p53motifDB: integration of genomic information and tumor suppressor p53 binding motifs.

The tumor suppressor gene TP53 encodes the DNA binding transcription factor p53 and is one of the most commonly mutated genes in human cancer. Tumor suppressor activity requires binding of p53 to its DNA response elements and subsequent transcriptional activation of a diverse set of target genes. Despite decades of close study, the logic underlying p53 interactions with its numerous potential genomic binding sites and target genes is not yet fully understood. Here, we present a database of DNA and chromatin-based information focused on putative p53 binding sites in the human genome to allow users to generate and test new hypotheses related to p53 activity in the genome. Users can query genomic locations based on experimentally observed p53 binding, regulatory element activity, genetic variation, evolutionary conservation, chromatin modification state, and chromatin structure. We present multiple use cases demonstrating the utility of this database for generating novel biological hypotheses, such as chromatin-based determinants of p53 binding and potential cell type-specific p53 activity. All database information is also available as a precompiled sqlite database for use in local analysis or as a Shiny web application.

Exploring patient perspectives: orthognathic surgery outcomes and experiences assessed by patient-reported outcome measures and patient-reported experience measures.

Evaluating the effectiveness of orthognathic treatment can be difficult. To address this issue, patient-reported outcome measures (PROMs) and patient-reported experience measures (PREMs) have been proposed as valuable instruments for understanding the quality of healthcare from the patients' standpoint. Therefore, the aim of this project was to employ PROMs and PREMs questionnaires to capture the patients' perspectives regarding their experience during the orthognathic treatment process, as well as their perception of their postoperative state. Preoperative and postoperative questionnaires were offered to patients at consenting appointment and at various timepoints after the surgery. The assessment of statistical relationships was carried out by means of Fisher's exact test. A total of 64 preoperative and 126 postoperative responses were received. The primary motivators for pursuing the surgery were the improvement of facial and dental aesthetics, as well as increased satisfaction with photographic and video appearances. These three factors were also cited as the most important postoperative benefits. Of the respondents, 58% reported experiencing altered sensation to the lower lip at the 24-month follow up (p = 0.02); however, the affected patients reported that this did not have an impact on their daily activities. The use of PROMs and PREMs to appraise the quality of life constitutes a valuable method for surgeons to gauge their treatment efficacy. Above all, such tools are particularly useful for evaluating patient satisfaction, which is the ultimate objective of any treatment.

Activation of ATF3 via the integrated stress response pathway regulates innate immune response to restrict Zika virus.

Zika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that can have devastating health consequences. The developmental and neurological effects of a ZIKV infection arise in part from the virus triggering cellular stress pathways and perturbing transcriptional programs. To date, the underlying mechanisms of transcriptional control directing viral restriction and virus-host interaction are understudied. Activating Transcription Factor 3 (ATF3) is a stress-induced transcriptional effector that modulates the expression of genes involved in a myriad of cellular processes, including inflammation and antiviral responses, to restore cellular homeostasis. While ATF3 is known to be upregulated during ZIKV infection, the mode by which ATF3 is activated, and the specific role of ATF3 during ZIKV infection is unknown. In this study, we show via inhibitor and RNA interference approaches that ZIKV infection initiates the integrated stress response pathway to activate ATF4 which in turn induces ATF3 expression. Additionally, by using CRISPR-Cas9 system to delete ATF3, we found that ATF3 acts to limit ZIKV gene expression in A549 cells. We also determined that ATF3 enhances the expression of antiviral genes such as STAT1 and other components in the innate immunity pathway to induce an ATF3-dependent anti-ZIKV response. Our study reveals crosstalk between the integrated stress response and innate immune response pathways and highlights an important role for ATF3 in establishing an antiviral effect during ZIKV infection. IMPORTANCE: Zika virus (ZIKV) is a re-emerging mosquito-borne flavivirus that co-opts cellular mechanisms to support viral processes that can reprogram the host transcriptional profile. Such viral-directed transcriptional changes and the pro- or anti-viral outcomes remain understudied. We previously showed that ATF3, a stress-induced transcription factor, is significantly upregulated in ZIKV-infected mammalian cells, along with other cellular and immune response genes. We now define the intracellular pathway responsible for ATF3 activation and elucidate the impact of ATF3 expression on ZIKV infection. We show that during ZIKV infection, the integrated stress response pathway stimulates ATF3 which enhances the innate immune response to antagonize ZIKV infection. This study establishes a link between viral-induced stress response and transcriptional regulation of host defense pathways and thus expands our knowledge of virus-mediated transcriptional mechanisms and transcriptional control of interferon-stimulated genes during ZIKV infection.

Predictive Biophysical Neural Network Modeling of a Compendium of in vivo Transcription Factor DNA Binding Profiles for Escherichia coli.

The DNA binding of most Escherichia coli Transcription Factors (TFs) has not been comprehensively mapped, and few have models that can quantitatively predict binding affinity. We report the global mapping of in vivo DNA binding for 139 E. coli TFs using ChIP-Seq. We used these data to train BoltzNet, a novel neural network that predicts TF binding energy from DNA sequence. BoltzNet mirrors a quantitative biophysical model and provides directly interpretable predictions genome-wide at nucleotide resolution. We used BoltzNet to quantitatively design novel binding sites, which we validated with biophysical experiments on purified protein. We have generated models for 125 TFs that provide insight into global features of TF binding, including clustering of sites, the role of accessory bases, the relevance of weak sites, and the background affinity of the genome. Our paper provides new paradigms for studying TF-DNA binding and for the development of biophysically motivated neural networks.

Context dependent activity of p63-bound gene regulatory elements.

The p53 family of transcription factors regulate numerous organismal processes including the development of skin and limbs, ciliogenesis, and preservation of genetic integrity and tumor suppression. p53 family members control these processes and gene expression networks through engagement with DNA sequences within gene regulatory elements. Whereas p53 binding to its cognate recognition sequence is strongly associated with transcriptional activation, p63 can mediate both activation and repression. How the DNA sequence of p63-bound gene regulatory elements is linked to these varied activities is not yet understood. Here, we use massively parallel reporter assays (MPRA) in a range of cellular and genetic contexts to investigate the influence of DNA sequence on p63-mediated transcription. Most regulatory elements with a p63 response element motif (p63RE) activate transcription, with those sites bound by p63 more frequently or adhering closer to canonical p53 family response element sequences driving higher transcriptional output. The most active regulatory elements are those also capable of binding p53. Elements uniquely bound by p63 have varied activity, with p63RE-mediated repression associated with lower overall GC content in flanking sequences. Comparison of activity across cell lines suggests differential activity of elements may be regulated by a combination of p63 abundance or context-specific cofactors. Finally, changes in p63 isoform expression dramatically alters regulatory element activity, primarily shifting inactive elements towards a strong p63-dependent activity. Our analysis of p63-bound gene regulatory elements provides new insight into how sequence, cellular context, and other transcription factors influence p63-dependent transcription. These studies provide a framework for understanding how p63 genomic binding locally regulates transcription. Additionally, these results can be extended to investigate the influence of sequence content, genomic context, chromatin structure on the interplay between p63 isoforms and p53 family paralogs.

Inappropriate behaviours in a dental training environment: pilot of a UK-wide questionnaire.

Incivility and inappropriate behaviour in the workplace are topics of growing interest due to their impact on patient care and safety. Several surveys and campaigns have emerged highlighting the existence of a problem. However, the true scale is difficult to ascertain. The aim of this study is to determine the existence of inappropriate behaviours within the UK dental training environment.An anonymous pilot questionnaire was distributed across multiple platforms reaching out to dental professionals within training environments, inviting responses between July 2022 and October 2022. A total of 215 responses were received. The vast majority (73.2%) felt that inappropriate behaviour is a problem within UK dental training. Senior colleagues were identified as perpetrators in 88% of responses. Most respondents (66%) reported feeling uncomfortable raising the issue, and when raised, 30% felt unsupported. Only 9% felt confident that action was taken after the issue was reported. Belittling was experienced and witnessed most commonly.The feedback received reveals the existence of inappropriate behaviours within dental training environments. Qualitative feedback indicates that if left unaddressed, the impact of such behaviour may persist long-term. Further research is required to address this issue, improve dental training conditions and job satisfaction.

Going paperless - Qualitative monitoring of staff morale during the transition from paper to electronic health records.

Background: Organisational change is an important part of development and growth. Transitioning from paper-based hospital records to electronic health records improves efficiency and patient safety by streamlining data access and reducing the risk of errors, ultimately leading to enhanced patient care and outcomes. In October 2020, a large NHS trust underwent the transition from paper notes to a fully electronic health records system. Therefore, the purpose of this study was to monitor staff morale during this organisational change; to highlight any issues arising that may impact on the smooth transition; to encourage feedback. Methods: A questionnaire was distributed to all members of the maxillofacial outpatients department on a regular basis. The qualitative responses were analysed using NVivo, following a framework analysis model. Results: The analysis generated 1319 codes, which were placed into 68 groups. The three main themes were 'Transformational Advancements in Healthcare Delivery'; 'Obstacles to Seamless EHR Integration; 'Navigating the Transition and Evolving Perceptions'. Discussion: Regular monitoring of morale and staff opinion allows for smoother transition in a large-scale organisational change. The results of this project will help future hospitals and trusts undergoing similar transitions.

E-cigarette side effects in otolaryngology: unveiling the vape mirage.

DATA SOURCES: The following databases were searched for publications up to May 2020: Web of Science, EMBASE, CENTRAL, Medline and CINAHL. Additionally, previously published reviews were hand searched. STUDY SELECTION: Clinical studies conducted in English language were considered, encompassing cohorts of more than four vaping individuals who have encountered inadvertent side effects. Both adult and paediatric populations were included. In vitro, animal studies and systematic or literature reviews were excluded from the analysis. DATA EXTRACTION AND SYNTHESIS: Two independent reviewers screened 1125 studies following deduplication. Two-hundred and eight full-text studies were assessed for eligibility. RESULTS: Thirty-two studies met the inclusion criteria. Diverse study designs were included, comprising of cross-sectional, randomised controlled trials, case-control studies, cohort studies, case series investigations and non-randomised trials. Of note, four studies focused on paediatric patients. Most reported side effects were cough, throat and mouth irritation and intra-oral lesions. CONCLUSIONS: While the direct side effects of e-cigarettes are well-documented, the long-term effects remain uncertain.

Appropriateness of two-week wait head and neck cancer referrals to a district general hospital.

Objectives The NHS advise urgent referral of patients with suspected head and neck cancers to secondary care to be seen via a two-week wait pathway. The objective of this review was to analyse the two-week wait head and neck cancer referrals to a district general hospital and to identify the prevalence of oral cancer.Materials and methods Patients referred via an urgent two-week wait cancer pathway during the period of 12 October 2020 to 19 January 2022 were identified. Data were extracted and analysed for referral source, patient sex, whether or not a biopsy was undertaken, and the number of patients with a final positive cancer diagnosis.Results Overall, 883 two-week wait referrals were received. Most referrals came from general medical practitioners (50%) followed by general dental practitioners (37%). A total of 379 patients (46%) underwent a biopsy, special investigations, or internal referral to another speciality. The overall prevalence of cancer was 6.2%. Most referrals received were for commonly occurring benign conditions.Conclusion Despite many two-week wait suspected cancer referrals, only a small percentage of patients go on to be diagnosed with head and neck cancer. These results highlight the number of avoidable referrals, which ultimately impact patient waiting lists and clinician time.

Shared Gene Targets of the ATF4 and p53 Transcriptional Networks.

The master tumor suppressor p53 regulates multiple cell fate decisions, such as cell cycle arrest and apoptosis, via transcriptional control of a broad gene network. Dysfunction in the p53 network is common in cancer, often through mutations that inactivate p53 or other members of the pathway. Induction of tumor-specific cell death by restoration of p53 activity without off-target effects has gained significant interest in the field. In this study, we explore the gene regulatory mechanisms underlying a putative anticancer strategy involving stimulation of the p53-independent integrated stress response (ISR). Our data demonstrate the p53 and ISR pathways converge to independently regulate common metabolic and proapoptotic genes. We investigated the architecture of multiple gene regulatory elements bound by p53 and the ISR effector ATF4 controlling this shared regulation. We identified additional key transcription factors that control basal and stress-induced regulation of these shared p53 and ATF4 target genes. Thus, our results provide significant new molecular and genetic insight into gene regulatory networks and transcription factors that are the target of numerous antitumor therapies.

How does diabetes mellitus impact on the prognosis of dental implants?

DATA SOURCES: Web of Science, Embase, PubMed and Cochrane Library databases were searched for publications up to August 2021. STUDY SELECTION: The study noted clear inclusion and exclusion criteria. Search terms were provided; only observational studies were considered. DATA EXTRACTION AND SYNTHESIS: A total of 122 studies were identified through the search strategy. Following deduplication, two reviewers conducted the screening. RESULTS: A total of 21 observational studies were included, involving cohort, case-control, and cross-sectional study designs. A meta-analysis identified increased risk of peri-implantitis in patients with diabetes mellitus and in smokers when compared to non-diabetic subjects and non-smokers. No significant association was found between poor plaque control or periodontal history and peri-implantitis. CONCLUSIONS: Patients with diabetes mellitus appear to have a higher risk of peri-implantitis.

Shared gene targets of the ATF4 and p53 transcriptional networks.

The master tumor suppressor p53 regulates multiple cell fate decisions, like cell cycle arrest and apoptosis, via transcriptional control of a broad gene network. Dysfunction in the p53 network is common in cancer, often through mutations that inactivate p53 or other members of the pathway. Induction of tumor-specific cell death by restoration of p53 activity without off-target effects has gained significant interest in the field. In this study, we explore the gene regulatory mechanisms underlying a putative anti-cancer strategy involving stimulation of the p53-independent Integrated Stress Response (ISR). Our data demonstrate the p53 and ISR pathways converge to independently regulate common metabolic and pro-apoptotic genes. We investigated the architecture of multiple gene regulatory elements bound by p53 and the ISR effector ATF4 controlling this shared regulation. We identified additional key transcription factors that control basal and stress-induced regulation of these shared p53 and ATF4 target genes. Thus, our results provide significant new molecular and genetic insight into gene regulatory networks and transcription factors that are the target of numerous antitumor therapies.

How harmful are e-cigarettes to the head and neck cells?

Data sources Medline, Cumulative Index to Nursing and Allied Health Literature, Chemical Abstracts Plus, Dentistry and Oral Sciences and Web of Science databases, as well as grey literature, were searched for publications up to December 2020.Study selection Search terms and concepts were mentioned in line with clear PICOS (population, intervention, comparison, outcomes and study) criteria. Inclusion and exclusion criteria were outlined. All study designs were considered.Data extraction and synthesis Two independent reviewers screened 233 articles using Rayyan software. In total, 49 full-text articles were retrieved.Results Overall, 18 studies fit the inclusion criteria, of which two were clinical trials and sixteen were in vitro research. Varying strengths of nicotine concentration were examined for toxicity on head and neck cells. The use of electronic cigarettes (e-cigarettes) caused changes to cell size and shape and reduced cell viability and cell proliferation.Conclusions Although less harmful than tobacco smoke, e-cigarettes appear to induce damaging changes in head and neck cells.

Five-year prospective fistula audit in a single center. TIG training negates consultant learning curve, but surgeons should beware the mid-range palatal defect.

The aim of primary palatoplasty is to achieve optimum speech with minimal morbidity. Symptomatic fistulae are well-recognised complications of palatoplasty and may require additional surgical intervention, increasing the burden of care. Our aims were to better understand fistula experience in our unit and compare fistula rates between an established consultant and a newly appointed training interface group (TIG) trained consultant. Post-operative fistulae were prospectively and independently recorded by Cleft Clinical Nurse Specialists as part of routine 6-week post-operative reviews. Cleft type and intra-operative hard-soft palate junction (HSPJ) width were prospectively recorded by operating surgeons. Data were collated and analysed using Microsoft Excel. Between 1 January 2014 and 31 December 2018, 250 primary palatoplasties were performed. The overall fistula rate was 8% (0% SMCP, ICP 7%, UCLP 8%, BCLP 22%). Fistulae clustered in clefts with a mid-range HSPJ width of 12-16 mm. Numerically, fistula rates remained similar over time despite increased unit activity (doubling of primary surgeries in 2017 and 2018). There was no significant difference in fistulae rates between surgeons (P > 0.05). Overall fistulae rate compared favourably with published data. TIG fellowships were designed in the context of cleft surgery to address issues relating to steep operative learning curves. These data demonstrate that results from a newly appointed TIG-trained surgeon are comparable to that of an established TIG-trained surgeon. Data also suggest surgeons should be aware of the risk of fistulae in the mid-range palatal defect and in HSPJ widths of 12-16 mm.

Guided tissue regeneration techniques involving blood-derived products in periradicular surgery: a systematic review and meta-analysis protocol.

OBJECTIVE: The objective of this review is to evaluate the clinical outcomes of standard periradicular surgery versus periradicular surgery with the use of guided tissue regeneration techniques involving blood-derived products in patients undergoing periradicular surgery. INTRODUCTION: Guided tissue regeneration techniques have been available in dentistry for decades. Primarily used during periodontal surgery and implant placement, their usefulness in periapical surgery has been garnering increased attention. According to current available evidence, guided tissue regeneration can improve clinical patient outcomes. No systematic reviews have been carried out to investigate guided tissue regeneration techniques involving blood-derived products in periradicular surgery. INCLUSION CRITERIA: Randomized controlled trials that investigate the outcomes of guided tissue regeneration techniques involving blood-derived products versus standard periradicular surgery technique, will be included for review. Studies will be excluded if they contain patients who have previously undergone periradicular surgery or the treatment was carried out on unrestorable teeth (ie, due to periodontal disease or root fractures). METHODS: The databases MEDLINE, Embase, Dentistry and Oral Sciences Source, and Cochrane CENTRAL will be used to locate published reports of studies. Reference lists of relevant past systematic reviews will be used to identify further studies. Unpublished studies will be sought using international trials registries and repositories. Two reviewers will carry out independent screening of records for inclusion and the selected studies will be critically appraised prior to data extraction and synthesis. Meta-analysis will be performed if appropriate. SYSTEMATIC REVIEW REGISTRATION NUMBER: PROSPERO CRD42020222663.

Regulatory roles of Escherichia coli 5' UTR and ORF-internal RNAs detected by 3' end mapping.

Many bacterial genes are regulated by RNA elements in their 5´ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3´ ends in 5´ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5´ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5´ UTRs and internal to ORFs.

In most organisms, specific segments of a cell's genetic information are copied to form single-stranded molecules of various sizes and purposes. Each of these RNA molecules, as they are known, is constructed as a chain that starts at the 5´ end and terminates at the 3´ end. Certain RNAs carry the information present in a gene, which provides the instructions that a cell needs to build proteins. Some, however, are 'non-coding' and instead act to fine-tune the activity of other RNAs. These regulatory RNAs can be separate from the RNAs they control, or they can be embedded in the very sequences they regulate; new evidence also shows that certain regulatory RNAs can act in both ways. Many regulatory RNAs are yet to be catalogued, even in simple, well-studied species such as the bacterium Escherichia coli. Here, Adams et al. aimed to better characterize the regulatory RNAs present in E. coli by mapping out the 3´ ends of every RNA molecule in the bacterium. This revealed many new regulatory RNAs and offered insights into where these sequences are located. For instance, the results show that several of these RNAs were embedded within RNA produced from larger genes. Some were nested in coding RNAs, and were parts of a longer RNA sequence that is adjacent to the protein coding segment. Others, however, were present within the instructions that code for a protein. The work by Adams et al. reveals that regulatory RNAs can be located in unexpected places, and provides a method for identifying them. This can be applied to other types of bacteria, in particular in species with few known RNA regulators.

Neisseria oralis septicaemia in a newborn: first recorded case.

Neisseria oralis is a bacterium which normally resides within the oral microflora. A female infant was born by emergency caesarean section owing to fetal distress with a gestational age of 38 weeks, a birthweight of 2250 g and a temperature of 36.5°C. The pregnancy had been normal. The delivery was complicated by prolonged rupture of membranes (48 hours) and meconium-stained and foul-smelling liquor. APGAR scores were 1 at 1 min, 9 at 5 min and 9 at 10 min. The infant looked pale and had respiratory distress requiring resuscitation for the first 4 minutes. After a septic screen, she was commenced on benzylpenicillin and gentamicin. On Day 1 of life she was diagnosed with neonatal sepsis, and N. oralis was identified in blood cultures and blood-stained cerebrospinal fluid (CSF). Although N. oralis was cultured from the CSF, it was considered that this was more likely owing to blood contamination of the CSF. In view of the blood and CSF cultures, antibiotics were changed to intravenous cefotaxime. By Day 6 blood infection markers were regarded as normal. Antibiotics were continued for 14 days. Although neonatal sepsis caused by N. oralis has not been reported before, it should be considered to be a pathogen able to cause neonatal sepsis.

Transcription termination and antitermination of bacterial CRISPR arrays.

A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ('repeats') interspersed with short, variable sequences ('spacers'). CRISPR arrays are transcribed and processed into individual CRISPR RNAs that each include a single spacer, and direct Cas proteins to complementary sequences in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho can prematurely terminate transcription of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of transcription termination and antitermination in the evolution of bacterial CRISPR-Cas systems.

Identification of regulatory targets for the bacterial Nus factor complex.

Nus factors are broadly conserved across bacterial species, and are often essential for viability. A complex of five Nus factors (NusB, NusE, NusA, NusG and SuhB) is considered to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent transcription termination. Here, we identify an additional cellular function for the Nus factor complex in Escherichia coli: repression of the Nus factor-encoding gene, suhB. This repression occurs primarily by translation inhibition, followed by Rho-dependent transcription termination. Thus, the Nus factor complex can prevent or promote Rho activity depending on the gene context. Conservation of putative NusB/E binding sites upstream of Nus factor genes suggests that Nus factor autoregulation occurs in many bacterial species. Additionally, many putative NusB/E binding sites are also found upstream of other genes in diverse species, and we demonstrate Nus factor regulation of one such gene in Citrobacter koseri. We conclude that Nus factors have an evolutionarily widespread regulatory function beyond ribosomal RNA, and that they are often autoregulatory.