to the outcomes. These findings have highly significant clinical implications in the treatment strategies of COVID-19 patients. Future vertical genomic studies would reveal more insights into the molecular and immunological mechanisms of these frequent bacterial species. Future large cohort multicenter studies would reveal more insights into the mechanisms of infection in COVID-19.

Tracheobronchitis caused by methicillin-resistant Staphylococcus aureus as a cause of chronic wheezing in a non-ventilated adult patient with tracheobronchomalacia.

Bacterial tracheobronchitis is an extremely rare entity, which was long considered to be a pediatric disease. We report the case of a 65-year-old woman who presented with persistent wheezing, worsening productive cough and sore throat. Computed tomography of the chest revealed the presence of tracheomalacia, confirmed at bronchoscopy. The presence of purulent exudate, coating the trachea and main bronchi, was consistent with bacterial tracheobronchitis. Culture of the tracheal aspirates grew methicillin-resistant Staphylococcus aureus (MRSA). As the patient was afebrile and not systemically ill, the clinical picture was consistent with exudative tracheobronchitis. To our knowledge, this is the first case of MRSA exudative tracheobronchitis and tracheomalacia in a non-ventilated adult. Other adult cases of bacterial tracheobronchitis and MRSA tracheobronchitis in mechanically ventilated patients reported in the literature are also reviewed.Physicians should be aware of the diagnosis of tracheomalacia in adults, which can masquerade as persistent asthma and may be associated with the development of serious infections including MRSA tracheobronchitis.

The incidence of ventilator-associated pneumonia (VAP) in a tertiary-care center: Comparison between pre- and post-VAP prevention bundle.

INTRODUCTION: Ventilator-associated pneumonia (VAP) is a nosocomial infection that develops 48h after the initiation of mechanical ventilatory support. Current evidence-based guidelines demonstrate that VAP prevention is feasible through the implementation of certain VAP prevention bundle of interventions simultaneously. We aimed in this study to investigate the effect of VAP prevention pre- and post- implementation. METHODS: This is a single-center, cohort study that took place at the Pediatric Intensive Care Unit (PICU) of King Abdulaziz Medical City (KAMC), Jeddah, Saudi Arabia from January 2015 to March 2018 and assessed the rate of VAP before and after implementation of the bundle. RESULTS: The study included 141 children, 95 were included from the pre-bundle group and 36 from the bundle group. VAP developed in 35% of the pre-bundle group compared to 31% of the bundle group (p=0.651) with incidence rates equaled to 18 and 12 per 1000 ventilator days, respectively. CONCLUSION: This study found that VAP bundle did not significantly reduce VAP rate in the PICU. Further large prospective multi-center studies with longer intervention duration are indicated to investigate the benefits of using VAP prevention bundle.

Emphysematous cystitis in the absence of known risk factors: an unusual clinical entity.

Emphysematous cystitis is a rare disorder that is usually associated with immunosuppression, poorly controlled diabetes mellitus, and other risk factors such as previous urinary tract infection and/or recent instrumentation of the urinary tract. The case of an 89-year-old woman with emphysematous cystitis who had no evidence of immunodeficiency or other risk factors except for advanced age is reported. A review of the literature on emphysematous cystitis in immunocompetent, nondiabetic individuals is presented.